The Modern concept of truth, which subjects truth to certainty, broke the harmonious relation between reality and truth, that prevailed in Ancient and Medieval Philosophy. Hans-Georg Gadamer thinks that the main task of contemporary Philosophy is to recover the original harmony of being and knowledge. To shed light on the nature of this problem, we expound the metaphysical-theological foundation of truth, which is at the roots of Aristotelian and Thomistic Philosophies. Specifically, we analyze here the relation between being, truth and (...) logos in the Aristotelian treatise Perì Hermeneías, and in its Thomistic commentary. (shrink)

Este capítulo se propone explorar cómo el replanteo de las causas finales en la ciencia natural suscitado por la Revolución Científica impactó en el desarrollo del materialismo y el ateísmo del Siglo de las luces. Con el surgimiento de la ciencia moderna en Europa, en el siglo XVII ocurrieron cambios sustantivos en la concepción de la causalidad. Ciertos estudios pioneros sobre el tema, sostenían que la nueva ciencia anulaba las causas finales y establecía que todos los fenómenos naturales debían explicarse (...) en términos de materia y movimiento (Burtt, 1952:98‒99; Schmitt, 1983:5). Más tarde, otros especialistas —con argumentos más sólidos y pruebas más convincentes— mostraron que la causalidad final no fue anulada por completo; siguió presente en muchos autores, aunque ya no como parte indispensable de la explicación científica, sino como un componente ontológico de la naturaleza (Osler, 1996 y 2001). Ahora bien, ¿qué sucedió con las causas finales en el siglo XVIII europeo, época de profundas turbulencias políticas y controversias filosóficas, en la cual el materialismo, el ateísmo y el deísmo fueron ganando terreno? Para hacer un recorte dentro de la vasta variedad de posiciones existentes en este escenario, comenzaremos por repasar la posición sobre las causas finales de Francis Bacon (1561‒1626), quien fue una figura muy influyente en la Ilustración. 2 Luego, analizaremos la recepción de esa posición por parte de algunos autores británicos (D. Stewart, S. Parker) y franceses en el siglo XVIII (D'Alembert, Naigeon, Diderot, Cabanis). (shrink)

"Sofò e Fefilìa" attinge dal mondo antico - dalla sua potenza -, ma possiede come sfondo del lucido meditare la contemporaneità. Un'analisi estrema, tragica, della vasta gamma dei sentimenti umani, che coniuga - in modo personale e innovativo - diverse anime: la poetica di d'Annunzio; la filosofia di Cioran, Weil, Heidegger, Schopenhauer, Leopardi, Pascal; la psicologia del profondo di Jung. Un tema, tanti temi: la vita-morte con le sue molteplici declinazioni in chiave gnostica. Sofò, perché Sofia è sapienza, lucetempo delle (...) menti, seme di salvezza. Il mito gnostico insegna, infatti, che l'uomo spirituale ritornerà alla luce e sarà la redenzione. Fefilìa, in quanto Fede e Amore costituiscono le cifre dell'e-sistenza. Prefazione: prof. Alberto Giovanni Biuso - Disponibile sul sito: BookSprint Edizioni -. (shrink)

This article documents our collaborative ongoing struggle to disrupt the reproduction of the coloniality of knowledge in the teaching of Gender Studies. We document how our decolonial feminist activism is actualised in our pedagogy, which is guided by feminist interpretations of ‘wonder’ (Irigaray, 1999; Ahmed, 2004; hooks, 2010) read alongside decolonial theory, including that of Ramón Grosfoguel, Walter D. Mignolo and María Lugones. Using notions of wonder as pedagogy, we attempt to create spaces in our classrooms where critical self-reflection and (...) critical intellectual and embodied engagement can emerge. Our attempts to create these spaces include multiple aspects or threads that, when woven together, might enable other ways of knowing-being-doing that works towards disrupting feminist complicity with coloniality in the Australian context. (shrink)

