Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (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)

While many bibliometric techniques have been employed to represent the structure of academic research communities over the years, much of this work has been conducted on scientific fields as opposed to those in the humanities. Here we use graphing techniques to present two networks that allow us to explore the structure of a subset of the philosophy community by mapping the citations between philosophical texts on the topic of ontology (the study of what exists). We find a citation gap between (...) philosophers studying material and abstract objects, and between analytic and continental ontologists, but other predictions were not confirmed by this method. We conclude by considering several additional methods for further exploring both the structure of philosophy and other disciplines in the humanities. (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)

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)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

An often-overlooked characteristic of the human mind is its propensity to wander. Despite growing interest in the science of mind-wandering, most studies operationalize mind-wandering by its task-unrelated contents. But these contents may be orthogonal to the processes that determine how thoughts unfold over time, remaining stable or wandering from one topic to another. In this chapter, we emphasize the importance of incorporating such processes into current definitions of mind-wandering, and propose that mind-wandering and other forms of spontaneous thought (such as (...) dreaming and creativity) are mental states that arise and transition relatively freely due to an absence of constraints on cognition. We review existing psychological, philosophical and neuroscientific research on spontaneous thought through the lens of this framework, and call for additional research into the dynamic properties of the mind and brain. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

I offer an interpretation of Carnap and Quine’s views on cognitive significance and insignificance. The basic idea behind their views is as follows: to judge an expression is insignificant is to recommend it not be used in or explicated into languages used to express truth-valued judgments in inquiry; to judge an expression is significant is to recommend it be used in or explicated into such languages. These judgments are pragmatic judgments, made in light of purposes for language use in inquiry. (...) For Carnap at least, these pragmatic judgments are non-cognitive. This basic idea is only a roughly correct statement of their views. This is because the details of the scientific languages they recommend for inquiry are necessary to understand their views and the way they understand their own views. Even so, I offer two reasons to suggest that this basic idea is worthy of our consideration today. First, it provides a conception of significance that captures the natural thought that epistemological concerns can lead us to consider expressions to be insignificant without requiring an objectionable form of verificationism. Second, if we appeal also to Carnap and Quine’s pluralistic attitude toward explication, we can make a pragmatic judgment that an expression is insignificant while judging it to be significant on a distinct explication of significance fit for describing and explaining natural language. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptual Spaces framework work, (...) the similarity values between the contents of observations on the one hand and the properties of the entities observed on the other needs to be found. This paper shows how to exploit Dempster-Shafer theory to implement a statistical approach for finding these similarities values. This approach will allow a user to identify the uncertainty involved in similarity value data, which can later be propagated through the developed mathematical model in order for the user to know the overall uncertainty in the observation-to-concept mappings needed for space event characterization. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Volume 19, Issue 9, September 2019, Page 64-66.

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Background Men with antisocial personality disorder show lifelong abnormalities in adaptive decision making guided by the weighing up of reward and punishment information. Among men with antisocial personality disorder, modifi cation of the behaviour of those with additional diagnoses of psychopathy seems particularly resistant to punishment. Methods We did a case-control functional MRI (fMRI) study in 50 men, of whom 12 were violent off enders with antisocial personality disorder and psychopathy, 20 were violent off enders with antisocial personality disorder but (...) not psychopathy, and 18 were healthy non-off enders. We used fMRI to measure brain activation associated with the representation of punishment or reward information during an event-related probabilistic response-reversal task, assessed with standard general linear-model-based analysis. Findings Offenders with antisocial personality disorder and psychopathy displayed discrete regions of increased activation in the posterior cingulate cortex and anterior insula in response to punished errors during the task reversal phase, and decreased activation to all correct rewarded responses in the superior temporal cortex. This finding was in contrast to results for off enders without psychopathy and healthy non-off enders. Interpretation Punishment prediction error signalling in off enders with antisocial personality disorder and psychopathy was highly atypical. This finding challenges the widely held view that such men are simply characterised by diminished neural sensitivity to punishment. Instead, this fi nding indicates altered organisation of the information processing system responsible for reinforcement learning and appropriate decision making. This difference between violent offenders with antisocial personality disorder with and without psychopathy has implications for the causes of these disorders and for treatment approaches. (shrink)

