Miranda Fricker's original presentation of Hermeneutical Injustice left open theoretical choice points leading to criticisms and subsequent clarifications with the resulting dialectic appearing largely verbal. The absence of perspicuous exposition of hallmarks of Hermeneutical Injustice might suggest scenarios exhibiting some – but not all – such hallmarks are within its purview when they are not. The lack of clear hallmarks of Hermeneutical Injustice, moreover, obscures both the extent to which Fricker's proposed remedy Hermeneutical Justice – roughly, virtuous communicative practices – (...) adequately addresses the injustice, and the accuracy of criticisms suggesting that Hermeneutical Justice is insufficient to the task. In what follows, after briefly defending necessary and sufficient conditions for what I take to be the best candidate interpretation of Hermeneutical Injustice, I build on recent work on moral responsibility to construct and defend a rigorous explication of Hermeneutical Justice. (shrink)

Although the last decade has seen a proliferation of ontological approaches to arguments, many of them employ ad hoc solutions to representing arguments, lack interoperability with other ontologies, or cover arguments only as part of a broader approach to evidence. To provide a better ontological representation of arguments, we present the Arguments Ontology (ArgO), a small ontology for arguments that is designed to be imported and easily extended by researchers who work in different upper-level ontology frameworks, different logics, and different (...) approaches to argument evaluation. Unlike most ontological approaches to arguments, ArgO utilizes Basic Formal Ontology (BFO) as an upper-level ontology, and may be used alongside other commonly used ontologies in the BFO framework, including boththe Information Artifact Ontology (IAO), and the Information Entity Ontology (INFO). Critically, our proposal is principled, based on rigorous definitions and formal axioms out of which characterizations of arguments naturally fall. It is our hope that ArgO may assist researchers in many projects, including: integrating heterogeneous sources of evidence, structuring the content of semantic wikis, and enhancing semantic reasoning. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and relations employing the (...) BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

Moeser suggested participants default to linear ordering elements but they can be primed to impose either linear or partial ordering. This study seems problematic insofar as ‘greater than’ might be understood to incline participants to favor linear orderings. Recent follow-up studies strongly suggest participants do not default to linear ordering. It seems plausible, moreover, that the observed priming effect is far more pervasive than Moeser countenanced. The present work explores the extent to which priming for linear or partial orders conflicts (...) with the construction of linear or partial ordering lists. Our two experiments suggest friction between priming and task, and also show once the priming tasks are cleared of potentially confounding semantic content, participants perform equally with respect to constructing linear or partial orders under similar priming conditions. (shrink)

If a person requires an organ or tissue donation to survive, many philosophers argue that whatever moral responsibility a biological relative may have to donate to the person in need will be grounded at least partially, if not entirely, in biological relations the potential donor bears to the recipient. We contend that such views ignore the role that a potential donor's unique ability to help the person in need plays in underwriting such judgments. If, for example, a sperm donor is (...) judged to have a significant moral responsibility to donate tissue to a child conceived with his sperm, we think this will not be due to the fact that the donor stands in a close biological relationship to the recipient. Rather, we think such judgments will largely be grounded in the presumed unique ability of the sperm donor to help the child due to the compatibility of his tissues and organs with those of the recipient. In this paper, we report the results of two studies designed to investigate the comparative roles that biological relatedness and unique ability play in generating judgments of moral responsibility in tissue donation cases. We found that biologically related individuals are deemed to have a significant moral responsibility to donate tissue only when they are one of a small number of people who have the capacity to help. (shrink)

Do biological relations ground responsibilities between biological fathers and their offspring? Few think biological relations ground either necessary or sufficient conditions for responsibility. Nevertheless, many think biological relations ground responsibility at least partially. Various scenarios, such as cases concerning the responsibilities of sperm donors, have been used to argue in favor of biological relations as partially grounding responsibilities. In this article, I seek to undermine the temptation to explain sperm donor scenarios via biological relations by appealing to an overlooked feature (...) of such scenarios. More specifically, I argue that sperm donor scenarios may be better explained by considering the unique abilities of agents involved. Appealing to unique ability does not eliminate the possibility of biological relations providing some explanation for perceived responsibilities on the part of biological fathers. However, since it is unclear exactly why biological relations are supposed to ground responsibility in the first place, and rather clear why unique ability grounds responsibility in those scenarios where it is exhibited, the burden of proof seems shifted to those advocating biological relations as grounds of responsibility to provide an explanation. Since this seems unlikely, I conclude it is best to avoid appealing to biological relations as providing grounds for responsibility. (shrink)

