Leo Strauss and Eric Voegelin were political theorists of the first rank whose impact on the study of political science in North America has been profound. A study of their writings is one of the most expeditious ways to explore the core of political science; comparing and contrasting the positions both theorists have taken in assessing that core provides a comprehensive appreciation of the main options of the Western tradition. In fifty-three recently discovered letters, Strauss and Voegelin explore the (...) nature of their similarities and differences, offering trenchant observations about one another's work, about the state of the discipline, and about the influences working on them. The correspondence fleshes out many assumptions made in their published writings, often with a frankness and directness that removes all vestiges of ambiguity. Included with the correspondence are four pivotal re-published essays—"Jerusalem and Athens: Some Preliminary Reflections", "The Gospel and Culture", "Immortality: Experience and Symbol", and "The Mutual Influence of Theology and Philosophy" —and commentaries by James L. Wiser, Hans-Georg Gadamer, Stanley Rosen, Thomas J. J. Altizer, Timothy Fuller, Ellis Sandoz, Thomas L. Pangle, and David Walsh. (shrink)

In 1924, not quite two years after receiving his doctorate from the University of Vienna, Eric Voegelin was named a Laura Spelman Rockefeller Memorial Fellow and thus given the opportunity to pursue postdoctoral studies in the United States. For the next twenty-four months, Voegelin worked with some of the most creative scholars in America and at several of the country's great universities, an experience that undoubtedly influenced his scholarly and personal perspectives throughout his life. A more immediate result was (...) the publication in 1928 of _On the Form of the American Mind,_ the young philosopher's first major work, in which his acute perceptions and analyses combine with a conceptual vocabulary struggling to find its own coherence and form. Voegelin begins his inquiry into the form of the American mind with a complex discussion of the concepts of time and existence in European and American philosophy and continues with an extended interpretation of George Santayana, a study of the Puritan mystic Jonathan Edwards, a presentation on Anglo-American jurisprudence, and a consideration of the historian, economist, and political scientist John R. Commons. Although admitting that this diversity of themes seems only loosely connected," Voegelin demonstrates the actual overall unity of these various subjects: each concerns linguistic expressions of a theoretical nature. Analysis of _On the Form of the American Mind_ indicates that Voegelin integrated the approaches of _Lebensphilosophie_ into what Georg Misch called the "philosophical combination of anthropology and history," which characterized contemporary trends within the discourse of the _Geisteswissenschaften_ and finally resulted in a theoretical paradigm of philosophical anthropology. Jürgen Gebhardt and Barry Cooper provide access to this brilliant study with their two-part introduction. The first part considers _On the Form of the American Mind_ in the context of methodological debates ongoing in Germany at the time Voegelin was writing the book; the second describes Voegelin's American experience and compares his work with similar studies written during the post-World War I period. (shrink)

Arsenic and phosphorus are group 15 elements with similar chemical properties. Is it possible that arsenate could replace phosphate in some of the chemicals that are required for life? Phosphate esters are ubiquitous in biomolecules and are essential for life, from the sugar phosphates of intermediary metabolism to ATP to phospholipids to the phosphate backbone of DNA and RNA. Some enzymes that form phosphate esters catalyze the formation of arsenate esters. Arsenate esters hydrolyze very rapidly in aqueous solution, which makes (...) it improbable that phosphorous could be completely replaced with arsenic to support life. Studies of bacterial growth at high arsenic:phosphorus ratios demonstrate that relatively high arsenic concentrations can be tolerated, and that arsenic can become involved in vital functions in the cell, though likely much less efficiently than phosphorus. Recently Wolfe‐Simon et al. 1 reported the isolation of a microorganism that they maintain uses arsenic in place of phosphorus for growth. Here, we examine and evaluate their data and conclusions. (shrink)

We investigate the expressive power of fragments of first-order logic that are defined in terms of prefixes. The main result establishes a strict hierarchy among these fragments over the signature consisting of a single binary relation. It implies that for each prefix p, there is a sentence in prenex normal form with prefix p, over a single binary relation, such that for all sentences θ in prenex normal form, if θ is equivalent to , then p can be embedded in (...) the prefix of θ. This strengthens a theorem of Walkoe. (shrink)

We investigate properties of propositional modal logic over the classof finite structures. In particular, we show that certain knownpreservation theorems remain true over this class. We prove that aclass of finite models is defined by a first-order sentence and closedunder bisimulations if and only if it is definable by a modal formula.We also prove that a class of finite models defined by a modal formulais closed under extensions if and only if it is defined by a -modal formula.

