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)

In this paper we compare the propositional logic of Frege’s Grundgesetze der Arithmetik to modern propositional systems, and show that Frege does not have a separable propositional logic, definable in terms of primitives of Grundgesetze, that corresponds to modern formulations of the logic of “not”, “and”, “or”, and “if…then…”. Along the way we prove a number of novel results about the system of propositional logic found in Grundgesetze, and the broader system obtained by including identity. In particular, we show that (...) the propositional connectives that are definable in terms of Frege’s horizontal, negation, and conditional are exactly the connectives that fuse with the horizontal, and we show that the logical operators that are definable in terms of the horizontal, negation, the conditional, and identity are exactly the operators that are invariant with respect to permutations on the domain that leave the truth-values fixed. We conclude with some general observations regarding how Frege understood his logic, and how this understanding differs from modern views. (shrink)

This dissertation presents a theory of online propaganda and radicalization which highlights the interaction between communication, epistemology, and technology. The central focus is providing an analysis of online media communications, content posted on social media platforms and transmitted by automated recommendation systems, which better explains how propaganda and radicalization have adapted so well to this technological environment. First, propaganda is interpreted as a unique approach to communication which manipulates the expectations an audience has of successful communications, and not simply as (...) a collection of individual acts with characteristic properties. A major aspect to this interpretation of propaganda is an emphasis on those environmental factors and sociological conditions involved in communication, which can have a direct impact on our experience and interpretation of reality. Second, considering these aspects a detailed account of how users experience the technical machinery facilitating social media platforms is presented, highlighting the problematic epistemic states users are forced to inhabit. Finally, online radicalization is explained through this new propaganda interpretation, the user experience of the technology underpinning social media platforms, and the epistemic states forced by online automation. (shrink)

Fifteen years after the September 11th terror attacks, the United States still exists in a state of exception or state of emergency, in which the executive branch claims extraordinary powers to carry out bombing strikes or drone attacks in foreign nations and to engage in surveillance against its citizens outside the boundaries of international and constitutional law. This blog-piece argues for a restoration of the constitutional limiuts on sovereign executive powers and a cessation of the war on terrorism.

Abstract: Giorgio Agamben's recent works have been preoccupied with a certain obscure passage from St. Paul's 'Second Epistle to the Thessalonians,' which describes the portentous events that must occur before the Second Coming of Jesus Christ can take place---specifically, the appearance of a 'man of lawlessness' (the Antichrist?) and the exposure of who or what is currently restraining the 'man of lawlessness' from being exposed as the Antichrist: a mysterious agency called the 'katechon.' In 'The Mystery of Evil: Benedict XVI (...) and the End of Days,' this obscure passage is connected with the abdication of Pope Benedict XVI through certain equally obscure references to the fourth century theologian, Tyconius, although the precise connection between these apocalyptic events and their mysterious agents remains obscure. This review attempts to shed some critical light upon this cryptic subject, both by considering the world-historical context of St. Paul's epistle, and by asking what role these apocalyptic figures play in Agamben's political theology. But, to begin with, the review also asks: Who, really, is the Antichrist? a scarcely rhetorical question that demands a sardonic answer. Although various candidates from contemporary politics are proposed, the review finally argues that the Antichrist and the katechon are not specific individuals or worldly institutions, but rather refer to world-historical trends within Western European Christian civilization itself that have resulted in what Friedrich Nietzsche called 'the devaluation of all higher values' and 'the desecration of the Christian moral world-view': an apocalyptic turn of events which Nietzsche equally sardonically referred to in 'The Antichrist.'. (shrink)

A review of Giorgio Agamben's The Mystery of Evil: Bendict XVI and the End of Days, which attempts to place Agamben's peculiar argument regarding Pope Benedict's abdication in the context of his reading of St. Paul's 2 Thessalonians 2:1-12, and, more generally, in terms of his political-theology in the Homo Sacer series. The questions, 'Who is the Antichrist?' and 'Who (or what) is the katechon?' are also explored, in the attempt to translate Agamben's obscure theology into contemporary political terms.