The field of AI has undergone a series of transformations, each marking a new phase of development. The initial phase emphasized curation of symbolic models which excelled in capturing reasoning but were fragile and not scalable. The next phase was characterized by machine learning models—most recently large language models (LLMs)—which were more robust and easier to scale but struggled with reasoning. Now, we are witnessing a return to symbolic models as complementing machine learning. Successes of LLMs contrast with their inscrutability, (...) inaccuracy, and hallucinations, which underwrite concerns over the reliability and trustworthiness of these systems, motivating investigations into commonsense reasoning, AI explainability, and formal verification techniques. Moreover, proper assessments of hybrid machine learning/symbolic systems require novel strategies to facilitate comparisons of performance and guide future AI progress. The EDGeS AAAI 2023 Spring symposium brought together researchers focusing on novel assessments and benchmarks for evaluating hybrid and artificial general intelligence (AGI) systems. This symposium revealed what was already suspected: research concerning evaluation of machine learning/symbolic hybrids and AGI is, unfortunately, lacking. Even so, the discussion was fruitful. (shrink)

Volume 19, Issue 11, November 2019, Page 32-34.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Dilip Ninan has raised a puzzle for centered world accounts of de re attitude reports extended to accommodate what he calls “counterfactual attitudes.” As a solution, Ninan introduces multiple centers to the standard centered world framework, resulting in a more robust semantics for de re attitude reports. However, while the so-called multi-centered world proposal solves Ninan’s counterfactual puzzle, this additional machinery is not without problems. In Section 1, I present the centered world account of attitude reports, followed by the extension (...) to counterfactual attitudes which Ninan targets with his puzzle. In Section 2, I pose the counterfactual puzzle and present Ninan’s multi-centered world solution, emphasizing similarities and differences between multi-centered and centered world accounts of attitude reports. In Section 3, I argue the counterfactual attitude wishing falls under the purview of the multi-centered proposal, but that the proposal generates false predictions for wish reports concerning unsatisfiable content. I canvass responses, ultimately concluding Ninan’s proposal requires substantial revisions. (shrink)

Imagine my surprise at discovering - tucked inside the cover of a first edition Alice in Wonderland – an unknown dialogue written by Lewis Carroll himself! It was scribbled on the back of a napkin, punctuated by Carroll’s tell-tale signature, and seems to have been written hastily. Carroll is known among laypersons as an absurdist, but he’s esteemed among formal thinkers as impressively logical. You can probably then imagine my further surprise at discovering various fallacies and confusions in the dialogue! (...) I counted equivocations over use/mention, identity/predication, measurements, and lexical/material parthood, but I’m sure there are more hiding. -/- If you share my interest in untangling these errors, I’ve copied Carroll’s dialogue below. I’ve found the task best pursued with help, whether students, interns, sisters, tarot readers, etc. As you’ll see, I’ve divided the dialogue into five sections, of varying difficulties. I recommend dividing helpers accordingly, assigning one section per group, then directing each to identify both good and bad reasoning in the section. After some time, groups should pass their discoveries to other groups for scrutiny. For example, if group 1 examined section 1, they’d pass their discoveries to group 2 who then checks group 1’s work against section 1. Proceed until each group has examined each section and – hopefully – you’ll find all the errors. Happy hunting! (shrink)

There is more responsibility on heaven and earth than dreamt of in most philosophy. This dissertation explores three debates in three sub-fields of philosophy, highlighting in each responsibilities agents find themselves with whether they like it or not. In the chapter "Trust Logic, Not Tortoises", I propose an answer to Wright’s Justification Question – to what extent are we justified in our knowledge of logic? – arguing early knowledge of logic is a species of know-how underwritten by dispositions to infer (...) that are themselves often refined into more sophisticated dispositions to infer as we develop. Given how foundational such know-how is to our understanding of the world, we find ourselves responsible for cultivating more sophisticated reasoning, whatever its provenance. In the chapter Ties that Undermine, I argue attributions to an agent of moral responsibility are largely influenced by the perceived rareness of that agent's ability to provide aid or prevent harm, degree of aid provided or harm prevented, and cost to that agent in providing aid or preventing harm. Voluntary adoption of such moral responsibility is not necessary for an agent to be morally responsible. I generalize this result to the epistemic domain in the chapter Speak No Evil: Understanding Hermeneutical (In)justice, arguing attributions to an agent of epistemic responsibility are also influenced by the perceived rareness of that agent's ability to generate true beliefs in themselves and others, extent of benefit provided and harm prevented by having such true beliefs, and cost to that agent in generating such true beliefs. Here, we see voluntary adoption of such epistemic responsibility is not necessary for an agent to be epistemically responsible. By exploring the relevance of such responsibility to three distinct debates in three distinct sub-fields of philosophy, this dissertation highlights how pervasive responsibility is to the lives of agents, and the work of philosophers. (shrink)

In the September 2020 edition of Perception, Alan Gilchrist published an editorial entitled “The Integrity of Vision” (Gilchrist, 2020). In it, Gilchrist critiques motivated perception research. His main points are as follows: (1) Motivated perception is compromised by experimental demand: Results do not actually show motivated perception but instead reflect subjects’ desires to comply with inferred predictions. (2) Motivated perception studies use designs that make predictions obvious to subjects. These transparent designs conspire with experimental demand to yield confirmatory but compromised (...) results. (3) Motivated perception research lacks guiding theory and cannot explain what appear to be contradictory results. (4) Motivated perception presents an unsupportable assault upon the impermeability of perception. The present commentary responds to these four assertions. (shrink)