A collection of newly commissioned papers on themes from David Albert's Time and Chance (HUP, 2000), with replies by Albert. Introduction [Barry Loewer, Brad Weslake, and Eric Winsberg] I. Overview of Time and Chance 1. The Mentaculus: A Probability Map of the Universe [Barry Loewer] II. Philosophical Foundations 2. The Metaphysical Foundations of Statistical Mechanics: On the Status of PROB and PH [Eric Winsberg] 3. The Logic of the Past Hypothesis [David Wallace] 4. In What Sense (...) Is the Early Universe Fine-Tuned? [Sean M. Carroll] 5. The Meta-Reversibility Objection [Christopher J. G. Meacham] 6. Typicality versus Humean Probabilities as the Foundation of Statistical Mechanics [Dustin Lazarovici] 7. The Past Hypothesis and the Nature of Physical Laws [Eddy Keming Chen] 8. On the Albertian Demon [Tim Maudlin] III. Underwriting the Asymmetries of Knowledge and Intervention 9. Reading the Past in the Present [Nick Huggett] 10. Causes, Randomness, and the Past Hypothesis [Mathias Frisch] 11. Time, Flies, and Why We Can’t Control the Past [Alison Fernandes] 12. The Concept of Intervention in Time and Chance [Sidney Felder] Conclusion [David Albert]. (shrink)

We prove a 0-1 law for the fragment of second order logic SO over parametric classes of finite structures which allow only one unary atomic type. This completes the investigation of 0-1 laws for fragments of second order logic defined in terms of first order quantifier prefixes over, e.g., simple graphs and tournaments. We also prove a low oscillation law, and establish the 0-1 law for Σ14 without any restriction on the number of unary types.

Model theory is concerned mainly, although not exclusively, with infinite structures. In recent years, finite structures have risen to greater prominence, both within the context of mainstream model theory, e.g., in work of Lachlan, Cherlin, Hrushovski, and others, and with the advent of finite model theory, which incorporates elements of classical model theory, combinatorics, and complexity theory. The purpose of this survey is to provide an overview of what might be called the model theory of finite structures. Some topics in (...) finite model theory have strong connections to theoretical computer science, especially descriptive complexity theory. In fact, it has been suggested that finite model theory really is, or should be, logic for computer science. These connections with computer science will, however, not be treated here.It is well-known that many classical results of ‘infinite model theory’ fail over the class of finite structures, including the compactness and completeness theorems, as well as many preservation and interpolation theorems. The failure of compactness in the finite, in particular, means that the standard proofs of many theorems are no longer valid in this context. At present, there is no known example of a classical theorem that remains true over finite structures, yet must be proved by substantially different methods. It is generally concluded that first-order logic is ‘badly behaved’ over finite structures.From the perspective of expressive power, first-order logic also behaves badly: it is both too weak and too strong. Too weak because many natural properties, such as the size of a structure being even or a graph being connected, cannot be defined by a single sentence. Too strong, because every class of finite structures with a finite signature can be defined by an infinite set of sentences. Even worse, every finite structure is defined up to isomorphism by a single sentence. In fact, it is perhaps because of this last point more than anything else that model theorists have not been very interested in finite structures. Modern model theory is concerned largely with complete first-order theories, which are completely trivial here. (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)

Background Bioethical debates about privacy, big data, and public health surveillance have not sufficiently engaged the perspectives of those being surveilled. The data justice framework suggests that big data applications have the potential to create disproportionate harm for socially marginalized groups. Using examples from our research on HIV surveillance for individuals incarcerated in jails, we analyze ethical issues in deploying big data in public health surveillance. -/- Methods We conducted qualitative, semi-structured interviews with 24 people living with HIV who had (...) been previously incarcerated in county jails about their perspectives on and experiences with HIV surveillance, as part of a larger study to characterize ethical considerations in leveraging big data techniques to enhance continuity of care for incarcerated people living with HIV. -/- Results Most participants expressed support for the state health department tracking HIV testing results and viral load data. Several viewed HIV surveillance as a violation of privacy, and several had actively avoided contact from state public health outreach workers. Participants were most likely to express reservations about surveillance when they viewed the state’s motives as self-interested. Perspectives highlight the mistrust that structurally vulnerable people may have in the state’s capacity to act as an agent of welfare. Findings suggest that adopting a nuanced, context-sensitive view on surveillance is essential. -/- Conclusions Establishing trustworthiness through interpersonal interactions with public health personnel is important to reversing historical legacies of harm to racial minorities and structurally vulnerable groups. Empowering stakeholders to participate in the design and implementation of data infrastructure and governance is critical for advancing a data justice agenda, and can offset privacy concerns. The next steps in advancing the data justice framework in public health surveillance will be to innovate ways to represent the voices of structurally vulnerable groups in the design and governance of big data initiatives. (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)