"Siamo come lucciole che hanno disimparato a illuminare e che prima si sono messe a girare attorno alla lanterna magica dell'ideale ascetico e ora attorno alle insegne pubblicitarie al neon. Lucciole che hanno scordato d’avere una potenzialità di orientatività preziosa nel proprio sistema affettivo" (G. Cusinato, La totalità incompiuta, Milano 2008, 314). Che cos'è una persona? Come si costituisce concretamente l'identità personale? Che rapporto c'è fra identità personale e identità psichica? C'è coincidenza fra persona e homo sapiens? La persona è (...) ancora oggi, nonostante tutto, al centro del dibattito filosofico, sociologico, giuridico e bioetico, eppure la sua dimensione sembra sfuggire continuamente alle reti concettuali e alle categorie epistemologiche della scienza. In questo lavoro si propone una fenomenologia della persona a partire dal confronto con la teoria dei sistemi autopoietici di Maturana e Varela e dei sistemi sociali di Luhmann, mettendo in luce che la persona non può essere considerata un sistema autopoietico. La persona si delinea piuttosto come un sistema excentrico che si costituisce mediante l'esecuzione dell'atto. Questa prospettiva viene esplorata attraverso un dialogo serrato con l'antropologia filosofica tedesca, la stessa che all'inizio del Novecento mette in luce che l'uomo non ha un'essenza precostituita e proprio per questo necessita di un processo di Bildung. L'antropologia filosofica di Scheler e Plessner nasce nella Germania degli anni Venti in un periodo ancora fluido in cui l'eclissi delle tradizionali concezioni dell'uomo non aveva ancora lasciato il posto alla cristallizzazione totalitaria dell'uomo di massa che si sarebbe imposta negli anni Trenta. (shrink)

Nella Premessa al "Discorso filosofico della modernità" (1985) Habermas scrive, in maniera enfatica, che il tema, ricco di sfaccettature, della “modernità come progetto in-compiuto” segna l’inizio la sua riflessione e dagli anni ’80 “non gli ha dato più pace”. In effetti, la “modernità” si presenta come un “oggetto d’analisi obbligato” anche solo dal punto di vista del necessario auto-chiarimento disciplinare. È con la formazione delle società moderne che si differenziano come “forme del sapere specialistico”, la scienza politica, l’economia politica, l’antropologia (...) culturale e la sociologia. Ed è, ancora, dalla prospettiva della “riflessione filosofica” che si avvia dal tardo secolo XVIII una rinnovata consapevolezza intellettuale intorno alla coscienza storica del tempo moderno, ai principi costitutivi del “nuovo mondo” e alle “cesure” rispetto alla cultura passata. Non si deve, però, ridurre il concetto di modernità alla visione filosofica del mondo. Anche questa prospettiva – peraltro presente negli scritti di Habermas –, deve essere ricondotta all’interno del programma di ricerca della “teoria dell’evoluzione sociale”, considerando assieme i processi di “razionalizzazione culturale” del mondo vitale e la “differenziazione” di nuovi “principi di organizzazione sociale” rispetto a quelli con cui si erano riprodotte le formazioni tradizionali. Il merito dei suoi studi, una volta ricondotti a unità, è di seguire la trasformazione delle sfere culturali di valore alla luce dei problemi che coinvolgono la riproduzione delle strutture sociali e delle forme di vita tradizionali, mediando le esigenze della teorizzazione astratta e le vicende della storia con-creta. In tal senso, egli segue la tradizione di ricerca dei classici del pensiero sociale, da Comte sino alla scuola di Parsons, attraverso Marx, Durkheim e Weber. Dopo aver esposto in che cosa consiste, secondo il nostro Autore, il “razionalismo occidentale”, qui, ci limitiamo a fornire un indice ragionato dei temi con cui Habermas ha ricostruito il concetto “formazione sociale moderna” attraverso l'analisi degli “albori della modernità”, delle “società capitalistico-liberali” e delle “società contemporanee”. (shrink)

L'antigiudaismo cristiano è essenzialmente la credenza che il popolo ebraico debba rinunciare alla propria fede e convertirsi al cristianesimo. In questo testo viene studiata la prima forma sistematica di antigiudaismo sviluppata in termini filosofici e teologici da Agostino d'Ippona. Alla luce dell'analisi filosofica sembra che l'avversione di Agostino per la fede ebraica si fondi su un'autentica rimozione della specificità del popolo eletto, della Legge e della Rivelazione sul Sinai.