With the naturalist worldview having become widely accepted, the trend of naturalistic Buddhism has likewise become popular in both academic and religious circles. In this article, I preliminarily reflect on this naturalized approach to Buddhism in two main sections. In section 1, I point out that the Buddha rejects theistic beliefs that claim absolute power over our destiny, opting instead to encourage us to inquire intellectually and behave morally. The distinguishing characteristics of naturalism such as a humanistic approach, rational enquiry, (...) empirical observation, as well as a pragmatic and realistic outlook can all be seen in the Buddha’s teachings. In section 2, however, I advance arguments to show that while the Buddha is opposed to theistic doctrines, his views are not entirely in accordance with the presuppositions of naturalism. Firstly, the Buddha’s foremost concern is not purely intellectual in nature—the purpose of his teachings is to realize a soteriological goal through spiritual practice. Secondly, naturalism tends to subscribe to ‘self-being,’ while the Buddha holds all things to exist conditionally and impermanently. Because of the dependent nature of all things, it is not possible to discover their essence through reduction. Thirdly, naturalized philosophy would be a kind of belief-habit that follows from certain preconditioned assumptions. But the Buddha encourages us to re-examine our conceptual proliferation leading to biased views, as that ultimately leads to suffering. I conclude by proposing a broader naturalist outlook that would allow for a more inclusive conception of the natural world that would take the axiological dimension of human transcendence into account and increase an overall understanding of human potentiality. (shrink)

Many philosophers have claimed that evidence for a theory is better when multiple independent tests yield the same result, i.e., when experimental results are robust. Little has been said about the grounds on which such a claim rests, however. The present essay presents an analysis of the evidential value of robustness that rests on the fallibility of assumptions about the reliability of testing procedures and a distinction between the strength of evidence and the security of an evidence claim. Robustness can (...) enhance the security of an evidence claim either by providing what I call second-order evidence, or by providing back-up evidence for a hypothesis. (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)

Forgiveness is mostly seen as a virtuous human response to wrongful conduct. But what happens when there is no acknowledgement of wrongdoing on the part of the wrongdoer? Does the forgiveness of the unrepentant still count as forgiveness? The Fourteenth Dalai Lama, for instance, is a figure who highly promotes the value of forgiveness. His homeland has been occupied by China since 1950, yet he maintains that he forgives and feels no enmity towards the Chinese government. The Chinese authorities, for (...) their part, have never admitted to wrongful invasion of the ‘roof of the world’, hence there has been no acceptance of the Dalai Lama’s forgiveness. Can the Dalai Lama’s forgiving under these circumstances, however, still be seen as forgiveness? In the present contribution, I shed light on the Buddhist view on forgiveness in the hope of inspiring ideas that might contribute to the pursuit of peace. Firstly, I explore certain matters surrounding the general idea of forgiveness and subsequently introduce Buddhist perspectives. Secondly, I respond to the key question of this paper by highlighting the Dalai Lama’s views as a means to elaborate on the Buddhist stance. I conclude by comparing Buddhist points of view with some contemporary philosophical perspectives and illustrating some distinguishing features of the Buddhist notion of forgiveness. From the above, I endeavour to establish that the Buddhist take on forgiveness is ultimately unconditional. (shrink)

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...) to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (shrink)

Daniel R. DeNicola’s Moral Philosophy: A Contemporary Introduction begins (pg. ix) with an anonymous reviewer’s quote, paraphrased here: ‘The author of an introductory ethics textbook has an impossible task, creating a work both accessible to undergraduates and rigorous enough for philosophers.’ DeNicola can of course be forgiven for not achieving this impossible task. Still, some attempts are better than others. After surveying the text content, I explain why I discourage instructors from using this textbook in introductory ethics courses.

Exploration of a hypothetical model of the structure of the Emergent Event. -/- Key Words: Emergent Event, Foundational Mathematical Categories, Emergent Meta-system, Orthogonal Centering Dialectic, Hegel, Sartre, Badiou, Derrida, Deleuze, Philosophy of Science.

