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)

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.

Until recently, Spinoza's standing in Anglophone studies of philosophy has been relatively low and has only seemed to confirm Friedrich Heinrich Jacobi's assessment of him as "a dead dog." However, an exuberant outburst of excellent scholarship on Spinoza has of late come to dominate work on early modern philosophy. This resurgence is due in no small part to the recent revival of metaphysics in contemporary philosophy and to the increased appreciation of Spinoza's role as an unorthodox, pivotal figure - indeed, (...) perhaps the pivotal figure - in the development of Enlightenment thinking. Spinoza's penetrating articulation of his extreme rationalism makes him a demanding philosopher who offers deep and prescient challenges to all subsequent, inevitably less radical approaches to philosophy. While the twenty-six essays in this volume - by many of the world's leading Spinoza specialists - grapple directly with Spinoza's most important arguments, these essays also seek to identify and explain Spinoza's debts to previous philosophy, his influence on later philosophers, and his significance for contemporary philosophy and for us. (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)

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)

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 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)

Rationalism is the thesis that the world and all the things in the world are intelligible, through and through. Nothing happens for no reason. On the contrary, whatever takes place, whatever exists, takes place or exists for a reason. Everything. On this view there are no brute facts. Each thing that exists has a reason that is sufficient for explaining the existence of the thing. According to perhaps the most extreme implication of this view, even the world itself, the totality (...) of all that exists, exists for a reason, has an explanation. Many philosophers today think that rationalism is a crazy view. However, this paper argues in support of rationalism, and explores its implications. (shrink)

Classification of sciences; Moslem scholars; Africa, North.

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)

Resumen: El discurso de la economía ha transitado por una tensión entre pertenecer a una Ciencia Social y presentar rasgos prototípicos de una Ciencia Básica. Ahora bien, evidenciar esta hibridez desafía a los investigadores del lenguaje, sobre todo si estos textos son parte de la formación de un economista. Particularmente, el Informe de Política Monetaria no ha sido estudiado desde el punto de vista lingüístico, por lo que se busca observar, en un corpus de 45 textos, si el género IPOM (...) evidencia dicha tensión discursiva de la disciplina. Para lograr ese objetivo, se ha optado por una metodología basada en dos dimensiones: Contexto de Producción y Organización Retórico-Funcional. Tras el análisis, los hallazgos del corpus IPOM-2013 integradamente muestran que el género IPOM efectivamente evidencia dicha tensión con rasgos más características de la CB como es el uso de recursos matemáticos y, por otro lado, rasgos de la CS, asociados a la modalización del discurso en su macromovida central.: The discourse of economy has gone by a constant tension between belonging to a Social Science and present prototypical features of a Basic Science. However, evidence this hybridity poses a challenge for researchers of language, especially if these texts are part of the training of an economist. In particular, the Monetary Policy Report has not been studied from the linguistic point of view. In this context, this research search to answer the question whether the gender IPOM evidences such discursive tension of the discipline. To achieve this objective, it has opted for a methodology based on 2 dimensions: Production Context and Rhetorical-Functional Organization. After the analysis, the findings Integrally shows that the IPOM genre effectively demonstrates this tension with features more characteristic of the BS such as the use of mathematical resources and, on the other hand, SC traits, mainly associated to the modalization of the discourse in its central macromove. (shrink)

This study shows how three Chilean media construct in their discourse the social actor ‘secondary students’, in a multimodal way. It focuses on the representation of Televisión Nacional de Chile (also known as TVN), El Dínamo and El Ciudadano of this social group which is often suppressed suppressed from the media sphere. It is a qualitative study with a social semiotic approach, following the guidelines of Visual Grammar and the typology of representation of social actors by van Leeuwen (2003). The (...) corpus comprised 15 multimodal texts of 2018 compiled from internet sites, which constitute a semiotic chain of a news event about education. The results suggest that TVN creates the meaning of an ‘aggressor student’, El Dínamo as a ‘student to be reformed’; whereas El Ciudadano, represents him as a social actor who is an ‘active participant’. (shrink)

Resumen: Este trabajo ofrece evidencia empírica a la premisa que sostiene que el acercamiento teórico y metodológico de la Lingüística al estudio de géneros del ámbito profesional, no ha tenido el mismo énfasis que el académico (Cassany y López, 2011; Montolío & López, 2010; Autor, 2016; Lillis, 2021). En este sentido, el objetivo de esta investigación fue describir el estudio de los géneros profesionales entre 2008 y 2017 en las 10 principales revistas de Lingüística en América Latina. Para ello se (...) utilizó un enfoque mixto en un corpus de 1.729 publicaciones. Los resultados indican que solo el 1,85% de los estudios abordan géneros profesionales, principalmente, acerca de Artículos de Investigación Científica (36,3%), Sentencias Judiciales (27,2%) y Noticias (18,1%), lo que evidencia un reto pendiente que tiene hasta hoy la Lingüística. Abstract: This paper provides empirical evidence to the premise that the theoretical and methodological approach of Linguistics to the study of genres of the professional field has not had the same emphasis as the academics ones (Cassany & López, 2011; Montolío & López, 2010; Author, 2006, Lillis, 2021). In this sense, the objective of this research was to describe the study of professional genres between 2008 and 2017 in the 10 leading journals of Linguistics in Latin America. For this, a mixed approach was used in a corpus of 1,729 publications. The results indicate that only 1.85% of the researchs analizes professional genres, mainly about Articles of Scientific Research (36.3%), Judicial Sentences (27.2%) and News (18.1%), which evidences a pending challenge in Linguistics. (shrink)

El presente ensayo se ocupa de una de las obras capitales de Rorty –Contingencia, ironía y solidaridad– en la que es posible encontrar las claves de su pensamiento ético y político. El sujeto de Rorty es “el ironista”, los ciudadanos de su sociedad liberal son quienes perciben la contingencia de su lenguaje de deliberación moral, aquella serie de palabras que le permiten justificar sus acciones, creencias y vida. Estas son las palabras con las que narramos prospectiva o retrospectivamente nuestras vidas, (...) un léxico último. Desde el neo-pragmatismo de Rorty se muestran las condiciones que han hecho posible que las sociedades se consideren a sí mismas como contingencias históricas antes que como expresiones de una subyacente naturaleza ahistórica o, si se quiere, realizaciones de metas suprahistóricas. Rorty sostiene que es en realidad la literatura, y no la filosofía, la que puede promover un sentido genuino de la solidaridad humana; esto a partir de la lectura de novelistas como Orwell y Nabokov. Se busca la descripción ya no de formulaciones abstractas, sino de experiencias humanas concretas, como el dolor o la traición, las que al ser compartidas, generen la necesaria empatía desde la cual se geste la solidaridad y la compasión. (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)

In Practicing Safe Sects F. LeRon Shults provides scientific and philosophical resources for having “the talk” about religious reproduction: where do gods come from – and what are the costs of bearing them in our culturally pluralistic, ecologically fragile environment?

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)