Abstract: Karl Jaspers describes The Axial Period (800-200 BCE) as a world-historical turning point in the spiritual evolution of the human species, characterized by the rise of Buddhism, Zoroastrianism, Pythagoreanism, and the Hebrew prophets, without precisely identifying what defines this world-historical period. What defines The Axial Period, I argue with Jaspers, is the sublimation of sacrifice, through which the sacrificial killing of domestic animals, characteristic of primitive religions, is sublimated into the self-sacrificial disciplines of prayer, meditation, and asceticism. This sublimation (...) of sacrifice involves a curiously duplicitous gesture, through which the sacred violence of primitive sacrifice is simultaneously sublimated into the self-sacrificial disciplines of the Western Indo-European religions, and demoted to the strictly physical violence of modern warfare, stripped of its sacred origins. I argue, against Jaspers, that there is no world-historical discontinuity between primitive and modern sacrifice, but rather a continuous trajectory of the sublimation of sacrifice in Western Indo-European cultures. The Brahminic sacred texts, the Rig Veda and the Brahmanas, for example, describe a sophisticated sacrificial ritualism that more effectively sublimates sacrificial violence than do Western European modern cultures, in which un-sacrificial violence continues to escalate, to challenge the survival of the contemporary world. (shrink)

Peter Sloterdijk's 'In the Shadow of Mt. Sinai' and Alain Badiou's 'Our Wounds Are Not So Recent' represent distinctly different attempts to come to grips with the conflict between the West (the US, the UK, France) and the Muslim world after the September 11th attacks. Although Sloterdijk finds the source of conflict in the religious zealotry of the Abrahamic religions, while Badiou blames the multinational capitalist system for drating a disaffected underclass, the two complementary perspectives work together to make this (...) ongoing conflict intelligible, if not, finally, to stop the war on terrorism. (shrink)

A review of Francoise Laruelle's General Theory of Victims, which places Laruelle's theory in the context of post-colonial theories of the subaltern subject after Gayatri Spivak and Edward Said. The review questions whether Laruelle's General Theory of Victims really allows the so-called victims to speak for themselves, or simply represents another attempt by Western (French?) intellectuals to speak to/through the victims, for their own political and theoretical purposes.

A review of Giorgio Agamben's The Use of Bodies that considers Agamben's Homo Sacer series as a contribution to Post-Marxist political theory, and attempts to place Agamben's politial theology in the context of 1970s Italian radical politics. The review also poses the question whether Agamben's anarchist/aestheticist theory is a helpful contribution to political praxis in the contemporary period of the global hegemony of multinational military-industrial technocratic capitalism.

Kostas Axelos' 'Introduction to a Future Way of Thought' attempts to bring together two strong thinkers often thought to represent diametrically opposed political traditions: Martin Heidegger and Karl Marx. This review considers this attempt as a result of Axelos' political background, as a Greek communist revolutionary who emigrated to France and came into contact with Postwar French Heideggerian thought. Axeols then helped to establish the Heideggerian Marxism characteristic of the influential journal, Arguments.

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

Susan Schneider (2019) has proposed two new tests for consciousness in AI (artificial intelligence) systems, the AI Consciousness Test and the Chip Test. On their face, the two tests seem to have the virtue of proving satisfactory to a wide range of consciousness theorists holding divergent theoretical positions, rather than narrowly relying on the truth of any particular theory of consciousness. Unfortunately, both tests are undermined in having an ‘audience problem’: Those theorists with the kind of architectural worries that motivate (...) the need for such tests should, on similar grounds, doubt that the tests establish the existence of genuine consciousness in the AI in question. Nonetheless, the proposed tests constitute progress, as they could find use by some theorists holding fitting views about consciousness and perhaps in conjunction with other tests for AI consciousness. (shrink)

We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for example that a (...) water pump has the function to pump water is to say that the pump exists because something was needed that would pump water. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (shrink)

