COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

El artículo estudia cómo la fenomenología puede contribuir al quehacer teológico. A tal fin, el prof. Gilbert comienza por identificar los inicios de la fenomenología. Seguidamente, presenta lo que él denomina fenomenología “descriptiva”, marcada por las ciencias humanas, que sirvió para reconocer las características esenciales de la religión. Pero la fenomenología puede dar un paso más, ya estrictamente filosófico, para elaborar un modo de fenomenología “especulativa”. Finalmente, el artículo indica las aportaciones de esta esta fenomenológica al desarrollo de la (...) teología, estudiando las propuestas de Michel Henry, Jean-Luc Marion y Emmanuel Falque. (shrink)

Throughout his life, John Tyler Bonner contributed to major transformations in the fields of developmental and evolutionary biology. He pondered the evolution of complexity and the significance of randomness in evolution, and was instrumental in the formation of evolutionary developmental biology. His contributions were vast, ranging from highly technical scientific articles to numerous books written for a broad audience. This historical vignette gathers reflections by several prominent researchers on the greatness of John Bonner and the implications of his work.

What is philosophy? How should we do it? Why should we bother to? These are the kinds of questions addressed by metaphilosophy - the philosophical study of the nature of philosophy itself. Students of philosophy today are faced with a confusing and daunting array of philosophical methods, approaches and styles and also deep divisions such as the notorious rift between analytic and Continental philosophy. This book takes readers through a full range of approaches - analytic versus Continental, scientistic versus humanistic, (...) 'pure' versus applied - enabling them to locate and understand these different ways of doing philosophy. Clearly and accessibly written, it will stimulate reflection on philosophical practice and will be invaluable for students of philosophy and other philosophically inclined readers. (shrink)

We report the results of an optical analogue of the fullerene molecule diffraction experiment. Our results, and an analysis of the fullerene experiment, suggest that the patterns observed in the latter can be explained using a localized particle model. There is no evidence that the grating period contributed to the published fullerene diffraction pattern. De Broglie waves, if they exist, are unlikely to have played a significant part in the fullerene diffraction experiment. The observed patterns are not consistent with those (...) expected according to wave theory for the experimental geometry corresponding to the slit-detector system and the de Broglie wavelength. The measurements were performed in the near field, making the demonstration of wave properties difficult. We outline a new classical approach to the electron and neutron interference experiments. The magnetic moment is crucial to this model, which emphasizes a mechanism for generating narrow-band continuum X-radiation. Some experiments are proposed which can decide between the suggested model and quantum mechanics, and which can also rule out an alternative stochastic model. (shrink)

Une autre face de la philosophie du monde anglo-saxon contemporain, qui nous fait grâce de l'empirisme logique. Francis Jacques en explique la portée dans une interminable préface. Il y avait de quoi.

Racially disparate policing, prosecution, and punishment harm individuals, families, and communities. These practices must be understood within the context of the development of the criminal legal system as a means of racialized social control. This context permits a critical examination of the way criminalization has been and is still deployed to subject poor and racialized communities to systemic injustices. This commentary frames a call for interventions to integrate a health justice approach to ensure that they advance racial and health equity (...) to promote the well-being of individuals, families, and communities. (shrink)

Le proslogion de saint Anselme n'est pas une oeuvre tres connue, bien que les commentaires de ses chapitres 2 a 4 sur l'argument appele par Kant ontologique soient en nombre infini.

This article explores a case study of a mindfulness teacher, Beth, and her experiences of teaching mindfulness to 11- to 16-year-olds in several English schools. It shows why Beth was drawn to teaching mindfulness, which was both to alleviate the stress amongst her pupils and improve her own mental health. It illustrates how and why she became a confident, successful mindfulness teacher: she learnt about mindfulness at various classes, retreats and teacher-education training sessions, spending thousands of pounds on her own (...) training. It argues that her positioning as a mindfulness teacher in an unmindful school system created an overwhelming demand for her services, but also huge stress upon her. It develops McCaw’s conceptions of ‘thin’ and ‘thick’ mindfulness (2020), arguing that while Beth began by practising ‘thin’ mindfulness – seeing it as a way of solving exam stress amongst her pupils – she became increasingly a ‘thick’ practitioner; her experiences of mindfulness led to profound personal change and, ultimately, to her becoming very disillusioned about teaching mindfulness in an unwelcoming educational, ‘unmindful’ environment. (shrink)

First published in 1949, Gilbert Ryle ’s The Concept of Mind is one of the classics of twentieth-century philosophy. Described by Ryle as a ‘sustained piece of analytical hatchet-work’ on Cartesian dualism, The Concept of Mind is a radical and controversial attempt to jettison once and for all what Ryle called ‘the ghost in the machine’: Descartes’ argument that mind and body are two separate entities. This sixtieth anniversary edition includes a substantial commentary by Julia Tanney and is essential (...) reading for new readers interested not only in the history of analytic philosophy but in its power to challenge major currents in philosophy of mind and language today. (shrink)

