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)

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)

Music can reduce stress and anxiety, enhance positive mood, and facilitate social bonding. However, little is known about the role of music and related personal or cultural variables in maintaining wellbeing during times of stress and social isolation as imposed by the COVID-19 crisis. In an online questionnaire, administered in 11 countries, participants rated the relevance of wellbeing goals during the pandemic, and the effectiveness of different activities in obtaining these goals. Music was found to be the most effective activity (...) for three out of five wellbeing goals: enjoyment, venting negative emotions, and self-connection. For diversion, music was equally good as entertainment, while it was second best to create a sense of togetherness, after socialization. This result was evident across different countries and gender, with minor effects of age on specific goals, and a clear effect of the importance of music in people's lives. Cultural effects were generally small and surfaced mainly in the use of music to obtain a sense of togetherness. Interestingly, culture moderated the use of negatively valenced and nostalgic music for those higher in distress. (shrink)

Deficits in social cognition and more specifically in communication have an important impact on the real-life functioning of people with schizophrenia. In particular, patients have severe problems in communicative-pragmatics, for example, in correctly inferring the speaker’s communicative intention in everyday conversational interactions. This limit is associated with morphological and functional alteration of the left middle temporal gyrus, a cerebral area involved in various communicative processes, in particular in the distinction of ironic communicative intention from sincere and deceitful ones. We performed (...) an fMRI study on 20 patients with SZ and 20 matched healthy controls while performing a pragmatic task testing the comprehension of sincere, deceitful, and ironic communicative intentions. We considered the L-MTG as the region of interest. SZ patients showed difficulties in the correct comprehension of all types of communicative intentions and, when correctly answering to the task, they exhibited a higher activation of the L-MTG, as compared to HC, under all experimental conditions. This greater involvement of the L-MTG in the group of patients could depend on different factors, such as the increasing inferential effort required in correctly understanding the speaker’s communicative intentions, and the higher integrative semantic processes involved in sentence processing. Future studies with a larger sample size and functional connectivity analysis are needed to study deeper the specific role of the L-MTG in pragmatic processes in SZ, also in relation to other brain areas. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:THE TRINITY AND FEMINISM * GREGORY RoccA, O.P. Dominican School of Philosophy and Theology Berkeley, California SPEAKING THE CHRISTIAN GOD is a substantial and fundamental theological response to the basic assumptions and conclusions of the burgeoning feminist movement within Christian theology. Its opponent is clearly theological feminism, not that egalitarian feminism which seeks justice for women within church and society. Noting the " paucity of critical response from (...) the theologians of the church " to the challenge of feminism, the editor states the book attempts " to substantively and critically engage specific feminist thinkers " about the doctrine of God and God-talk, and " to offer constructive discussion and analysis of the crucial and often very complex theological issues." With only a couple of exceptions, the individual articles succeed admirably in the second aim, though only about half offer a substantive engagement with specific feminist thinkers (the most frequent debate partners are Sallie McFague and Rose~ mary Radford Ruether, and the single most cited line is Mary Daly's " If God is male, then the male is God "). The editor also warns us that polemic has often not been avoided, for " when the gospel of Jesus Christ is at stake, passion also must enter into theology." However, again with only a couple of exceptions, I found the individual essays to be models of rational criticism and controversy which avoid the kind of emotional attack that delights in sarcasm, personal vituperation, and ad feminam arguments. *Speaking the Christian God: The Holy Trinity and the Challenge of Feminism. Edited by Alvin F. Kimel, Jr. Grand Rapids, Michigan/Leominster, England: Eerdmans/Gracewing, 1992. Pp. x + 337. 509 510 GREGORY ROCCA, O.P. The book's eighteen contributors (thirteen men and five women) share the fundamentals of Christian belief and span the various Christian confessions, though the great majority are from the Protestant traditions. This collection does not entirely escape the anthological bane of uneven quality (though almost all the essays are excellent), repetition, and lack of focal unity (the common target is feminism but the responses to it are varied). As an aid in discerning the focal unity behind these diverse rejoinders to feminism, I will synthesize the essays under four basic questions : How do we speak the Christian God? Why do we speak the Christian God as Father? What does speaking the Christian God as Father teach us about God and ourselves? Why does theological feminism have trouble with speaking the Christian God as Father? First Question: How do we speak the Christian God? According to different essayists-by simile, metaphor, analogy qualified by negative theology, and personal name. Some point out the differences between these various ways of speaking God and then try to show how, in at least one of the ways, Father is God's ineradicable and eternal name. Thus, they defend Father as the Trinity's nomen primum and critique the feminists for conflating the distinct ways by which we speak God. Roland Frye, Garrett Green, Colin Gunton and Janet Martin Soskice all focus on Father as a metaphorical name for God. Frye maintains there is an essential difference between simile and metaphor, and that Father is God's most fitting metaphorical name. While God is a few times compared to a mother by illustrative simile (mainly in Second and Third Isaiah), he is never named mother or addressed as mother; more positively, the appellative and predicative metaphor Father is said of God directly or vocatively about 250 times in the Old and New Testaments. One might wonder, however, whether the division between metaphor and simile is so airtight. Are not all metaphors immediately translatable back into similes? The answer is No, according to Garrett Green, who explains how contemporary thinkers see metaphor not as atomistic and substitutional (the classical view) but as contextualized and THE TRINITY AND FEMINISM 511 unique. Thus, Father is God's unique metaphorical name which transcends mere simile. Still, one might counter that metaphors are protean and plastic: if Father can be said uniquely of God, then why not also Mother? Gunton addresses himself to this objection in dialogue with Sallie McFague, contending that a realist theological epistemology shows that divine metaphor cannot be totally protean but... (shrink)