ENGLISH: The author investigates whether the model prevalent today of an “humble reason” - based on fallibilism and epistemic humility - is the most appropriate to express the theological truth, even in the light of the debate within the contemporary theism (rational theology). To answer this question it is necessary to examine the epistemological status of “human truth” and the “truth of faith”, in order to develop a common approach to sciences, philosophy and theology. Finally, the author shows how the (...) communitarian dimension and the “choice” (a call for freedom) are inherent to theology understood as “critical faith”, whose peculiarity is to posit itself without nostalgia in the middle between fideism, rationalism and a certain relativism. From the path, finally, it emerges the proposal of a new “cristeologia”. ITALIAN: Il rapporto tra fede e ragione è la questione meta-teologica per eccellenza. L’autore si propone dunque d’indagare se il modello oggi prevalente di “ragione umile” – basato su fallibilismo e umiltà epistemica – sia il più adeguato per esprimere le verità teologiche, anche alla luce del dibattito interno al teismo contemporaneo (teologia razionale). Per rispondere a questa domanda è necessario esaminare lo statuto epistemologico della verità umana e della verità di fede, per poter elaborare un metodo comune alle discipline scientifiche, filosofiche e teologiche, capace di trovare un equilibrio tra fideismo e positivismo teologico. Dopo una breve panoramica storica dei rapporti tra fede e ragione nel pensiero occidentale (con particolare attenzione alla dottrina dei praeambula fidei), l’articolo cercherà di mostrare come, nel paradigma della verità relazionale e del fallibilismo sia necessario integrare il problema delle fonti, dell’autorità, del concetto di ispirazione e della nozione di “rivelazione”, giacché contraddistinguono la teologia rispetto alla filosofia. Si mostrerà infine come la dimensione comunitaria e della scelta (appello alla libertà) siano connaturate alla teologia intesa come fede critica, la cui peculiarità è di collocarsi senza nostalgie nel mezzo tra fideismo, razionalismo e un certo relativismo. Dal percorso emergerà infine la proposta di una nuova "cristeologia". (shrink)

L’Exercitium academicum circa praescientiam daemonum (1666), pubblicato nella riformata Jena, tematizza una questione dibattuta nella Scolastica fra XIII e XIV secolo ma le cui radici risalgono ad Agostino d'Ippona, cui si deve il primo testo sull'argomento: la prescienza dei demoni. L'analisi segue la traccia del De divinatione daemonum agostiniano, mentre appare critica nei confronti delle posizioni di Tommaso d'Aquino e dei tomisti. Ad esse, in particolare riguardo alla natura delle facoltà intellettive demoniche, egli contrappone Giovanni Duns Scoto, Durando di san (...) Porziano e non meglio specificati nominales, accomunati in un indistinto riferimento alla teoria delle species. Ciò non toglie che il testo segua poi Tommaso nell'articolazione delle forme di prescienza dei demoni e nella definizione di questa come conoscenza congetturale. Scopo del nostro intervento sarà infatti mostrare, attraverso l'analisi che per la prima volta sarà condotta sul testo, lo spaccato di una comunità conversazionale nella quale le linee di forza e le distinzioni che animano il dibattito si mostrano autonome rispetto alle posizioni storiche di cattolici e riformati. Nell’Exercitium, Duns Scoto è contrapposto ai tomisti e, con Agostino e Durando di san Porziano – che costituisce una fonte comune del dibattito secentesco insieme a Bonaventura, Aureolo, Suarez, Vazquez, Gregorio di Valencia, e in tale veste sarà ripreso di lì a poco da Leibniz -, è cooptato tra gli autori a sostegno della sua tesi. Lungi dall'essere un esercizio di eclettismo o la stanca ripetizione di formule scolastiche, lo scritto getta luce su un dibattito universitario nel quale le fonti sono usate non come auctoritates ma quale repertorio di teorie da smontare e rimontare; ad esse l’Exercitium attinge per soluzioni che si definiscono in relazione a finalità filosofiche o dottrinali, ma non politiche né confessionali. (shrink)

A new translation and edition of Aristotle's Protrepticus (with critical comments on the fragments) -/- Welcome -/- The Protrepticus was an early work of Aristotle, written while he was still a member of Plato's Academy, but it soon became one of the most famous works in the whole history of philosophy. Unfortunately it was not directly copied in the middle ages and so did not survive in its own manuscript tradition. But substantial fragments of it have been preserved in several (...) works by Iamblichus of Chalcis, a third century A.D. neo-Pythagorean philosopher and educator. On the basis of a close study of Iamblichus' extensive use and excerption of Aristotle's Protrepticus, it is possible to reconstruct the backbone of the lost work, and then to flesh it out with the other surviving reports about the work from antiquity (for example in Alexander of Aphrodisias and other ancient commentators on Aristotle). It is also possible to identify several papyrus fragments of the work, and many references and literary allusions in later authors, especially Cicero, whose own lost dialogue Hortensius was a defense of philosophy modeleld on Aristotle's. (shrink)