Behavior, language, development, identity, and science—all of these phenomena are commonly characterized as 'social' in nature. But what does it mean to be 'social'? Is there any intrinsic 'mark' of the social shared by these phenomena? In the first book to shed light on this foundational question, twelve distinguished philosophers and social scientists from several disciplines debate the mark of the social. Their varied answers will be of interest to sociologists, anthropologists, philosophers, psychologists, and anyone interested in the theoretical foundations (...) of the social sciences. (shrink)

One important concern regarding implantable Brain Computer Interfaces is the fear that the intervention will negatively change a patient’s sense of identity or agency. In particular, there is concern that the user will be psychologically worse-off following treatment despite postoperative functional improvements. Clinical observations from similar implantable brain technologies, such as deep brain stimulation, show a small but significant proportion of patients report feelings of strangeness or difficulty adjusting to a new concept of themselves characterized by a maladaptive je ne (...) sais quoi despite clear motor improvement. Despite the growing number of cases in the DBS literature, there is currently no accepted or standardized tool in neuroethics specifically designed to capture the phenomenological postoperative experience of patients implanted with DBS or BCI devices. Given potential risks of postoperative maladaptation, it is important for the field of neuroethics to develop a qualitative instrument that can serve as a shared method for capturing postoperative variations in patient experience of identity and agency. The goal of this article is to introduce an instrument we have developed for this purpose and call for further neuroethical efforts to assess the phenomenology of implantable brain device use. (shrink)

We argue for peace education as a process of improving the quality of everyday relationships. This is vital, as children bring their habits formed largely by social and political institutions such as the family, religion, law, cultural mores, to the classroom (Splitter, 1993; Furlong & Morrison, 2000) and vice versa. It is inevitable that the classroom habitat, as a microcosm of the community in which it is situated, will perpetuate the epistemic practices and injustices of that community, manifested in attitudes, (...) beliefs, behaviours and actions that can limit the child’s ability to learn. The educational task then, is to create opportunities for children to problematize the very environment they inhabit. To this end, our concern is for peace education aimed at addressing epistemic violence; a form of harm brought about by a particular rationality of domination. -/- The classroom community of inquiry, initially developed by Matthew Lipman and Ann Sharp as the methodology for the Philosophy for Children (P4C) approach to education (Lipman & Sharp, 1978; Lipman, Sharp & Oscanyan, 1980), is often viewed as a solution to inequality in the classroom—an intellectually safe environment which allows students to explore, practice and internalize good reasoning through philosophy so that they can make school relevant to their lives. Traditionally, the teacher’s role is to take a ‘neutral stance’ in discussion during the conduct of a community of inquiry. However, we argue that it is misplaced to assume that the community of inquiry is a safe intellectual environment in which the teacher as co-inquirer also facilitates the discussion procedurally, letting the argument lead, which Lipman took as the guiding principle for his process of inquiry. For, as Paulo Freire (1987) put it: -/- ... the dominant ideology makes its presence in the classroom partly felt by trying to convince the teacher that he or she must be neutral in order to respect the student. This kind of neutrality is a false respect for students. On the contrary, the more I say nothing about agreeing or not agreeing out of respect for the others, the more I am leaving the dominant ideology in peace! (p. 174). -/- Teachers must be aware of the possibility of epistemic violence to be able to detect and disrupt it, in order to facilitate a peaceful inquiry. We do not consider peace in the negative, as the absence of conflict, but in the positive as the capacity to respond skilfully to conflict as a way of life. Therefore, we concentrate on peace education that prepares students to turn conflict into inquiry, rather than peace education as values education or character education that instils values of ‘fraternity and non-violence’ (Gregory, 2004, p. 277). The community of inquiry provides such a framework, however, we argue that it must be facilitated in a way that mitigates the effects of epistemic violence by creating an educational habitat in which multiple ways of knowing can flourish. (shrink)

What is a social rule? This paper first notes three important problems for H.L.A. Hart’s famous answer in the Concept of Law. An alternative account that avoids the problems is then sketched. It is less individualistic than Hart’s and related accounts. This alternative account can explain a phenomenon observed but downplayed by Hart: the parties to a social rule feel that they are in some sense ‘bound’ to conform to it.

World news can be discouraging these days. In order to counteract the effects of fake news and corruption, scientists have a duty to present the truth and propose ethical solutions acceptable to the world at large. -/- By starting from scratch, we can lay down the scientific principles underlying our very existence, and reach reasonable conclusions on all major topics including quantum physics, infinity, timelessness, free will, mathematical Platonism, happiness, ethics and religion, all the way to creation and a special (...) type of multiverse. -/- This article amounts to a summary of my personal Theory of Everything. -/- DOI: 10.13140/RG.2.2.36046.31049. (shrink)