In his recent The Parmenidean Ascent, Michael Della Rocca develops a regress-theoretic case, reminiscent of F.H. Bradley’s famous argument in Appearance and Reality, against the intelligibility of relations and in favor of a monistic conception of reality. I argue that Della Rocca illicitly supposes that “internal” relations – in one sense of that word – lead to a “chain” regress, a regress of relations relating relations and relata. In contrast, I contend that if “internal” or grounded relations lead (...) to a regress at all, it is a kind of “fission” regress within the relata themselves, and that a chain regress for relations only arises, if at all, for so-called “external” relations, relations not grounded in their relata. In this way, I contend that Della Rocca pursues a regress for so-called “internal” or grounded relations that only arises, if at all, for so-called “external” relations, relations not grounded in their relata. I compare Della Rocca’s case against relations with Bradley’s reasoning in Appearance and Reality, and suggest in this context that Bradley may, perhaps, have the upper hand. (shrink)

In his recent _The Parmenidean Ascent_, Michael Della Rocca develops a regress-theoretic case, reminiscent of F. H. Bradley’s famous argument in _Appearance and Reality_, against the intelligibility of relations and in favor of a monistic conception of reality. I argue that Della Rocca illicitly supposes that “internal” relations — in one sense of that word — lead to a “chain” regress, a regress of relations relating relations and relata. In contrast, I contend that if “internal” or grounded relations (...) lead to a regress at all, it is a kind of “fission” regress within the relata themselves, and that a chain regress for relations only arises, if at all, for so-called “external” relations, relations not grounded in their relata. In this way, I contend that Della Rocca pursues a regress for so-called “internal” or grounded relations that only arise, if at all, for so-called “external” relations, relations not grounded in their relata. I compare Della Rocca’s case against relations with Bradley’s reasoning in _Appearance and Reality_ and suggest in this context that Bradley may, perhaps, have the upper hand. (shrink)

The Principle of Sufficient Reason (PSR) holds that, for everything that exists or occurs or holds true, there is a reason why that is the case. I consider three possible ways of relating physics to the PSR: past states as reasons for present states, reasons why the laws of physics take the form that they do, and reasons why there is anything at all. In each case I suggest that the PSR is not the best way of thinking about how (...) and why physics works. -/- Invited reflection for The Principle of Sufficient Reason (Oxford Philosophical Concepts), Eds. F. Amijee and M. Della Rocca (forthcoming 2024). (shrink)

This article focusses on the generality of the entities involved in a geometric proof of the kind found in ancient Greek treatises: it shows that the standard modern translation of Greek mathematical propositions falsifies crucial syntactical elements, and employs an incorrect conception of the denotative letters in a Greek geometric proof; epigraphic evidence is adduced to show that these denotative letters are ‘letter-labels’. On this basis, the article explores the consequences of seeing that a Greek mathematical proposition is fully general, (...) and the ontological commitments underlying the stylistic practice. (shrink)

In my dissertation I approach the subject of the attributes of God in Spinoza's metaphysics by considering three pivotal and closely linked problems. I discuss the problem of the relation of God to the attributes, the problem of the essence of God, and the problem of the true conception of God. ;I examine three interpretations of God and the attributes in Spinoza: that of Jonathan Bennett, according to which God is the thing that has the attributes and modes as properties, (...) that of Edwin Curley and Alan Donagan, according to which God is the collection of attributes, and that of H. F. Hallett and Steven Parchment, according to which God is the totality of attributes. I examine each stance relative to the three problems. I reveal the weaknesses of each interpretation by making explicit the problems that each interpretation is unable to deal with successfully and by exposing new problems that some of the interpretations create. I then discuss topics in Spinoza that need to be understood in order to arrive at the correct answers to the three problems. For example, I carefully examine 2D2---a definition that commentators on Spinoza generally consider imperative in the discussion of the essence of God. ;I then suggest an interpretation of God and the attributes that is motivated by Spinoza's claim in 1P34 that God's power is God's essence. I claim that an adequate idea of the essence of God is a de re conception of God; and I invoke Michael Della Rocca's account of the opacity of attribute-contexts in order to support my view of de re conceptions of God. I show that, for Spinoza, the essence of a thing is given by the definition of the thing; and I show that 1D6 correlates with his claim in 1P34 that God's power is God's essence. I argue that God's essence is absolutely infinite and eternal power, and that power is what is constituted and expressed by each of the infinite attributes. (shrink)