A new advanced systems theory concerning the emergent nature of the Social, Consciousness, and Life based on Mathematics and Physical Analogies is presented. This meta-theory concerns the distance between the emergent levels of these phenomena and their ultra-efficacious nature. The theory is based on the distinction between Systems and Meta-systems (organized Openscape environments). We first realize that we can understand the difference between the System and the Meta-system in terms of the relationship between a ‘Whole greater than the sum of (...) the parts’ and a ‘Whole less than the sum of its parts’, i.e., a whole full of holes (like a sponge) that provide niches for systems in the environment. Once we understand this distinction and clarify the nature of the unusual organization of the Meta-system, then it is possible to understand that there is a third possibility which is a whole exactly equal to the sum of its parts that is only supervenient like perfect numbers. In fact, there are three kinds of Special System corresponding to the perfect, amicable, and sociable aliquot numbers. These are all equal to the sum of their parts but with different degrees of differing and deferring in what Jacques Derrida calls “differance”. All other numbers are either excessive (systemic) or deficient (metasystemic) in this regard. The Special Systems are based on various mathematical analogies and some physical analogies. But the most important of the mathematical analogies are the hypercomplex algebras, which include the Complex Numbers, Quaternions, and Octonions, with the Sedenions corresponding to the Emergent Meta-system. However, other analogies are the Hopf fibrations between hyperspheres of various dimensions, nonorientable surfaces, soliton solutions, etc. These Special Systems have a long history within the tradition since they can be traced back to the imaginary cities of Plato. The Emergent Meta-system is a higher order global structure that includes the System with the three Special Systems as a cycle. An example of this from our tradition is in the Monadology of Gottfried Wilhelm von Leibniz. There is a conjunctive relationship between the System schema and the Special Systems that produce the Meta-system schema cycle. The Special Systems are a meta-model for the relationship between the emergent levels of Consciousness (Dissipative Ordering based on the theory of negative entropy of Prigogine), Living (Autopoietic Symbiotic based on the theory of Maturana and Varela), and Social (Reflexive based on the theory of John O’Malley and Barry Sandywell). These different special systems are related to the various existenitals identified by Martin Heidegger in Being and Time and various temporal reference frames identified by Richard M. Pico. We also relate the special systems to morphodynamic and teleodynamic systems of Terrence Deacon in Incomplete Nature to which we add sociodynamic systems to complete the series of Special Systems. (shrink)

After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.

Explorations in Systems Phenomenology in Relation to Ontology, Hermeneutics and the Meta-dialectics of Design -/- SYNOPSIS A Phenomenological Analysis of Emergent Design is performed based on the foundations of General Schemas Theory. The concept of Sign Engineering is explored in terms of Hermeneutics, Dialectics, and Ontology in order to define Emergent Systems and Metasystems Engineering based on the concept of Meta-dialectics. -/- ABSTRACT Phenomenology, Ontology, Hermeneutics, and Dialectics will dominate our inquiry into the nature of the Emergent Design of the (...) System and its inverse dual, the Meta-system. This is an speculative dissertation that attempts to produce a philosophical, mathematical, and theoretical view of the nature of Systems Engineering Design. Emergent System Design, i.e., the design of yet unheard of and/or hitherto non-existent Systems and Metasystems is the focus. This study is a frontal assault on the hard problem of explaining how Engineering produces new things, rather than a repetition or reordering of concepts that already exist. In this work the philosophies of E. Husserl, A. Gurwitsch, M. Heidegger, J. Derrida, G. Deleuze, A. Badiou, G. Hegel, I. Kant and other Continental Philosophers are brought to bear on different aspects of how new technological systems come into existence through the midwifery of Systems Engineering. Sign Engineering is singled out as the most important aspect of Systems Engineering. We will build on the work of Pieter Wisse and extend his theory of Sign Engineering to define Meta-dialectics in the form of Quadralectics and then Pentalectics. Along the way the various ontological levels of Being are explored in conjunction with the discovery that the Quadralectic is related to the possibility of design primarily at the Third Meta-level of Being, called Hyper Being. Design Process is dependent upon the emergent possibilities that appear in Hyper Being. Hyper Being, termed by Heidegger as Being (Being crossed-out) and termed by Derrida as Differance, also appears as the widest space within the Design Field at the third meta-level of Being and therefore provides the most leverage that is needed to produce emergent effects. Hyper Being is where possibilities appear within our worldview. Possibility is necessary for emergent events to occur. Hyper Being possibilities are extended by Wild Being propensities to allow the embodiment of new things. We discuss how this philosophical background relates to meta-methods such as the Gurevich Abstract State Machine and the Wisse Metapattern methods, as well as real-time architectural design methods as described in the Integral Software Engineering Methodology. One aim of this research is to find the foundation for extending the ISEM methodology to become a general purpose Systems Design Methodology. Our purpose is also to bring these philosophical considerations into the practical realm by examining P. Bourdieu’s ideas on the relationship between theoretical and practical reason and M. de Certeau’s ideas on practice. The relationship between design and implementation is seen in terms of the Set/Mass conceptual opposition. General Schemas Theory is used as a way of critiquing the dependence of Set based mathematics as a basis for Design. The dissertation delineates a new foundation for Systems Engineering as Emergent Engineering based on General Schemas Theory, and provides an advanced theory of Design based on the understanding of the meta-levels of Being, particularly focusing upon the relationship between Hyper Being and Wild Being in the context of Pure and Process Being. (shrink)