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

In real-time, Twitter strongly imprints world events, popular culture, and the day-to-day; Twitter records an ever growing compendium of language use and change; and Twitter has been shown to enable certain kinds of prediction. Vitally, and absent from many standard corpora such as books and news archives, Twitter also encodes popularity and spreading through retweets. Here, we describe Storywrangler, an ongoing, day-scale curation of over 100 billion tweets containing around 1 trillion 1-grams from 2008 to 2020. For each day, we (...) break tweets into 1-, 2-, and 3-grams across 150+ languages, record usage frequencies, and generate Zipf distributions. We make the data set available through an interactive time series viewer, and as downloadable time series and daily distributions. We showcase a few examples of the many possible avenues of study we aim to enable including how social amplification can be visualized through ‘contagiograms’. (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 translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

That uses of language not only can, but even normally do, have the character of actions was a fact largely unrealised by those engaged in the study of language before the present century, at least in the sense that there was lacking any attempt to come to terms systematically with the action-theoretic peculiarities of language use. Where the action-character of linguistic phenomena was acknowledged, it was normally regarded as a peripheral matter, relating to derivative or nonstandard aspects of language which (...) could afford to be ignored. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

I contend that Adam Smith and David Hume offer re-interpretations of Aristotle’s notion of greatness of soul, focusing on the kind of magnanimity Aristotle attributes to Socrates. Someone with Socratic magnanimity is worthy of honor, responds moderately to fortune, and is virtuous—just and benevolent. Recent theorists err in claiming that magnanimity is less important to Hume’s account of human excellence than benevolence. In fact, benevolence is a necessary ingredient for the best sort of greatness. Smith’s “Letter to Strahan” (...) attributes this greatness to Hume. It encourages us to admire Hume as an exemplar of human excellence, to seek Hume’s virtues for ourselves, and to approve of the “love of literary fame” which Hume calls his “ruling passion.”. (shrink)

Sometimes it’s not certain which of several mutually exclusive moral views is correct. Like almost everyone, I think that there’s some sense in which what one should do depends on which of these theories is correct, plus the way the world is non-morally. But I also think there’s an important sense in which what one should do depends upon the probabilities of each of these views being correct. Call this second claim “moral uncertaintism”. In this paper, I want to address (...) an argument against moral uncertaintism offered in the pages of this journal by Brian Weatherson, and seconded elsewhere by Brian Hedden, the crucial premises of which are: that acting on moral uncertaintist norms necessarily involves motivation by reasons or rightness as such, and that such motivation is bad. I will argue that and are false, and that at any rate, the quality of an agent’s motivation is not pertinent to the truth or falsity of moral uncertaintism in the way that Weatherson’s and Hedden’s arguments require. (shrink)

Most of our memories are inferential, so says Sven Bernecker in Memory: A Philosophical Study. I show that his account of inferentially remembering that p is too strong. A revision of the account that avoids the difficulty is proposed. Since inferential memory that p is memory that q (a proposition distinct from p) with an admixture of inference from one’s memory that q and a true thought one has that r, its analysis presupposes an adequate account of the (presumably non-inferential) (...) memory that q. Bernecker’s account of non-inferentially remembering that is shown to be inadequate. A remedy lies in strengthening the account by requiring the rememberer to have had prima facie justification to believe that q, any defeaters of which were misleading. (shrink)

Gruber and Smith (2019) have conducted some interesting virtual reality (VR) experiments, but we think that these experiments fail to illuminate why people think that the present is special. Their experiments attempted to test a suggestion by Hartle (2005) that with VR one might construct scenarios in which people experience the same present twice. If that’s possible, then it could give us a reason to think that when we experience the present as being special, that’s not because it’s objectively (...) so. Instead, our experience of the present being special is a feature of having a psychology like ours. While we are sympathetic to the thought that there is no objective present, we do not think that these experiments give us a reason to think this. That said, VR experiments, such as Gruber and Smith’s, hold much promise for being able to illuminate various aspects of our temporal psychology.According to Hartle’s (2005) IGUS model (which is meant to resemble entities like us) sensory information is routed to two kinds of processes: conscious processes C, which cause behavior, and unconscious processes, U, which construct a schematic representation of the environment. Hartle proposed that we experience the present as being special because of the sensory information at a time entering into C. For Gruber et al. (2020), the succession of sensory information entering into C underpins our experience of time passing. Our experience of time passing is illusory because it fails to be verid... (shrink)

This paper argues against the correctness of the more popular -first views (fittingness first, reasons first, and value first). The aim of this paper is to argue that there are at least two categories of normative properties that are basic and that one of those categories is value. Although the emphasis of this paper is on reductionist -first accounts, most of the arguments work equally well against weaker views that are only committed to different categories of normative properties' being linked (...) by a necessary bi-conditional. -/- . (shrink)