The 1996 European Summer Meeting of the Association of Symbolic Logic was held held the University of the Basque Country, at Donostia (San Se bastian) Spain, on July 9-15, 1996. It was organised by the Institute for Logic, Cognition, Language and Information (ILCLI) and the Department of Logic and Philosophy of Sciences of the University of the Basque Coun try. It was supported by: the University of Pais Vasco/Euskal Herriko Unib ertsitatea, the Ministerio de Education y Ciencia (DGCYT), Hezkuntza Saila (...) (Eusko Jaurlaritza), Gipuzkoako Foru Aldundia, and Kuxta Fun dazioa. The main topics of the meeting were Model Theory, Proof Theory, Re cursion and Complexity Theory, Models of Arithmetic, Logic for Artifi cial Intelligence, Formal Semantics of Natural Language and Philosophy of Contemporary Logic. The Program Committee consisted of K. Ambos Spies (Heidelberg), J.L. Balcazar (Barcelona), J.E. Fenstad (Oslo), D. Israel (Stanford), H. Kamp (Stuttgart), R. Kaye (Birmingham), J.M. Larrazabal (San Sebastian), D. Lascar (Paris, chairman), A. Marcja (Firenze), G. Mints (Stanford), M. Otero (Madrid), S. Ronchi della Rocca (Torino), K. Segerberg (Uppsala) and L. Vega (Madrid). The organizing Committee consisted of X. Arrazola (San Sebastian), A. Arrieta (San Sebastian), R. Beneyeto (Valencia), B. Carrascal (San Se bastian), K. Korta (San Sebastian), J.M. Larrazabal (San Sebastian, chair man), J.C. Martinez (Barcelona), J.M. Mendez (Salamanca), F. Migura (Victoria) and J. Perez (Victoria). (shrink)

Arthur Danto has made important contributions to both aesthetics and philosophy of history. Furthermore, as I shall try to show in this essay, his aesthetics is of great relevance to his philosophy of history, while his philosophy of history is of no less interest for his aesthetics.By focusing on the notions of representation, identity, and the identity of indiscernibles we shall discover how fruitful this cooperation of aesthetics and philosophy of history may be. Crucial to all historical writing and, hence, (...) to all philosophy of history, is the notion of identity through time and change. How could the historian write the history of x if x cannot be said to remain the same in the course of its history? It will become clear that aesthetics will provide us with a satisfactory solution for the problem, for the aestheticist notion of representation will enable us to define the notion of identity that the historian needs.Nevertheless, a certain friction can be observed between Danto's aesthetics and his philosophy of history. At the end of this essay I hope to show that Danto's philosophy of history will be our best guide to dealing adequately with this friction. (shrink)

Interdisciplinary dialogue with contemporary sciences question the coherence and plausibility of many traditional Christological formulations. This book attempts to show that engaging in this interdisciplinary endeavour is both possible and promising.

This chapter contains sections titled: Introduction Origins of the Contemporary Debate Historiographic Research and Writing Two Variants of Narrativist Philosophy of Historiography The Philosophical Approach The Transcendentalization of Narrativist Philosophy of Historiography Rhetorical Narrativist Philosophy Hayden White Conclusion Bibliography.

This paper considers papers on conceptual analysis by Laudan (1981) and Whitt (1989) and relates them to three biochemical episodes: (1) the modern 'biochemical explanation' of acupuncture; (2) the chemio-osmotic hypothesis of oxidative phosphorylation; (3) the theory of the complete digestion of proteins in the gut. The advantages of including philosophical debate in chemical/biochemical undergraduate courses is then discussed.

We initiate the study of computable presentations of real and complex C*-algebras under the program of effective metric structure theory. With the group situation as a model, we develop corresponding notions of recursive presentations and word problems for C*-algebras, and show some analogous results hold in this setting. Famously, every finitely generated group with a computable presentation is computably categorical, but we provide a counterexample in the case of C*-algebras. On the other hand, we show every finite-dimensional C*-algebra is computably (...) categorical. (shrink)