Gilbert Ryle’s The Concept of Mind (1949/2002. Chicago, IL: University of Chicago Press) is generally considered a landmark in the quest to refute Cartesian dualism. The work contains many inspirational ideas and mainly posits behavioral disposition as the referent of mind in order to refute mind–body dualism. In this article, I show that the Buddhist theory of ‘non-self’ is also at odds with the belief that a substantial soul exists distinct from the physical body and further point out similarities between (...) the Buddhist outlook and Ryle’s ideas in three parts. First, I illustrate that Ryle’s ‘category mistake’ has certain points in common with the Buddhist refutation of ‘self’. Within the Buddhist framework, referents such as ‘mind’ and ‘self’ are merely imputed terms. The presumed existence of an independent substance such as a ‘soul’, when considered in isolation from the expedient usage of the term ‘mind’, can therefore also be viewed as a ‘category mistake’. Second, attempting to solve the questions of ‘what mind is’ and ‘how mind operates’ are two entirely different approaches to the study of mind. I argue that it is necessary to focus on ‘knowing-how’ rather than ‘knowing-that’, if we are to gain a more comprehensive understanding of mind and avoid any kind of category mistake such as those that follow from isolating the physical properties of brain or drawing inferences from a mystical soul. Third, I aim to show why investigating mind from the perspective of ‘dispositions’ of behavior is a valid approach. The Buddhist concept of karma-vāsanā elucidates the habitual tendency to act or not act in various situations. Based on this theory, I argue that the workings of the human mind bears strong links to the formation of karma and as such have important axiological implications that cannot be ignored. I conclude by pointing out that Ryle’s insightful ideas could in certain ways be complemented by the Buddhist theory of mind. In my view, his philosophy is not only a mediator between Analytic Philosophy and Phenomenology, but could perhaps also be seen as a mediator between traditional Eastern systems of thought and contemporary philosophies of mind. (shrink)

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 Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (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)

Purpose – With the growing demand for ethical standards in the prevailing business environment, ethical leadership has been under increasingly more focus. Based on the social exchange theory and social learning theory, this study scrutinized the impact of ethical leadership on the presentation of ethical conduct by employees through the ethical climate. Notably, this study scrutinized the moderating function of the person organization fit (P-O fit) in relation to ethical climate and the ethical conduct of employees. -/- Design/methodology/approach – To (...) evaluate the research hypotheses, two-wave data were collected from 295 individuals who are currently employed in various Iraqi organizations (i.e. manufacturing, medical, and insurance industries). -/- Findings – In line with the hypotheses, the outcomes from a sample of 295 workers working in different Iraqi entities exhibited a positive relationship between the ethical behavior of leaders and the ethical conduct of employees in the ethical climate. Moreover, it was observed that the P-O fit of employees moderated the relationship between ethical climate and the ethical conduct of employees such that the relationship was more robust for those with a high P-O fit in comparison to those with a low P-O fit. -/- Research limitations/implications – The primary limitation of this study is in the data, which was obtained from a single source. Although the study conducted two surveys and utilized a mediation and moderation variables model that was less likely to be influenced by common method bias (CMB) (Podsakoff et al., 2012), one cannot completely rule out CMB. Apart from the potential effects of the CMB, the consistency of the empirical findings could have also been compromised since self-reported data were utilized in measuring ethical behavior, which can be a very complex and sensitive issue. For this reason, the social desirability response bias cannot be ruled out completely. When possible, future studies must gather data from multiple sources. Furthermore, supervisors must evaluate the ethical behavior of employees. Another limitation was that the findings of this study were based on a sample in a Middle Eastern cultural context such as in Iraq. Perhaps, the particular cultural features of this context, which encompassed, among other things, strong adherence to religious values (Moaddel, 2010), could have influenced the findings of this study. It is true that the effects of differences (P–O fit) are highly likely to replicate across cultural contexts (Triandis et al., 1988). However, it can be seen that further studies are needed to evaluate the context-sensitivity of these findings (Whetten, 2009) by analyzing other cultures, where the importance of religiosity is on the decline (i.e. in Western countries, Ribberink et al., 2018) or where the cultural features are very much different from those that apply to Iraq. Lastly, other external factors were not taken into account by this study as it tried to explain ethical behavior. Ethics is a highly complex subject and is influenced by numerous variables at the organizational, individual, and external environment levels. Thus, caution must be observed when making inferences from the present study which, to a certain degree, offered a simplified version of ethical behavior by concentrating on a few variables such as the Arab culture’s traditional ideology, which dominates even science (Abu Khalil, 1992). In addition, there are political conflicts in the Middle Eastern cultural context such as what is happening in Iraq (Harff, 2018). Thus, it is important to include such aspects in future researches. -/- Practical implications – In terms of management, the findings send a clear signal to those in the upper echelon that, without ignoring the issue of ethics in organizations, employees are a critical aspect to be taken into account to encourage ethical behavior at the workplace. This study has important practical implications. First, this study determined that ethical leadership (here, of the supervisors) positively influences the behavior of subordinates (refers to the supervisors here); this, in turn, further improves the ethical behavior of employees. It is vital that managers or supervisors are motivated to practice ethical leadership because they directly influence the employees. It has been suggested that top managers, especially chief executive officers, have the ability to shape the ethical climate, which also influences the ethical behavior of employees further. This study offered several feasible ways that managers can apply to achieve that. In particular, top managers may utilize the ethical climate as a way of communicating the ethical values that they have to their subordinates, thereby serving as a motivation for the subordinates to adopt ethical behavior. It was also suggested by this study that ethical climate and the P–O fit may, to some degree, substitute each other as they influence the ethical behavior of employees. Therefore, firms that were identified to have a low level of ethical standards, practices, and policies, at least from the employees’ perspective, are better poised to conduct ethical issues in order to construct the ethical behavior of their subordinates. More importantly, it is highly essential that the value congruence between an organization and its followers be considered. -/- Social implications – This study highlighted the notion of ethics and how it’s essential for society. Ethics refers to the norms, standards, and values that direct the behavior of an individual. Ethical behavior is vital in society because we need to be treated with respect as human beings. -/- Originality/value – This study responds to recent calls for more research to identify factors that may strengthen or mitigate the influence of ethical behavior in the workplace such as ethical leadership, ethical climate, and Person–Organization. (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)