In December 2013, the Nonhuman Rights Project (NhRP) filed a petition for a common law writ of habeas corpus in the New York State Supreme Court on behalf of Tommy, a chimpanzee living alone in a cage in a shed in rural New York (Barlow, 2017). Under animal welfare laws, Tommy’s owners, the Laverys, were doing nothing illegal by keeping him in those conditions. Nonetheless, the NhRP argued that given the cognitive, social, and emotional capacities of chimpanzees, Tommy’s confinement constituted (...) a profound wrong that demanded remedy by the courts. Soon thereafter, the NhRP filed habeas corpus petitions on behalf of Kiko, another chimpanzee housed alone in Niagara Falls, and Hercules and Leo, two chimpanzees held in research facilities at Stony Brook University. Thus began the legal struggle to move these chimpanzees from captivity to a sanctuary, an effort that has led the NhRP to argue in multiple courts before multiple judges. The central point of contention has been whether Tommy, Kiko, Hercules, and Leo have legal rights. To date, no judge has been willing to issue a writ of habeas corpus on their behalf. Such a ruling would mean that these chimpanzees have rights that confinement might violate. Instead, the judges have argued that chimpanzees cannot be bearers of legal rights because they are not, and cannot be persons. In this book we argue that chimpanzees are persons because they are autonomous. (shrink)

How might emerging and future technologies—sex robots, love drugs, anti-love drugs, or algorithms to track, quantify, and ‘gamify’ romantic relationships—change how we understand and value love? We canvass some of the main ethical worries posed by such technologies, while also considering whether there are reasons for “cautious optimism” about their implications for our lives. Along the way, we touch on some key ideas from the philosophies of love and technology.

The growth of self-tracking and personal surveillance has given rise to the Quantified Self movement. Members of this movement seek to enhance their personal well-being, productivity, and self-actualization through the tracking and gamification of personal data. The technologies that make this possible can also track and gamify aspects of our interpersonal, romantic relationships. Several authors have begun to challenge the ethical and normative implications of this development. In this article, we build upon this work to provide a detailed ethical analysis (...) of the Quantified Relationship. We identify eight core objections to the QR and subject them to critical scrutiny. We argue that although critics raise legitimate concerns, there are ways in which tracking technologies can be used to support and facilitate good relationships. We thus adopt a stance of cautious openness toward this technology and advocate the development of a research agenda for the positive use of QR technologies. (shrink)

Now it is plain that such consequences as these conflict sharply with common-sense notions of morality. If we had been obliged to accept Psychological Egoism, in any of its narrower forms, on its merits, we should have had to say: 'So much the worse for the common-sense notions of morality!' But, if I am right, the morality of common sense, with all its difficulties and incoherences, is immune at least to attacks from the basis of Psychological Egoism.

Standard Analytic Epistemology (SAE) names a contingently clustered class of methods and theses that have dominated English-speaking epistemology for about the past half-century. The major contemporary theories of SAE include versions of foundationalism, coherentism, reliabilism, and contextualism. While proponents of SAE don’t agree about how to define naturalized epistemology, most agree that a thoroughgoing naturalism in epistemology can’t work. For the purposes of this paper, we will suppose that a naturalistic theory of epistemology takes as its core, as its starting-point, (...) an empirical theory. The standard argument against naturalistic approaches to epistemology is that empirical theories are essentially descriptive, while epistemology is essentially prescriptive, and a descriptive theory cannot yield normative, evaluative prescriptions. In short, naturalistic theories cannot overcome the is-ought divide. Our main goal in this paper is to show that the standard argument against naturalized epistemology has it almost exactly backwards. (shrink)