In his [1937, 1938], Paul Dirac proposed his “Large Number Hypothesis” (LNH), as a speculative law, based upon what we will call the “Large Number Coincidences” (LNC’s), which are essentially “coincidences” in the ratios of about six large dimensionless numbers in physics. Dirac’s LNH postulates that these numerical coincidences reflect a deeper set of law-like relations, pointing to a revolutionary theory of cosmology. This led to substantial work, including the development of Dirac’s later [1969/74] cosmology, and other alternative cosmologies, such (...) as the Brans-Dicke modification of GTR, and to extensive empirical tests. We may refer to the generic hypothesis of “Large Number Relations” (LNR’s), as the proposal that there are lawlike relations of some kind between the dimensionless numbers, not necessarily those proposed in Dirac’s early LNH. Such relations would have a profound effect on our concepts of physics, but they remain shrouded in mystery. Although Dirac’s specific proposals for LNR theories have been largely rejected, the subject retains interest, especially among cosmologists seeking to test possible variations in fundamental constants, and to explain dark energy or the cosmological constant. In the first two sections here we briefly summarize the basic concepts of LNR’s. We then introduce an alternative LNR theory, using a systematic formalism to express variable transformations between conventional measurement variables and the true variables of the theory. We demonstrate some consistency results and review the evidence for changes in the gravitational constant G. The theory adopted in the strongest tests of Ġ/G, by the Lunar Laser Ranging (LLR) experiments, assumes: Ġ/G = 3(dr/dt)/r – 2(dP/dt)/P – (dm/dt)/m, as a fundamental relationship. Experimental measurements show the RHS to be close to zero, so it is inferred that significant changes in G are ruled out. However when the relation is derived in our alternative theory it gives: Ġ/G = 3(dr/dt)/r – 2(dP/dt)/P – (dm/dt)/m – (dR/dt)/R. The extra final term (which is the Hubble constant) is not taken into account in conventional derivations. This means the LLR experiments are consistent with our LNR theory (and others), and they do not really test for a changing value of G at all. This failure to transform predictions of LNR theories correctly is a serious conceptual flaw in current experiment and theory. (shrink)

According to the theological worldview of J. R. R. Tolkien, the principal work of a Christian is to know, love, and serve God. Why, then, did he devote so much time to creating an entire family of imaginary languages for imaginary peoples in an imaginary world? This paper argues that the stories of these peoples, with their ‘eucatastrophes,’ have consoling value amid the incomplete stories of our own lives. But more fundamentally, secondary creation is proper to the adopted children of (...) God and can be a way of drawing closer to God. Such work also witnesses to the freedom of the children of God, not only to receive salvation from God, but to contribute to the enrichment of creation and eternal life. (shrink)

This is Part 2 of a four part paper, intended as an introduction to the key concepts and issues of time directionality for physicists and philosophers. It redresses some fundamental confusions in the subject. These need to be corrected in introductory courses for physics and philosophy of physics students. Here we analyze the quantum mechanical time reversal operator and the reversal of the deterministic Schrodinger equation. It is argued that quantum mechanics is anti-symmetric w.r.t. time reversal in its deterministic laws. (...) This contradicts the orthodox analysis, found throughout the conventional literature on physical time, which claims that quantum mechanics is time symmetric (reversible), and that we must adopt the anti-unitary operator (T*) instead of the unitary time reversal operator (T) for time reversal in quantum mechanics. This is widely claimed as settled scientific fact, and large metaphysical conclusions about the symmetry of time are drawn from it. But it is an error. (shrink)

As so often with his published texts, the experience of reading Nietzsche’s notebooks is at once mesmerising and infuriating. One is in the presence of a thinker who, on the one hand, meditates deeply on fundamental issues in philosophy and psychology but who, on the other, refuses to be pinned down. The fact that Nietzsche’s style is so elusive can account for the enormously disparate interpretations of his work and it is no surprise that his notebooks have been read in (...) the most extreme fashion. The notebooks have a chequered history having been variously touted as the crowning achievement of his philosophy, and as not repaying the effort of reading. (shrink)

Wittgenstein's farcical clash with literary critic F. R. Leavis over the analysis of Empson's poem "Legal Fiction" is well known to devotees of Wittgenstein's life (Ludwig Wittgenstein: Personal Recollections (1981), edited by Rush Rhees, Oxford: Basil Blackwell, 80). Less well known is the value of studying Empson's artistic and intellectual achievement as part of the wider cultural background for the appreciation of Wittgenstein's views and influence, early and late. This talk sketches some diverting byways awaiting further exploration. A recurrent theme (...) is contradiction. (shrink)