Identification of factors that predict recurrent antisocial behavior is integral to the social sciences, criminal justice procedures, and the effective treatment of high-risk individuals. Here we show that error-related brain activity elicited during performance of an in- hibitory task prospectively predicted subsequent rearrest among adult offenders within 4 y of release (N =96). The odds that an offender with relatively low anterior cingulate activity would be rearrested were approximately double that of an offender with high activity in this region, holding (...) constant other observed risk factors. These results suggest a potential neurocognitive biomarker for persistent antisocial behavior. (shrink)

WHO in 2019 established the Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing, which has recently published a Draft Governance Framework on Human Genome Editing. Although the Draft Framework is a good point of departure, there are four areas of concern: first, it does not sufficiently address issues related to establishing safety and efficacy. Second, issues that are a source of tension between global standard setting and state sovereignty need to be addressed in a (...) more nuanced fashion. Third, it fails to meaningfully engage with the extent to which the conceptualisation of human dignity may justifiably vary between jurisdictions. Fourth, the meaning of harm to the interests of a future person requires clarity. Provided these four areas of concern can be addressed, the future of the global governance of human genome editing may hold promise. (shrink)

Psychopathy is a personality disorder characterized by callous antisocial behavior and criminal recidivism. Here we examine whether psychopathy is associated with alterations in functional connectivity in three large-scale cortical networks. Using fMRI in 142 adult male prison inmates, we computed resting-state functional connectivity using seeds from the default mode network, frontoparietal network, and cingulo-opercular network. To determine the specificity of our findings to these cortical networks, we also calculated functional connectivity using seeds from two comparison primary sensory networks: visual and (...) auditory networks. Regression analyses related network connectivity to overall psychopathy scores and to subscores for the “factors” and “facets” of psychopathy: Factor 1, interpersonal/affective traits; Factor 2, lifestyle/antisocial traits; Facet 1, interpersonal; Facet 2, affective; Facet 3, lifestyle; Facet 4, antisocial. Overall psychopathy severity was associated with reduced functional connectivity between lateral parietal cortex and dorsal anterior cingulate cortex. The two factor scores exhibited contrasting relationships with functional connectivity: Factor 1 scores were associated with reduced functional connectivity in the three cortical networks, whereas Factor 2 scores were associated with heightened connectivity in the same networks. This dissociation was evident particularly in the functional connectivity between anterior insula and dorsal anterior cingulate cortex. The facet scores also demonstrated distinct patterns of connectivity. We found no associations between psychopathy scores and functional connectivity within visual or auditory networks. These findings provide novel evidence on the neural correlates of psychopathy and suggest that connectivity between cortical association hubs, such as the dorsal anterior cingulate cortex, may be a neurobiological marker of the disorder. (shrink)

Neuroimaging studies have found that adult male psychopaths show reduced engagement of limbic and paralimbic circuitry while making moral judgments. The goal of this study was to investigate whether these findings extend to adolescent males with psychopathic traits. Functional MRI was used to record hemodynamic activity in 111 incarcerated male adolescents while they viewed unpleasant pictures that did or did not depict moral transgressions and rated each on “moral violation severity”. Adolescents were assessed for psychopathic traits using the Psychopathy Checklist-Youth (...) Version (PCL-YV), Kiddie Schedule for Affective Disorders and Schizophrenia-Present and Lifetime Version (KSADS-PL) Conduct Disorder supplement, and Inventory of Callous and Unemotional Traits-Youth Version (ICU-Y). While viewing pictures depicting moral transgressions, CD scores were negatively correlated with hemodynamic responses in the anterior temporal cortex. Adolescents scoring low on the ICU-Y showed a positive correlation between right amygdala responses and severity of violation ratings; those with high ICU-Y scores showed a negative correlation. While viewing unpleasant pictures with and without moral transgressions, PCL-YV scores were negatively correlated with hemodynamic responses in the left amygdala. Overall, the results are consistent with those previously found in adult male psychopaths, but vary depending on the type of psychopathy assessment. (shrink)