A general insight of 20th-century philosophy of science is that the acceptance of a scientific theory is grounded, not merely on a theory's relation to data, but on its status as having no, or being superior to its, competitors. I explore the ways in which scientific realists might be thought to utilise this insight, have in fact utilised it, and can legitimately utilise it. In more detail, I point out that, barring a natural but mistaken characterisation of scientific realism, traditional (...) realism has not utilised that insight regarding scientific theories, i.e., has not explicitly factored that insight into, and invoked it as justification for, what realists believe. Nonetheless, a new form of realism has. In response to a key historical threat, two of the most thoroughly developed contemporary versions of realism—one put forward by Jarrett Leplin, another by Stathis Psillos—are anchored on the sensible tactic of requiring that the theories to which realists commit themselves have no competitors. I argue, however, that the particular kind of non-competitor condition they invoke is illegitimate in the context of the realism debate. I contend further that invoking a non-competitor condition that is legitimate, sensible, and even, as it turns out, required in the context of the debate threatens to eliminate the possibility of scientific realism altogether. (shrink)

Peter Baumann offers the tantalizing suggestion that Thomas Reid is almost, but not quite, a pragmatist. He motivates this claim by posing a dilemma for common sense philosophy: Will it be dogmatism or scepticism? Baumann claims that Reid points to but does not embrace a pragmatist third way between these unsavory options. If we understand `pragmatism' differently than Baumann does, however, we need not be so equivocal in attributing it to Reid. Reid makes what we could call an argument from (...) practical commitment, and this is plausibly an instance of what William James calls the pragmatic method. (shrink)

In this paper we distinguish two issues that are often run together in discussions about physicalism. The first issue concerns levels. How do entities picked out by non-physical terminology, such as biological or psychological terminology, relate to physical entities? Are the former identical to, or metaphysically supervenient on, the latter? The second issue concerns physical parts and wholes. How do macroscopic physical entities relate to their microscopic parts? Are the former generally determined by the latter? We argue that views on (...) these two issues are independent of one another and should not be conflated. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

The article begins by describing two longstanding problems associated with direct inference. One problem concerns the role of uninformative frequency statements in inferring probabilities by direct inference. A second problem concerns the role of frequency statements with gerrymandered reference classes. I show that past approaches to the problem associated with uninformative frequency statements yield the wrong conclusions in some cases. I propose a modification of Kyburg’s approach to the problem that yields the right conclusions. Past theories of direct inference have (...) postponed treatment of the problem associated with gerrymandered reference classes by appealing to an unexplicated notion of projectability . I address the lacuna in past theories by introducing criteria for being a relevant statistic . The prescription that only relevant statistics play a role in direct inference corresponds to the sort of projectability constraints envisioned by past theories. (shrink)

Traditionally, the term ’God’ has been understood either as a proper name or as a description. However, according to a new view, the term God’ in a sentence like "Jesus Christ is God" functions as a kind term, much as the term ’tiger’ functions in the sentence "Tigger is a tiger." In this paper I examine the claim that divinity can be construed as a ’supernatural’ kind, developing the outlines of an account of the semantics of God’ along these lines, (...) and suggest that it might solve an important philosophical problem concerning the Incarnation. (shrink)

There are two senses of ‘what scientists know’: An individual sense (the separate opinions of individual scientists) and a collective sense (the state of the discipline). The latter is what matters for policy and planning, but it is not something that can be directly observed or reported. A function can be defined to map individual judgments onto an aggregate judgment. I argue that such a function cannot effectively capture community opinion, especially in cases that matter to us.

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

In a recent article, Joel Pust argued that direct inference based on reference properties of differing arity are incommensurable, and so direct inference cannot be used to resolve the Sleeping Beauty problem. After discussing the defects of Pust's argument, I offer reasons for thinking that direct inferences based on reference properties of differing arity are commensurable, and that we should prefer direct inferences based on logically stronger reference properties, regardless of arity.

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (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)