Define teleology as the view that requirements hold in virtue of facts about value or goodness. Teleological views are quite popular, and in fact some philosophers (e.g. Dreier, Smith) argue that all (plausible) moral theories can be understood teleologically. I argue, however, that certain well-known cases show that the teleologist must at minimum assume that there are certain facts that an agent ought to know, and that this means that requirements can't, in general, hold in virtue of facts about (...) value or goodness. I then show that even if we grant those 'ought's teleology still runs into problems. A positive justification of teleology looks like it will require an argument of this form: O(X); if X, then O(Y); therefore O(Y). But this form of argument isn't in general valid. I conclude by offering two positive suggestions for those attracted to a teleological outlook. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

Adam Smith is respected as the father of contemporary economics for his work on systemizing classical economics as an independent field of study in The Wealth of Nations. But he was also a significant moral philosopher of the Scottish Enlightenment, with its characteristic concern for integrating sentiments and rationality. This article considers Adam Smith as a key moral philosopher of commercial society whose critical reflection upon the particular ethical challenges posed by the new pressures and possibilities of commercial (...) society remains relevant today. The discussion has three parts. First I address the artificial separation between self-interest and morality often attributed to Smith, in which his work on economics is stripped of its ethical context. Second I outline Smith’s ethical approach to economics, focusing on his vigorous but qualified defence of commercial society for its contributions to prosperity, justice, and freedom. Third I outline Smith’s moral philosophy proper as combining a naturalistic account of moral psychology with a virtue ethics based on propriety in commercial society. (shrink)

Scrutiny (1932-1953) was one of the most important critical reviews of the last century. Its editors and contributors included F. R. Leavis, Q. D. Leavis, Denys Thompson, L. C. Knights, D. W. Harding, W. H. Mellers, H. A. Mason, among others. In recasting Scrutiny’s critique of mass culture by way of Alisdair MacIntyre’s After Virtue (1981), I hope to show that the Scrutiny project not only dramatizes the conflicts internal to what MacIntyre calls emotivist culture, but provides a new way (...) of looking at the group’s relation to the culture industry, its purported elitism, and its deep ties with a communitarian rather than socialist politics. (shrink)

We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A (...) problem arises for this theory for cases involving 'free-standing Y terms', as for example in the case of money in a computerized bank account. Here there is no physical X to which a status function might be attached. We conclude by arguing that Searle's response to this problem creates difficulties for his naturalistic framework. (shrink)

Preliminary version of “Towards a History of Speech Act Theory”, in A. Burkhardt (ed.), Speech Acts, Meanings and Intentions. Critical Approaches to the Philosophy of John R. Searle, Berlin/New York: de Gruyter, 1990, 29–61.

Analytical philosophy of the last one hundred years has been heavily influenced by a doctrine to the effect that one can arrive at a correct ontology by paying attention to certain superficial (syntactic) features of first-order predicate logic as conceived by Frege and Russell. More specifically, it is a doctrine to the effect that the key to the ontological structure of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of first-order logic, where ‘F’ (...) stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects), the relation between these two kinds of entity being revealed in the predicate-argument structure of atomic formulas in first-order logic. (shrink)

Why be moral? Why, in the language of Adam Smith, act on what you think is praiseworthy even when it does not get you praise from other people? Because, answers Smith, you love praiseworthiness. But what is this love of praiseworthiness, and where does it come from? In this article, 1) I argue that we start to love praiseworthiness when we redirect our love of praise away from other people toward the ‘impartial spectator’-aspect of ourselves, and 2) show (...) how this fits with evidence that the rudimentary moral compass which guides us early in childhood needs correction through socialisation to develop into a mature moral conscience. (shrink)

A critique of dubious contrasts between "science" and "religion" drawn on the basis of cognitive-evolutionary accounts of human psychology, e.g.,. the claim that religious concepts are “likely” and “natural” for the human mind whereas scientific thinking is “rare” and “unnatural.” Initially made by biologist Lewis Wolpert in *The Unnatural Nature of Science* (1993) and anthropologist Pascal Boyer in *Religion Explained: The Evolutionary Origins of Religious Thought* (2001), they are developed at length by philosopher R. N. McCauley in a*Why Religion is (...) Natural and Science is Not* (2011). These contrasts involve tendentiously narrow or broad definitions of the terms “science” and “religion” and the obliteration of the complex historical and intellectual relations between the ideas and practices currently identified by those terms. (shrink)