Everybody knows that Superman is Clark Kent. Nobody knows that Superman is Clark Kent. Located between these two absolute statements is the epistemological limit that separates the superhero fictitious universe from our universe of causal reality. The superheroic double identity is a secret shared by the superhero and the reader of the comic or the viewer of the movie, and quite often the superhero winks at the outside world, thus breaking the 4th wall and establishing this collusive relationship. (...) However, in our hypothesis, we are interested in Superman not as a fictitious archetype, but rather as a fictitious metaphor. We are not interested in his double identity as the matrix of superheroic attributes and narratives, but rather as the differential limit between superhuman and human within the fictional universe. Because, the reader or the viewer may share the secret identity with Superman and also with Spiderman or Batman or any other superhuman, but the secret equivalence of Superman and Clark Kent contains another hidden antithesis. (shrink)

Contextualism (the view that ‘knowledge’ and its variants are context-sensitive) has been supported in large part through appeal to intuitions about Keith DeRose’s Bank Cases. Recently, however, the contextualist construal of these cases has come under fire from Kent Bach and Jennifer Nagel who question whether the Bank Case subject’s confidence can remain constant in both low- and high-stakes cases. Having explained the Bank Cases and this challenge to them, I argue that DeRose has given a reasonable reply to (...) this initial challenge. However, I proceed to argue that the current stalemate can be broken. Seeking to extend the Bach-Nagel critique, I offer a novel interpretation of the Bank Cases according to which the subject’s evidence changes between low- and high-stakes cases. If I am correct, then, given the amount of support the Bank Cases have been thought to lend contextualism, the case for contextualism is seriously weakened. (shrink)

Agents have powers to bring about change. Do agents have normative powers to bring about normative change directly? This chapter distinguishes between direct normative change and descriptive and institutional changes, which may indirectly be normatively significant. This article argues that agents do indeed have the powers to bring about normative change directly. It responds to a challenge claiming that all normativity is institutional and another claiming that exercises of normative powers would violate considerations of supervenience. The article also responds to (...) a challenge - generalizing Kent Hurtig’s recent challenge about consent - which states that exercises of normative powers are valid only in cases that do not matter - they never bring about a “normative transformation” of what the agent overall ought to do. It turns out that consent is normatively transformative in some cases, but the main contribution of exercises of normative powers is at the contributory level not that of overall oughts. Invalid exercises of normative powers are void of any normative effects. Rational agents as possessors of normative powers are not merely responsive to pre-existing normative reasons, but they can also create normative reasons. A “responsive” view of rational agency sees us as being able to track existing normative reasons and make descriptive changes (on which normative changes supervene). The “creative” view of rational agency sees us as being able not only to construct institutions but also to create normative reasons directly. The chapter concludes that agents are both responsive and creative. (shrink)

This paper defends the claim that although ‘Superman is Clark Kent and some people who believe that Superman flies do not believe that Clark Kent flies’ is a logically inconsistent sentence, we can still utter this sentence, while speaking literally, without asserting anything false. The key idea is that the context-sensitivity of attitude reports can be - and often is - resolved in different ways within a single sentence.

On Kripke’s intended definition, a term designates an object x rigidly if the term designates x with respect to every possible world in which x exists and does not designate anything else with respect to worlds in which x does not exist. Kripke evidently holds in Naming and Necessity, hereafter N&N (pp. 117–144, passim, and especially at 134, 139–140), that certain general terms – including natural-kind terms like ‘‘water’’ and ‘‘tiger’’, phenomenon terms like ‘‘heat’’ and ‘‘hot’’, and color terms like (...) ‘‘blue’’ – are rigid designators solely as a matter of philosophical semantics (independently of empirical, extra-linguistic facts). As a consequence, Kripke argues, identity statements involving these general terms are like identity statements involving proper names (e.g., ‘‘Clark Kent=Superman’’) in that, solely as a matter of philosophical semantics, they express necessary truths if they are true at all. But whereas it is reasonably clear what it is for a (first-order) singular term to designate, Kripke does not explicitly say what it is for a general term to designate. General terms are standardly treated in modern logic as predicates, usually monadic predicates. There are very forceful reasons – due independently to Church and Godel, and ultimately to Frege – for taking predicates to designate their semantic extensions. But insofar as the extension of the general term ‘‘tiger’’ is the class of actual tigers (or its characteristic function), it is clear that the term does not rigidly designate its extension, since the class of tigers in one possible world may differ from the class of tigers in another. What, then, is it for ‘‘tiger’’ to be rigid? (shrink)

I argue that Frege's puzzle can extend beyond semantics and to, for example, pictures and scent. Accordingly, attempted solutions to the puzzle should not focus solely on semantics. Solutions that do so can at best provide a partial solution to the puzzle. They will not provide a solution that explains the broader phenomenon, including the one where I, as a child, learned the identity of Clark Kent and Superman without possessing their names. Below I will provide a solution that (...) accounts for the typical Frege case as well as my childhood case. The solution will, accordingly, not be a semantic solution. Instead it will focus on information we have on objects and how we organize and access the information. The solution I will provide is psychological and not semantic in nature. At the same time I will show that the solution I provide aligns itself well with Millianism. (shrink)

