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)

JOHN CORCORAN AND WILIAM FRANK. Surprises in logic. Bulletin of Symbolic Logic. 19 253. Some people, not just beginning students, are at first surprised to learn that the proposition “If zero is odd, then zero is not odd” is not self-contradictory. Some people are surprised to find out that there are logically equivalent false universal propositions that have no counterexamples in common, i. e., that no counterexample for one is a counterexample for the other. Some people would be surprised (...) to find out that in normal first-order logic existential import is quite common: some universals “Everything that is S is P” —actually quite a few—imply their corresponding existentials “Something that is S is P”. Anyway, perhaps contrary to its title, this paper is not a cataloging of surprises in logic but rather about the mistakes that did or might have or might still lead people to think that there are no surprises in logic. The paper cataloging of surprises in logic is on our “to-do” list. -/- ► JOHN CORCORAN AND WILIAM FRANK, Surprises in logic. Philosophy, University at Buffalo, Buffalo, NY 14260-4150, USA E-mail: corcoran@buffalo.edu There are many surprises in logic. Peirce gave us a few. Russell gave Frege one. Löwenheim gave Zermelo one. Gödel gave some to Hilbert. Tarski gave us several. When we get a surprise, we are often delighted, puzzled, or skeptical. Sometimes we feel or say “Nice!”, “Wow, I didn’t know that!”, “Is that so?”, or the like. Every surprise belongs to someone. There are no disembodied surprises. Saying there are surprises in logic means that logicians experience surprises doing logic—not that among logical propositions some are intrinsically or objectively “surprising”. The expression “That isn’t surprising” often denigrates logical results. Logicians often aim for surprises. In fact, [1] argues that logic’s potential for surprises helps motivate its study and, indeed, helps justify logic’s existence as a discipline. Besides big surprises that change logicians’ perspectives, the logician’s daily life brings little surprises, e.g. that Gödel’s induction axiom alone implies Robinson’s axiom. Sometimes wild guesses succeed. Sometimes promising ideas fail. Perhaps one of the least surprising things about logic is that it is full of surprises. Against the above is Wittgenstein’s surprising conclusion : “Hence there can never be surprises in logic”. This paper unearths basic mistakes in [2] that might help to explain how Wittgenstein arrived at his false conclusion and why he never caught it. The mistakes include: unawareness that surprise is personal, confusing logicians having certainty with propositions having logical necessity, confusing definitions with criteria, and thinking that facts demonstrate truths. People demonstrate truths using their deductive know-how and their knowledge of facts: facts per se are epistemically inert. [1] JOHN CORCORAN, Hidden consequence and hidden independence. This Bulletin, vol.16, p. 443. [2] LUDWIG WITTGENSTEIN, Tractatus Logico-Philosophicus, Kegan Paul, London, 1921. -/-. (shrink)

This paper provides an analysis of the way in which two foundational principles of medical ethics–the trusted doctor and patient autonomy–can be undermined by the use of machine learning (ML) algorithms and addresses its legal significance. This paper can be a guide to both health care providers and other stakeholders about how to anticipate and in some cases mitigate ethical conflicts caused by the use of ML in healthcare. It can also be read as a road map as to what (...) needs to be done to achieve an acceptable level of explainability in an ML algorithm when it is used in a healthcare context. (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?

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)

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)

Volume 19, Issue 7, July 2019, Page 39-40.

Engineering an artificial intelligence to play an advisory role in morally charged decision making will inevitably introduce meta-ethical positions into the design. Some of these positions, by informing the design and operation of the AI, will introduce risks. This paper offers an analysis of these potential risks along the realism/anti-realism dimension in metaethics and reveals that realism poses greater risks, but, on the other hand, anti-realism undermines the motivation for engineering a moral AI in the first place.

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)

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)

Definitions of terms that are central to a theoretical understanding of the Royal Government of Bhutan's policy of Gross National Happiness.

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)

This chapter describes the potential far‐reaching consequences of contemplative higher education for the fields of science and medicine.

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)

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 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)

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)

Cosmic Justice Hypotheses. -/- This applied-logic lecture builds on [1] arguing that character traits fostered by logic serve clarity and understanding in ethics, confirming hopeful views of Alfred Tarski [2, Preface, and personal communication]. Hypotheses in one strict usage are propositions not known to be true and not known to be false or—more loosely—propositions so considered for discussion purposes [1, p. 38]. Logic studies hypotheses by determining their implications (propositions they imply) and their implicants (propositions that imply them). Logic also (...) studies hypotheses by seeing how variations affect implications and implicants. People versed in logical methods are more inclined to enjoy working with hypotheses and less inclined to dismiss them or to accept them without sufficient evidence. Cosmic Justice Hypotheses (CJHs), such as “in the fullness of time every act will be rewarded or punished in exact proportion to its goodness or badness”, have been entertained by intelligent thinkers. Absolute CJHs, ACHJs, imply that it is pointless to make sacrifices, make pilgrimages, or ask divine forgiveness: once acts are done, doers must ready themselves for the inevitable payback, since the cosmos works inexorably toward justice. Ceteris Paribus CJHs, CPCJHs, on the other hand, such as “in the fullness of time every act will be rewarded or punished in exact proportion to its goodness or badness—other things being equal”, leave room for exceptions. For example, some people subscribing to Ceteris Paribus CJHs think that certain bad acts can be performed with impunity as long as certain procedures are carried out previous to, or simultaneous with, or even after the acts. Belief Ceteris Paribus CJHs has been exploited by unscrupulous “spiritual leaders” who claim to have power to grant exceptions. In opposition to belief in CPCJHs are CJHs that hold belief in CPCJHs to be inherently wrong and subject to punishment. Other variants of CJHs are Cumulative Cosmic Justice Hypotheses, such as “in the fullness of time every person will be rewarded or punished in exact proportion to the net goodness or badness of their acts”. Still other variants include the Hereditary Cumulative Cosmic Justice Hypotheses, such as “in the fullness of time every person will be rewarded or punished in exact proportion to the net goodness or badness of their ancestors’ acts”. [1] JOHN CORCORAN, Inseparability of Logic and Ethics, Free Inquiry, S. 1989, pp. 37–40. [2] ALFRED TARSKI, Introduction to Logic, Dover, 1995. (shrink)

