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)

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)

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)

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)

I argue that the standard counterexamples to the identity of indiscernibles fail because they involve a commitment to a certain kind of primitive or brute identity that has certain very unpalatable consequences involving the possibility of objects of the same kind completely overlapping and sharing all the same proper parts. The only way to avoid these consequences is to reject brute identity and thus to accept the identity of indiscernibles. I also show how the rejection of the identity of indiscernibles (...) derives some of its support from its affinity with a Kripkean account of trans-world identity and theories of direct reference. (shrink)

This paper analyzes and evaluates Spinoza way of carrying out his naturalistic program in psychology. I begin by examining Spinoza’s general metaphysical doctrine according to which each thing strives to preserve itself. While this doctrine cannot be true in its unqualified form, it does receive some support from Spinoza’s views on the nature of complex individuals. I then explore the problematic way in which Spinoza applies the doctrine of self -preservation to human psychology. The paper goes on the investigate the (...) naturalistic character of Spinoza’s views on such topics as irrational action, prudence, altruism, mental causation and the nature and classification of affects. (shrink)

Gregory Rocca's nuanced discussion prevents Aquinas's thought from being capsulized in familiar slogans and is an antidote to unilateralist or monochrome views about God-talk.

The article addresses some aspects of Gava’s book, highlighting two main points: (1) the notion of philosophy in a cosmic sense; (2) its connection with the meaning of the concept of method. Regarding (1) I show how Gava’s interpretation of the systematic concept of philosophy does not account adequately for the scholastic concept. This has consequences for the notion of philosophy in a cosmic sense itself; its nature as an objective archetype and its personification in the ideal of a master (...) of wisdom are not properly emphasized. These features are closely related to Kant’s claim that philosophy cannot be learned, which is connected with Kant’s peculiar idea of method. Regarding (2), I argue that ‘method’ for Kant does not concern only the construction of scientific systems, but also the establishment of a way of thinking, a stance embracing thought and action. The meaning of the postulates and the notion of ‘faith’ thus acquire a ‘weaker’ connotation, as an attitude, habitus, aimed at the establishment and promotion of a ‘life-structuring’ rationality, and not as an alternative route to a theoretical ‘commitment’. (shrink)

This paper critically examines a prominent and perennial strategy—found in thinkers as diverse as Kant and Shamik Dasgupta—of simultaneously embracing the Principle of Sufficient Reason and also limiting it so as to avoid certain apparently negative consequences of an unrestricted PSR. I will argue that this strategy of taming the PSR faces significant challenges and may even be incoherent. And for my purposes, I will enlist a generally derided argument by Leibniz for the PSR which will help us to see (...) the connections between the PSR and a radical form of monism. (shrink)

What are Descartes's criteria for substance, and how many material objects meet them? A passage in the Synopsis of the Meditations has led some to portray him as a monist about extended substance and others to say that he does not even use “extended substance” as a count term. After considering Descartes's two criteria for substance, as well as his account of transubstantiation, we see that these answers are mistaken. Descartes countenances an infinity of extended substances. These are quantities of (...) matter that can survive any rearrangement or scattering of their parts, but not the annihilation of any of them. (shrink)

The Parmenidean Ascent is a full-throated and wide-ranging defense of an extreme form of monism or the denial of all distinctions, a form of monism rarely seen since the time of the pre-Socratic philosopher, Parmenides. At once historically sensitive and deeply engaged with trends in recent and contemporary metaphysics, philosophy of action, epistemology, and philosophy of language, The Parmenidean Ascent aims, on rationalist grounds and in a skeptical spirit, to challenge the content of-and to overturn the methods of much of (...) contemporary philosophy. (shrink)

Spinoza's response to a certain radical form of scepticism has deep and surprising roots in his rationalist metaphysics. I argue that Spinoza's commitment to the Principle of Sufficient Reason leads to his naturalistic rejection of certain sharp, inexplicable bifurcations in reality such as the bifurcations that a Cartesian system posits between mind and body and between will and intellect. I show how Spinoza identies and rejects a similar bifurcation between the representational character of ideas or mental states and the epistemic (...) status of these ideas, a bifurcation to which Spinoza sees the radical sceptic committed. Spinoza's rejection of this bifurcation helps to explain some of his most cryptic statements concerning scepticism and also reveals a promising and highly metaphysical strategy for understanding and responding to scepticism. (shrink)

This paper presents an argument for the Principle of Sufficient Reason, the PSR, the principle according to which each thing that exists has an explanation. I begin with several widespread and extremely plausible arguments that I call explicability arguments in which a certain situation is rejected precisely because it would be arbitrary. Building on these plausible cases, I construct a series of explicability arguments that culminates in an explicability argument concerning existence itself. This argument amounts to the claim that the (...) PSR is true. The plausibility of the initial cases in the series provides the basis of an argument for the PSR, an argument that can be rebutted only by drawing a line between the plausible early cases in the series and the apparently unacceptable later cases. I argue that no principled reason for drawing this line has been found and that one cannot draw an unprincipled or arbitrary line without begging the question. The paper concludes that, therefore, this defense of the PSR remains unrebutted and that we have a powerful, new reason to embrace the PSR. (shrink)