Background Analysis of aphasic narratives can be a challenge for clinicians. Previous studies have mainly employed measures that categorized speech samples at the word level. They included quantification of the use and misuse of different word classes, presence and absence of narrative contents and errors, paraphasias, and perseverations, as well as morphological structures and errors within a narrative. In other words, a great amount of research has been conducted in the aphasiology literature focusing on micro-linguistic structures of oral narratives. Aspects (...) of macro- linguistic structures, such as the analysis of content information by a speaker, consistency of using cohesive devices to present information within a narrative, and order of presenting information necessary to form a coherent discourse, have not been extensively investigated. The current investigation proposes a clinical analytic system to target three aspects of macro-linguistic structures in narratives among speakers with aphasia. Specifically, (1) the presence of search events (i.e., the mentioning of key events that allow the listener to understand; Capilouto, Wright, &Wagovich, 2006) within a narrative, (2) the sequence of the mentioned events, and (3) the informativeness (i.e., the fulfillment of lexical items that allow the user to understand what the event is detailing) of the event contents, were focused in the proposed framework. Method Ten controls transcripts from were selected from the AphasiaBank (MacWhinney, Fromm, Forbes, & Holland, 2011). Three narrative tasks, including sequential picture description of ‘Refused Umbrella’, procedural narrative of making a ‘Peanut Butter and Jelly Sandwich’, and telling of ‘Cinderella’ story, were used to establish normative data for the basis of analysis. Specifically, the Search Events (e) and Informative Words (i) used by at least 70% of the speakers were listed for each genre. The sequential order of mentioning the Search Events, i.e., common order of events in 90% of the speakers, (s.total) was determined. Twelve speakers with aphasia (nine fluent and three non-fluent) were recruited and administered the Western Aphasia Battery and Object and Action Naming Battery. Their performance in the above three discourse tasks were orthographically transcribed and analyzed using the following measures: e.total, e.matched with norm, e.missed, e.irrlevant, e.extra, s.total, i.pb&j, i.umbr, i.cind, and i.total. Three samples were randomly chosen to be re-analyzed for inter- and intra-rater reliability. Results Results of an independent t-test suggested significant differences between the fluent and non-fluent subjects in sequential order of Search Events for all genres (s.total) and i.total, suggesting sensitivity of this framework to differentiate between the two fluency groups. Results of Pearson product-moment correlations revealed significant relation between Informative Words and WAB spontaneous speech scores, AQ, as well as OAB scores, for both aphasic groups. The mean value of coefficients for intra-rater reliability (0.992), with significant correlations on e.match, e.miss, and e.extra, was higher than that of inter-rater reliability (0.897). Discussion Based on our preliminary results, this objective framework allowed clinical evaluation of impairment in macro-linguistic structures present in aphasic discourse. Further extension should involve more subjects encompassing a wider range of severity with different types of aphasia. (shrink)

The badness of having conflicting emotions is a familiar theme in academic ethics, clinical psychology, and commercial self-help, where emotional harmony is often put forward as an ideal. Many philosophers give emotional harmony pride of place in their theories of practical reason.1 Here we offer a defense of a particular species of emotional conflict, namely, ambivalence. We articulate an conception of ambivalence, on which ambivalence is unresolved inconsistent desire (§1) and present a case of appropriate ambivalence (§2), before considering two (...) alternative defenses of emotional conflict (§3). We then argue that inconsistent desires can be fitting (§4) and that it can be reasonable not to resolve inconsistent desires (§5), before considering an objection (§6) and concluding the discussion (§7). (shrink)

This paper focuses on invasive therapeutic procedures, defined as procedures requiring the introduction of hands, instruments, or devices into the body via incisions or punctures of the skin or mucous membranes performed with the intent of changing the natural history of a human disease or condition for the better. Ethical and methodological concerns have been expressed about studies designed to evaluate the effects of invasive therapeutic procedures. Can such studies meet the same standards demanded of those, for example, evaluating pharmaceutical (...) agents? This paper describes a research project aimed at examining the interplay and sometimes apparent conflict between ethical standards for human research and standards for methodological rigor in trials of invasive procedures. The paper discusses how the authors plan to develop a set of consensus standards that, if met, would result in substantial and much-needed improvements in the methodological and ethical quality of such trials. (shrink)

According to standard scientific realism, science seeks truth and we can justifiably believe that our successful theories achieve, or at least approximate, that goal. In this paper, I discuss the implications of the following competitor thesis: Any theory we may favor has competitors such that we cannot justifiably deny that they are approximately true. After defending that thesis, I articulate three specific threats it poses for standard scientific realism; one is epistemic, the other two are axiological (that is, pertaining to (...) the claim that science seeks truth). I also flag an additional axiological “challenge,” that of how one might justify the pursuit of a primary aim, such as truth. Bracketing epistemic realism, I argue that the axiological threats can be addressed by embracing a refined realist axiological hypothesis, one that specifies a specific subclass of true claims sought in science. And after identifying three potential responses to the axiological “challenge,” I contend that, while standard axiological realism appears to lack the resources required to utilize any of the responses, the refined realist axiology I embrace is well suited to each. (shrink)