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Plato on Knowledge as a Power1Nicholas D. SmithAt 471C4 in Plato’s Republic, the argument takes a sudden turn when Glaucon becomes impatient with all of the specific prescriptions Socrates has been making, and asks to return to the issue Socrates had earlier set aside—whether or not the city he was describing could ever be brought into being. In response to Glaucon’s impatient question, Socrates articulates his “third wave of (...) paradox” (472ag–7), namely, that the ills of the cities will never be ended until either philosophers become rulers or rulers become philosophers (473c11–d6). Glaucon immediately responds that such a view is likely to be greeted with violence and scorn (473e6–474a4), and so Socrates must hasten to explain his odd claim. His explanation, it turns out, is that true philosophers have an enormous cognitive advantage over non-philosophers—philosophers have and use knowledge (ἐπιστήμη), whereas non-philosophers have and use only opinion (δόξα).2 This distinction, between επιστήμη and δόξα, turns out: to be a distinction between two different cognitive powers (δυνάμεις—477d7–e3). And different powers, Plato clearly tells us, apply to or take as their objects (Plato says they are “ἐπί”) different things (477dl).In this paper, I shall argue that the relationship between the cognitive powers and their various objects has been fundamentally misunderstood, which has led scholars into one or more misinterpretations of important and explicit features of the text. At the heart of these misunderstandings, I claim, is [End Page 145] their shared misconception of the relation between the cognitive power and its objects as interpretable in terms of the relationship between a cognitive stale and what the content of that state is of or about.3 One consequence of the view for which I shall argue is that what has come to be known as the “two-worlds theory”4 of Plato’s epistemology is seriously mistaken, but no less mistaken than the alternatives given by its recent critics. Another consequence that I shall draw from my argument is that Plato should be understood neither as a kind of foundationalist with regard to knowledge and warrant, as some have supposed him to be,5 nor as a coherentist, as others have supposed,6 but, rather, as a kind of causal reliabilist. [End Page 146]1. KNOWLEDGE AS A POWERScholarly interpretations of Plato’s epistemology have routinely sought to understand the relationships between each cognitive power of Republic Book V and the objects of the ἐφ’ ᾦ (“what it is related to”) condition by which it is differentiated from other δυνάμεις as Plato’s way of telling us what each sort of cognition is of or aboul. 7 So, for example, we find Gail Fine using the expressions “belief [δόξα] is set over [Fine’s translation of Plato’s ἐπί] …” and “knowledge is set over …” interchangeably with “belief is of …” or “belief is about…” and “knowledge is of …” or “knowledge is about …”8 Against the “two-worlds theory,” Fine argues that, for Plato, there can be knowledge of sensibles and beliefs about Forms. Accordingly, since she assimilates the power-ἐπί-object set of relations to the cognilion-of/about-object relation, she concludes—in order to account for knowledge of sensibles and beliefs about Forms—that the objects of knowledge and opinion must be propositions. Plato’s claims that knowledge is ἐπί what is, whereas opinion is ἐπί what is and is not, Fine understands as, “One can only know true propositions; one can believe both true and false propositions.”9 We shall see later that this “veridical” understanding of what Plato means to identify as “what is,” and “what is and is not” fails to account for important and explicit elements of Plato’s exposition of the epistemological and metaphysical distinctions he is making. For now, it is enough to note that Fine understands the ἐφ’ᾦ) relation in terms of our cognition-of/about-object relation. One finds the same assimilation made by those who advance existential readings of Plato’s “is” and “is not,”10 as [End Page 147] well as those who have urged that we adopt predicative readings of “is” and “is not.”11But I think there are very serious problems with this assimilation. Plato is very... (shrink)

Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...) Consider” (P2C) document, and convened a national expert panel to review and critique the P2C. -/- Results: We developed the P2C to aid informaticists designing an advanced query tool for an electronic health record (EHR) system in Indianapolis. The P2C consists of six questions (“Points”) that frame important ethical issues, apply accepted principles of bioethics and Fair Information Practices, comment on how questions might be answered, and address implications for patient care. -/- Discussion: The P2C is intended to clarify whatis at stake when designers try to accommodate potentially competing ethical commitments and logistical realities. The P2C was developed to guide informaticists who were designing a query tool in an existing EHR that would permit patient granular control. While consideration of ethical issues is coming to the forefront of medical informatics design and development practices, more reflection is needed to facilitate optimal collaboration between designers and ethicists. This report contributes to that discussion. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis. Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato’s dialogues, is sfounded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then show (...) how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato’s dialogues by date, more general challenges to historicist interpretations of Plato’s dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

Plato recognizes faction as a serious threat to any political community. The Republic’s proposed solution to faction relies on bringing citizens into a relation of ὁμόνοια. On the dominant line of interpretation, ὁμόνοια is understood along the lines of “explicit agreement” or “consensus.” Commentators have consequently thought that the καλλίπολις becomes resistant to faction when all or most of its members explicitly agree with one another about certain fundamentals of their political association—for example, they agree regarding who should govern in (...) the καλλίπολις.We argue that ὁμόνοια in Plato’s political philosophy has been under-analyzed and misunderstood. We show that, in Alcibiades I, rendering ὁμόνοια simply as agreement results in confusion about how expertise, political friendship, and civic unity are compossible in a well-ordered political community. In our view, Plato refines and adds philosophical depth to the concept of ὁμόνοια in the Republic. We claim that ὁμόνοια is a relation of psychological “like-mindedness” that obtains among members of different occupational classes in a political community. A community is rendered resistant to faction, then, when its members are, in some significant way, psychologically alike. Additionally, while Platonic ὁμόνοια can naturally be expected to result in substantive agreement among citizens, we argue that Platonic ὁμόνοια does not consist solely in agreement. (shrink)

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)

We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...) to other types of military and nonmilitary unmanned vehicle operations. (shrink)

An ontology of geographic kinds is designed to yield a better understanding of the structure of the geographic world, and to support the development of geographic information systems that are conceptually sound. This paper first demonstrates that geographical objects and kinds are not just larger versions of the everyday objects and kinds previously studied in cognitive science. Geographic objects are not merely located in space, as are the manipulable objects of table-top space. Rather, they are tied intrinsically to space, and (...) this means that their spatial boundaries are in many cases the most salient features for categorization. The ontology presented here will accordingly be based on topology (the theory of boundary, contact and separation) and on mereology (the theory of extended wholes and parts). Geographic reality comprehends mesoscopic entities, many of which are best viewed as shadows cast onto the spatial plane by human reasoning and language. Because of this, geographic categories are much more likely to show cultural differences in category definitions than are the manipulable objects of table-top space. (shrink)

In the Nintendo game Animal Crossing: New Horizons, players move to an uninhabited island and quickly become instrumental to the naming, aesthetic development, and biodiversity of the island. In some ways, the game can foster a love for and curiosity about nature. In other ways, the game reinforces harmful colonialist values and attitudes that are ultimately an obstacle to conservation in the real world. Here I critique the game values relevant to conservation, both the values that benefit and the values (...) that hinder conservation. I discuss possibilities for a future version of the game that reinforces values better aligned with conservation. (shrink)

In this paper we argue that Socrates is a cognitivist about emotions, but then ask how the beliefs that constitute emotions can come into being, and why those beliefs seem more resistant to change through rational persuasion than other beliefs.

It has been argued that Plato sought to make his rulers invulnerable to any kind of wrongdoing. In this paper we argue that this (humanly impossible) claim misunderstand the ways in which Plato shapes his state precisely in order to make the rulers safe from what could corrupt them.