Poniższa praca odnosi się głównie do tezy Huberta Orłowskiego, według której „niemiecka dyskusja o Polsce miała legitymujące, nic do pominięcia znaczenie dla wynalezienia niemieckiego narodu”. Wobec rozmiarów i rozdrobnienia społeczno-wyznaniowego Rzeszy Niemieckiej ok. 1700 r. temat ten ograniczony jest do Prus Zachodnich i głównego problemu (teoria państwowości, religia, historia) debaty o przyczynach funkcjonowania powstałego obrazu Polski. Koncentracja na Prusach Zachodnich wynika z modalnego charakteru, jaki musiał mieć „problem Polski” jako odzwierciedlenie procesów tworzenia się granic na danym obszarze, którego niemiecki rejon (...) kulturalny miał polską przynależność państwową. Przedstawia się tu sposób, w jaki nowa, w dyskusyjnych ramach europejskiego wczesnego Oświecenia powstająca świadomość wnosiła stopniowy odwrót od rozpadającej się polskiej Republiki Szlacheckiej, a tym samym konieczność poszukiwania nowej władzy ochronnej. Wynikała z tego pewna opcja narodowa, która następnie zmieniła regionalnie obraz Polski. Ta trafnie podkreślana przez Orłowskiego konccplualizacja obrazu Polski służyła do przekształcenia stanowo uformowanej boruskiej świadomości regionalnej w nowożytną (pozytywnie lub negatywnie) skupioną na Prusach świadomość państwową. Punktem wyjścia poniższych rozważań jest spór o to, czy forma państwa polskiej Republiki Szlacheckiej w drugiej połowie XVII w. mogła jeszcze być wystarczającą dla ekonomicznych i politycznych potrzeb mieszczaństwa. Rozważania te wskazują zarówno z obcej jak też z własnej perspektywy na ten w tamtym okresie z mieszczańskiego punktu widzenia mało atrakcyjny obraz Polski. Obcy znaczy tu jednak nie tyle trochę specyficzny „polski”, ile nie do zaakceptowania jako patriotyczny i nierozsądny ekonomicznie dla mieszczanina sposób postępowania polskiego szlachcica. W tymże sensie informuje zrekonstruowana tu debata o wczesnym mieszczańskim (nie zabarwionym jeszcze narodowo) obrazie Polski. Przedstawia ona jednocześnie, w jak wielkim stopniu konstruowany był portret własny mieszczaństwa w kulturalnie niemiecko ukształtowanych miastach Polski, według etosu protestanckiego w przeciwieństwie do katolickiej szlachty polskiej. Rozwijający się z tego późny pruski obraz Polski jest następnie podejmowany jako kompleks dalej działających i umacniających się uprzedzeń, które powstają na początku XVIII w. i oddzielają się stopniowo od ich prawdziwych kulis. Jako stereotyp ma to więc swoje korzenie w przeciwieństwie mieszczańsko-boruskich i polskich, skierowanych na konstelacje władzy w Republice Szlacheckiej interesów i poczynań. Teza ta uwidacznia też, że nie chodziło tylko o opis stereotypowej struktury dziś rozprzestrzenionych opinii o Polsce. Dużo większe zainteresowanie skierowane zostało na „ziarenko prawdy” , które, z historycznego punktu widzenia, zawarte jest w każdym stereotypie. (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.

On the work of Frank Ramsey, emphasizing topics most relevant to philosophy of science.

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)

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)

The aim of this paper is to show that the French philosopher and historian of science Abel Rey played a more influential role in the formative phase of the Vienna Circle than hitherto supposed. On the whole, it will be argued that Rey's contribution had political impact. His interpretation of "modern physics" in 1907 in the face of the alleged "bankruptcy of science" should be appreciated as a masterpiece of applied enlightenment thought. As such, it was especially paradigmatic for Philipp (...) Frank's "positivist" defense of the theory of relativity and quantum mechanics against the irrationalist tendencies of the 1920s and 1930s. (shrink)

This paper consists of two parts. In the first part, I give an in-depth comparison and analysis of the theories of Frank Ankersmit and Eelco Runia, in which I highlight their most important resemblances and differences. What both have in common is their notion of the presence of the past as a ‘presence in absence’. They differ, however, with respect to the character of this past and the role representation plays in making it present. Second, I also argue that (...) for both Ankersmit and Runia, the presence of the past is always the present of our past, which excludes the experience of the otherness of the past, and which opens both theories to the criticisms of being self-centered and nationalistic. (shrink)