This first extensive study of Spinoza's philosophy of mind concentrates on two problems crucial to the philosopher's thoughts on the matter: the requirements for having a thought about a particular object, and the problem of the mind's relation to the body. Della Rocca contends that Spinoza's positions are systematically connected with each other and with a principle at the heart of his metaphysical system: his denial of causal or explanatory relations between the mental and the physical. In this way, (...) Della Rocca's exploration of these two problems provides a new and illuminating perspective on Spinoza's philosophy as a system. (shrink)

This paper offers a defense of a much-maligned Leibnizian argument for the Principle of Sufficient Reason, the principle according to which whatever is has a sufficient reason or explanation. While Leibniz’s argument is widely thought to rely on a question-begging premise, the paper offers a wholly original and non-question-begging defense of that premise, a defense that Leibniz did not anticipate. The paper does not present this defense of Leibniz's argument as an interpretation of Leibniz; rather, the paper—more modestly in one (...) way, less modestly in another—simply claims that this argument succeeds. (shrink)

Scientific risk evaluations are constructed by specific evidence, value judgements and biological background assumptions. The latter are the framework-setting suppositions we apply in order to understand some new phenomenon. That background assumptions co-determine choice of methodology, data interpretation, and choice of relevant evidence is an uncontroversial claim in modern basic science. Furthermore, it is commonly accepted that, unless explicated, disagreements in background assumptions can lead to misunderstanding as well as miscommunication. Here, we extend the discussion on background assumptions from basic (...) science to the debate over genetically modified (GM) plants risk assessment. In this realm, while the different political, social and economic values are often mentioned, the identity and role of background assumptions at play are rarely examined. We use an example from the debate over risk assessment of stacked genetically modified plants (GM stacks), obtained by applying conventional breeding techniques to GM plants. There are two main regulatory practices of GM stacks: (i) regulate as conventional hybrids and (ii) regulate as new GM plants. We analyzed eight papers representative of these positions and found that, in all cases, additional premises are needed to reach the stated conclusions. We suggest that these premises play the role of biological background assumptions and argue that the most effective way toward a unified framework for risk analysis and regulation of GM stacks is by explicating and examining the biological background assumptions of each position. Once explicated, it is possible to either evaluate which background assumptions best reflect contemporary biological knowledge, or to apply Douglas' 'inductive risk' argument. (shrink)

Appearing in English for the first time, Schelling’s 1842 lectures develop the idea that many philosophical concepts are born of religious-mythological notions.

By invoking surprising rationalist considerations that Bernard Williams does not anticipate, this paper defends Williams’s claim that that moral criticism on the basis of purported external reasons amounts to ‘bluff’. After strengthening this rejection of external reasons by drawing parallels to compelling rationalist arguments in other domains, the paper mounts a similarly rationalist critique of internal reasons invoked by Kantian moral philosophers. The paper closes with an apocalyptic line of thought that develops the preceding rationalist arguments into a challenge to (...) the notion of acting for reasons in general. (shrink)

The intelligibility of change in Descartes Content Type Journal Article DOI 10.1007/s11016-010-9494-0 Authors Michael Della Rocca, Department of Philosophy, Yale University, P.O. Box 208306, New Haven, CT 06520-8306, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.

Se busca dar cuenta del origen y naturaleza de la noción ética y psicoanalítica de culpa. Tanto Freud como Nietzsche se han ocupado de la genealogía de este concepto; cada uno, desde ámbitos distintos, pero que en forma sorprendente confluyen. Asimismo se examina como la noción de culpa es el motivo literario y clave hermenéutica de la sobrecogedora obra de Kafka, lector de Freud. Obras como El proceso, La condena, etc., lo evidencian. La tesis central que aúna este amplio registro (...) de obras y autores referidos ―y en la que radica el valor de este trabajo― es la idea freudiana que la conciencia de culpa preexiste a la falta, esto es, de la existencia de una culpabilidad constitutiva o internalizada que podría ser atribuida a la tradición judeo-cristiana, según la imputación de Nietzsche que se funda en un entramado genealógico más complejo. (shrink)

This paper starts with one of Chalmers’ basic points: first-hand experience is an irreducible field of phenomena. I claim there is no ‘theoretical fix’ or ‘extra ingredient’ in nature that can possibly bridge this gap. Instead, the field of conscious phenomena requires a rigorous method and an explicit pragmatics for its exploration and analysis. My proposed approach, inspired by the style of inquiry of phenomenology, I have called neurophenomenology. It seeks articulations by mutual constraints between phenomena present in experience and (...) the correlative field of phenomena established by the cognitive sciences. It needs to expand into a widening research community in which the method is cultivated further. (shrink)