This synthesis of 5 prominent conflict management paradigms uses power differential as the single most contributing variable to their process and outcome of conflict. Efforts of scholars to integrate or synthesize conflict paradigms have been unsuccessful or clumsy by the scholars’ own assessments. The 5 selected paradigms represent an interdisciplinary set of normative and descriptive paradigms from different social contexts and intellectual frameworks. The 5 share the common traits of rival goals, three levels of socially constructed power differential, and outcomes (...) relative to the total value of the rival goal. An inverse relationship between power differential and the total value of conflict outcomes is supported by all 5 paradigms and empirical data. Explanatory metatheory is the methodology used for synthesis. An increase in power differential results in a decrease in total value of the rival goal. Power differential is constructed using Max Weber’s ideal-type method. The power differentials are abstracted from the paradigms themselves. Empirical work form secondary sources and case studies complete the analysis. (shrink)

I argue that Smith proposed a new kind of imperialism, which we would describe as a species of ‘federalism,’ and that his plan influenced Bentham and Kant in their federal projects, although they seem to have been unaware of each other’s proposals. In what follows, I outline Smith’s position. I then describe Kant’s and Bentham’s debts to Smith in turn. This will also allow for greater clarity about the nature of early liberalism.

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

In this chapter, I identify a distinctive use of ‘sublime’ in Adam Smith’s philosophy of science. I show that for Smith a scientific discipline and its theories can be sublime. I trace this idea back to Malebranche. I show that in Smith it is a way to convey something about the irrational nature of the natural order lurking behind’s science’s intellectual achievements. In section 1, I diagnose and distinguish three uses of ‘sublime’ in Smith. I situate (...) two of these in the early modern discussions of the sublime in the wake of Boileau's and William Smith’s translations of Longinus. 1 I argue that the third in which Smith treats intellectual disciplines as themselves sublime is relatively distinctive, although not wholly unique to Smith. In section 2, I put this notion in context and trace it, somewhat speculatively, back to the reception of Isaac Newton by Smith and Smith’s reading of Malebranche. In the third section I conclude with some reflections on the significance of this discussion for Smith’s conception of the nature of scientific rationality. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

I frame my argument by way of Hayek's tendency to treat Hume and Smith as central articulations of the rule of law. The rest of the paper explores their defense of clientelism. First, I introduce Hume’s ideas on the utility of patronage in his essay, “Of the Independency of Parliament.” I argue that in Hume clientelism just is a feature of parliamentary business. It seems ineliminable. I then contextualize Hume’s account by comparing it to Montesquieu’s account of this system (...) of patronage in Book XIX, chapter 27 of The Spirit of the Laws. Montesquieu primarily treats it as a species of bad corruption. However, he also sees some benefits to it. I then turn to Smith and I show that he echoes Hume’s analysis of corruption in an easily ignored passage in Wealth of Nations. I then show that for Smith one argument in favor of a kind of federal parliamentary union between Great Brittain and her American colonies lies in its ability to facilitate and make more efficient the system of patronage by the Crown. While Smith’s account of these matters is quite Humean, one can discern in Smith a distinct cost-benefit argument for the acceptance of the necessity of a system of patronage in the service of the peaceful expansion and entrenchment of the rule of law in his proposal for parliamentary union. (shrink)

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding, melting. Among this plethora of what we can think of as ‘mere dispositions’ is a subset of dispositions in whose realizations we have an interest – a car responding well when driven on ice, a rabbit’s lungs responding well when it is chased by a wolf, and so on. We (...) call the latter ‘capabilities’ and we attempt to provide an ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are being collected in siloed fashion. (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)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

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 theses exposed by Alexius Meinong in two newspaper articles in 1873 are taken as the paradigm of a feeling that was common to young Austrian intelligentsia. Meinong upholds a conception of life as struggle and of history as a series of struggles among nations. In his view, the defence of the interests of a people is absolute and generates conflicts among nations that will increasingly dominate future scenarios. The concept of nation has an identification function inward and one of (...) dissociation outward. This discourse is contextualised within the framework of the various student corporations of the University of Vienna, where the new ruling class was forming which, despite different political ideas, was united by nationalism. Finally, the paper analyses the opposing views of Eric J. Hobsbawm and Anthony D. Smith on the idea of nation and suggests some similarities between the Habsburg Empire and the European Union. (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)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)