Previous work demonstrates that music with more surprising chords tends to be perceived as more enjoyable than music with more conventional harmonic structures. In that work, harmonic surprise was computed based upon a static distribution of chords. This would assume that harmonic surprise is constant over time, and the effect of harmonic surprise on music preference is similarly static. In this study we assess that assumption and establish that the relationship between harmonic surprise and music preference is not constant as (...) time goes on. Analyses of harmonic surprise and preference from 1958 to 1991 showed increased harmonic surprise over time, and that this increase was significantly more pronounced in preferred songs. Separate analyses showed similar increases over the years from 2000 to 2019. As such, these findings provide evidence that the human perception of tonality is influenced by exposure. Baseline harmonic expectations that were developed through listening to the music of “yesterday” are violated in the music of “today,” leading to preference. Then, once the music of “today” provides the baseline expectations for the music of “tomorrow,” more pronounced violations—and with them, higher harmonic surprise values—become associated with preference formation. We call this phenomenon the “Inflationary-Surprise Hypothesis.” Support for this hypothesis could impact the understanding of how the perception of tonality, and other statistical regularities, are developed in the human brain. (shrink)

It is a classical result of Mortimer that $L^2$ , first-order logic with two variables, is decidable for satisfiability. We show that going beyond $L^2$ by adding any one of the following leads to an undecidable logic:– very weak forms of recursion, viz.¶(i) transitive closure operations¶(ii) (restricted) monadic fixed-point operations¶– weak access to cardinalities, through the Härtig (or equicardinality) quantifier¶– a choice construct known as Hilbert's $\epsilon$ -operator.In fact all these extensions of $L^2$ prove to be undecidable both for satisfiability, (...) and for satisfiability in finite structures. Moreover most of them are hard for $\Sigma^1_1$ , the first level of the analytical hierachy, and thus have a much higher degree of undecidability than first-order logic. (shrink)

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)

In medical research, it is not unusual that risks are ruled out without any specification the exact risk that was ruled out. This makes it difficult to balance expected health benefits and risk of harm when choosing between alternative treatment options. International guidelines for reporting medical research results are sufficiently specific when it comes to establishing health benefits. However, there is a lack of standards for reporting on ruling out risks. We argue that transparency is needed, as in the case (...) of non-inferiority trials. The Consolidated Standards of Reporting Trials and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statements should be revised accordingly. (shrink)

We show that the existential preservation theorem fails for two-variable first-order logic FO2. It is known that for all k ≥ 3, FOk does not have an existential preservation theorem, so this settles the last open case, answering a question of Andreka, van Benthem, and Németi. In contrast, we prove that the homomorphism preservation theorem holds for FO2.

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)

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)

Early career scientists sometimes observe senior scientists engage in apparent scientific misconduct, but feel powerless to intervene, lest they imperil their careers. We propose a Secure Reporting Procedure that both protects them, when pursuing those concerns, and treats the senior scientists fairly. The proposed procedure is, we argue, consistent with the ethical principles of the scientific community, as expressed in the codes of its professional organizations. However, its implementation will require changes in procedures and regulations. Those efforts will be a (...) small price to pay for protecting the scientific community’s integrity and fidelity to its principles. We begin by describing the circumstances motivating the proposal, then sketch its design, and, finally, illustrate next steps in its application in two national settings. (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)

Web scraping involves using computer programs for automated extraction and organization of data from the Web for the purpose of further data analysis and use. It is frequently used by commercial companies, but also has become a valuable tool in epidemiological research and public health planning. In this paper, we explore ethical issues in a project that “scrapes” public websites of U.S. county jails as part of an effort to develop a comprehensive database to enhance HIV surveillance and improve continuity (...) of care for incarcerated populations. We argue that the well-known framework of Emanuel et al. provides only partial ethical guidance for the activities we describe, which lie at a complex intersection of public health research and public health practice. We suggest some ethical considerations from the ethics of public health practice to help fill gaps in this relatively unexplored area. (shrink)

This important new work is a major analysis of the foundation of Eric Voegelin's political science.