Después de varios años bajo los efectos del boom del posmodernismo, en la década de los 90 la intelectualidad latinoamericana comenzó а recibir uп nuevo paquete de propuestas teóricas reunidas en torno al concepto “poscolonialidad”. Bajo el iпflujo de las teorías poscoloniales у los estudios subalternos se crea oficialmente en los Estados Unidos en 1994 el Grupo Latinoamericano de Estudios Subalternos (Latin American Subaltern Studies Gгoup). А el pertenecían intelectuales como Walter Mignolo, John Beverley, Alberto Moreiras, Ileana Rodríguez у (...) Norma Alarcón. Este grupo nace con la loable finalidad básica realizaг una renovación poscolonial de los llamados "Estudios de Área" norteamericanos, en particularг, de los "Latin American Studies”. En el trabajo, luego de describir algunas de las ideas más importante del grupo, se pasa a exponer, en forma de interrogantes, algunas reflexiones críticas sobre sus propuestas. (shrink)

Después de varios años bajo los efectos del boom del posmodernismo, en la década de los 90 la intelectualidad latinoamericana comenzó а recibir uп nuevo paquete de propuestas teóricas reunidas en torno al concepto “poscolonialidad”. Bajo el iпflujo de las teorías poscoloniales у los estudios subalternos se crea oficialmente en los Estados Unidos en 1994 el Grupo Latinoamericano de Estudios Subalternos (Latin American Subaltern Studies Gгoup). А el pertenecían intelectuales como Walter Mignolo, John Beverley, Alberto Moreiras, Ileana Rodríguez у (...) Norma Alarcón. Este grupo nace con la loable finalidad básica realizaг una renovación poscolonial de los llamados "Estudios de Área" norteamericanos, en particularг, de los "Latin American Studies”. En el trabajo, luego de describir algunas de las ideas más importante del grupo, se pasa a exponer, en forma de interrogantes, algunas reflexiones críticas sobre sus propuestas. (shrink)

Sfruttando alcune considerazioni, presenti in Richard (1997), riguardo questioni pragmatiche e psicologiche connesse alla semantica russelliana per i verbi psicologici si propone un modello teorico in cui, attraverso l’introduzione di alcuni enunciati strategici, ad es. “Lois non realizza che Superman è Clark Kent”, alcuni problemi connessi al diverso comportamento di Lois con gli individui Superman e Clark Kent, sembrerebbero risolti fornendoci corrette predizioni riguardo il comportamento di un agente razionale. Scopo di questo lavoro è estendere il modello ad (...) alcuni casi riguardanti l’etica delle credenze e mostrare, attraverso un caso paradigmatico nella letteratura specialistica, alcune potenziali conferme empiriche del modello stesso. (shrink)

These days the two most popular approaches to belief ascription are Millianism and Contextualism. The former approach is inconsistent with the existence of ordinary Frege cases, such as Lois believing that Superman flies while failing to believe that Clark Kent flies. The Millian holds that the only truth-conditionally relevant aspect of a proper name is its referent or extension. Contextualism, as I will define it for the purposes of this essay, includes all theories according to which ascriptions of the (...) form ‘S believes that a is F’ and ‘S believes that b is F’, where ‘a’ and ‘b’ are coreferential proper names, may, depending on the context, differ in truth-value even though in those very contexts each ascription relates the same believer to the very same proposition. What the two theories have in common is the claim that names are Millian. What separates the two theories is what they say about belief contexts. In this essay I prove that Millianism is true, Contextualism is true, or our intuitions regarding belief ascriptions are hopelessly inaccurate. As a consequence, my argument is a proof that either names and many general terms are Millian or our intuitions regarding belief ascriptions are hopelessly inaccurate. (shrink)

Propositional attitude sentences, such as (1) Pierre believes that snow is white, have proved to be formidably difficult to account for in a semantic theory. It is generally agreed that the that-clause ‘that snow is white’ purports to refer to the proposition that snow is white, but no agreement has been reached on what this proposition is. Sententialism is a semantic theory which tries to undermine the very enterprise of understanding what proposition is referred to in (1): according to sententialists, (...) in (1) reference is made to the sentence “Snow is white”. Sententialism is generally considered doomed. The two main reasons why are the famous translation argument, firstly suggested by Alonzo Church, and a problem raised by Stephen Schiffer. The purpose of this paper is to provide a unified solution to both criticisms. What I take to be the key ingredient sententialists may exploit is an observation that concerns the nature of languages and quotations: since quotation marks display the quoted material, if you are a speaker of the language the quoted material belongs to, you usually cannot but understand what is quoted. Moreover, I show that sententialists may appeal to that very observation also in order to answer another problem, pointed out by Kent Bach. I conclude that there are good reasons for resisting the temptation of introducing propositions in order to account for propositional attitude sentences. (shrink)