Daniel Dennett (1996) has disputed David Chalmers' (1995) assertion that there is a "hard problem of consciousness" worth solving in the philosophy of mind. In this paper I defend Chalmers against Dennett on this point: I argue that there is a hard problem of consciousness, that it is distinct in kind from the so-called easy problems, and that it is vital for the sake of honest and productive research in the cognitive sciences to be clear about the difference. But I (...) have my own rebuke for Chalmers on the point of explanation. Chalmers (1995, 1996) proposes to "solve" the hard problem of consciousness by positing qualia as fundamental features of the universe, alongside such ontological basics as mass and space-time. But this is an inadequate solution: to posit, I will urge, is not to explain. To bolster this view, I borrow from an account of explanation by which it must provide "epistemic satisfaction" to be considered successful (Rowlands, 2001; Campbell, 2009), and show that Chalmers' proposal fails on this account. I conclude that research in the science of consciousness cannot move forward without greater conceptual clarity in the field. (shrink)

Timothy O’Connor’s book Theism and Ultimate Explanation offers a defense of a new version of the cosmological argument. In his discussion, O’Connor argues against the coherence of a brute fact “explanation” of the universe and for the claim that the God of theism cannot be logically contingent. In this paper, I take issue with both of these arguments. Regarding the former, I claim that contrary to what O’Connor asserts, we have no good reason to prefer an account according to which (...) the universe is explained via a necessary being to that of a naturalist who thinks that the universe is contingent and ultimately unexplained. Regarding the latter, I argue that the possibility of a logically contingent God is fully consistent with traditional theism. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

Our aim in this paper is to explicate some unexpected and striking similarities and equally important differences, which have not been discussed in the literature, between Wittgenstein's methodology and the approach of Chinese Chan or Japanese Zen Buddhism. We say ?unexpected? similarities because it is not a common practice, especially in the analytic tradition, to invest very much in comparative philosophy. The peculiarity of this study will be further accentuated in the view of those of the ?old school? who see (...) Wittgenstein as a logical positivist, and Zen as a religious excuse for militarism or sadomasochism. If the second claim were true, the following investigation would not only be futile but also impossible. That the first claim, concerning the ?old school? perspective on Wittgenstein, is incorrect, we will demonstrate in the ensuing discussion. By now more experts have come to accept this claim and we hope that our comparative perspective will add even more momentum. (shrink)

This entry surveys a range of proposed solutions to the problem of intentionality, that is, the problem of explaining how human thoughts can be about, or be directed toward, objects. The family of solutions described here takes the content of a mental representation—what that concept represents or is about—to be a function of causal relations between mental representations and their typically external objects. This emphasis on causal relations should be understood broadly, however, so as to cover theories couched in terms (...) of law-like natural relations or the law-governed way in which one natural event carries information about another. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (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)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Transoral laser microsurgery applies to the piecemeal removal of malignant tumours of the upper aerodigestive tract using the CO2 laser under the operating microscope. This method of surgery is being increasingly popularised as a single modality treatment of choice in early laryngeal cancers (T1 and T2) and occasionally in the more advanced forms of the disease (T3 and T4), predomi- nantly within the supraglottis. Thomas Kuhn, the American physicist turned philosopher and historian of science, coined the phrase ‘paradigm shift’ in (...) his groundbreaking book The Structure of Scientific Revolutions. He argued that the arrival of the new and often incompatible idea forms the core of a new paradigm, the birth of an entirely new way of thinking. This article discusses whether Steiner and col- leagues truly brought about a paradigm shift in oncological surgery. By rejecting the principle of en block resection and by replacing it with the belief that not only is it oncologically safe to cut through the substance of the tumour but in doing so one can actually achieve better results, Steiner was able to truly revolutionise the man- agement of laryngeal cancer. Even though within this article the repercussions of his insight are limited to the upper aerodigestive tract oncological surgery, his willingness to question other peoples’ dogma makes his contribution truly a genuine paradigm shift. (shrink)

In Supersizing the Mind: Embodiment, Action, and Cognitive Extension (Clark, 2008), Andy Clark bolsters his case for the extended mind thesis and casts a critical eye on some related views for which he has less enthusiasm. To these ends, the book canvasses a wide range of empirical results concerning the subtle manner in which the human organism and its environment interact in the production of intelligent behavior. This fascinating research notwithstanding, Supersizing does little to assuage my skepticism about the hypotheses (...) of extended cognition and extended mind. In particular, Supersizing fails to make the case for the extended view as a revolutionary thesis in the theoretical foundations of cognitive science. (shrink)