Loneliness—perceived social isolation—is defined as a discrepancy between existing social relationships and desired quality of relationships. Whereas most research has focused on existing relationships, we consider the standards against which people compare them. Participants who made downward social or temporal comparisons that depicted their contact with others as better reported less loneliness than participants who made upward comparisons that depicted their contact with others as worse. Extending these causal results, in a survey of British adults, upward social comparisons predicted current (...) loneliness, even when controlling for loneliness at a previous point in time. Finally, content analyses of interviews with American adults who lived alone showed that social and temporal comparisons about contact with others were both prevalent and linked to expressed loneliness. These findings contribute to understanding the social cognition of loneliness, extend the effects of comparisons about social connection to the important public health problem of loneliness, and provide a novel tool for acutely manipulating loneliness. (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 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 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)

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)

Consciousness and Politics begins with an analysis of the problem of the historicity of truth as it was formulated shortly before Voegelin abandoned his eight-volume History of Political Ideas. The analysis then follows a more or less chronological path, discussing the arguments developed in The New Science of Politics, Voegelin's most famous book, the differentiation of consciousness and the problems of myth and nature as presented in the early volumes of Order and History. Starting in the 1960s, Voegelin began a (...) lengthy argument in several volumes that resumed his concern with the philosophy of consciousness, which he had outlined in his early writings, and its connection to what we conventionally call philosophy of history. Voegelin's late and often difficult essays, lectures, and the final volume of Order and History, many scholars have noticed, emphasize the meditative origins of his political science and, more broadly, of philosophy. The concluding chapters analyze this subject-matter and a perennial question that so many of Voegelin's readers have raised: what is the relation of his political science or philosophy to Christianity? (shrink)

A new realislic local model of light propagation and detection is described. The authors propose a novel stochastic model of low-intensity photon detection in which background noise is added to a part of the photon prior to absorption. In this model, in agreement with Planck, there is no quantization of the propagating field. The model has some similarities to theories advanced by E. Santos and T. Marshall in the last decade, but also has substantial deviations from these. A mechanism, conserving (...) energy and momentum, is proposed by which a sudden collapse of the wave-packet is avoided. The experimental Bell inequality violation of Aspect. Grangier and Roger [Phys. Rev. Lett.47, 460 (1981)]is discussed. The authors have carried out a computer simulation of a radio frequency (RF) analogue of the Einstein-Podolsky-Rosen thought experiment to illustrate how the manipulation of certain factors, especially signal to noise ratio, detector threshold and characteristics of the noise, enables the same Bell inequality to be either satisfied or violated by a realistic local model. Building on arguments by Santos. [Phys. Rev. A46. 3646 (1992)],the appropriateness of this Bell lest is discussed. Neither the authors' stochastic-optical model, nor their RF analogue, involves an enhancement assumption of the type defined by Clauser and Horne [Phys. Rev. D10, 526 (1974)]. (shrink)

Eric Voegelin's new study of Greek civilization, part of his continuing study of Order and History, contains elements of both such approaches to antiquity. In briefest compass, it is Voegelin's contention that order in history depends upon the recognition of the transcendental source of order; disorder is engendered by the "immanentization" of this source. Nevertheless, the transcendental source of order, the Christian God, is experienced within history, and civilizations are evaluated in terms of their anticipation of, approach to, or (...) withdrawal from this God. In terms of Christ's revelation, Greek thought is prejudged as a defective preliminary vision of historical and metaphysical truth. Just as Christ completes the Greek vision in "existential" terms, so Thomas Aquinas remedies the faults of Greek theory. In the process of being rejected or completed, classical thought takes on a remarkably Christian appearance. Despite his conservative or transcendental intentions, Voegelin's version of Christianity places great emphasis upon history as "open" to the future, and so the christianization of the Greeks produces anachronisms of the most extreme liberalism. At the same time, however, the Greek failure to transcend either the polis as a form of temporal order or an immanent conception of Being is severely criticized. (shrink)

The primary argument against mereological singularism—the view that definite plural noun phrases like ‘the students’ refer to “set-like entities”—is that it is ultimately incoherent. The most forceful form of this charge is due to Barry Schein, who argues that singularists must accept a certain comprehension principle which entails the existence of things having the contradictory property of being both atomic and non-atomic. The purpose of this paper is to defuse Schein’s argument, by noting three necessary and independently motivated restrictions (...) on the metalinguistic predicates ‘atom’ and ‘non-atom’: both are sort, property, and context-relative. With these restrictions in place, Schein’s problematic assumption becomes evident: his presumed singularist analysis of ‘non-atom’ conflates the metalanguage with the meta-metalanguage, i.e. the language used to talk about the metalanguage. (shrink)