This article is featured in a special issue dedicated to theme, "the human being in the digital era: awareness, critical thinking and political space in the age of the internet and artificial intelligence." In this article, I consider the way that social-media companies nudge us to spend more time on their platforms, and I argue that, in principle, these nudges are morally permissible: they are not manipulative and do not violate any obvious moral rules. The moral problem, I argue, is (...) not with nudging in principle but is instead with the fact that users are being nudged towards something bad for them. In practice, this often involves being nudged to spend an unhealthy amount of time using a social-media app or being nudged towards content that is bad for us, such as by promoting eating-disorder content to young girls. Since nudging is morally permissible, it is open to these companies to use the same technologies to nudge us towards the good. (shrink)

I argue that Plato thinks that a sunaition is a mere tool used by a soul (or by the cosmic nous) to promote an intended outcome. In the first section, I develop the connection between sunaitia and Plato’s teleology. In the second section, I argue that sunaitia belong to Plato’s theory of the soul as a self-mover: specifically, they are those things that are set in motion by the soul in the service of some goal. I also argue against several (...) popular and long-standing interpretations, namely, that sunaitia correspond to Aristotle’s idea of hypothetical necessity, that sunaitia are the ‘how’ in an explanation (whereas the true cause is the ‘why’), and that Plato’s causal views should be read through Aristotle’s fourfold schema. I conclude the article by surveying the history of sunaitia after Plato’s usage. (shrink)

I argue that Plato believes that the soul must be both the principle of motion and the subject of cognition because it moves things specifically by means of its thoughts. I begin by arguing that the soul moves things by means of such acts as examination and deliberation, and that this view is developed in response to Anaxagoras. I then argue that every kind of soul enjoys a kind of cognition, with even plant souls having a form of Aristotelian discrimination (...) (krisis), and that there is therefore no completely unintelligent, evil soul in the cosmos that can explain disorderly motions; as a result, the soul is not the principle of all motion but only motion in the cosmos after it has been ordered by the Demiurge. (shrink)

I argue that, according to Plato, the body is the sole cause of psychic disorders. This view is expressed at Timaeus 86b in an ambiguous sentence that has been widely misunderstood by translators and commentators. The goal of this article is to offer a new understanding of Plato’s text and view. In the first section, I argue that although the body is the result of the gods’ best efforts, their sub-optimal materials meant that the soul is constantly vulnerable to the (...) body’s influences. In the second section, I argue that every psychic disorder is a disruption of the motions of the inner psychic circles by the body; moreover, I defend my translation of 86b. In the final section, I argue that the goal of education is to restore the circles to their original orbits, and I disarm a possible objection that bad education is also a cause of psychic disorder. (shrink)

This article concerns the place of Plato’s eschatology in his philosophy. I argue that the theory of reincarnation appeals to Plato due to its power to explain how non-human animals came to be. Further, the outlines of this theory are entailed by other commitments, such as that embodiment disrupts psychic functioning, that virtue is always rewarded and vice punished, and that the soul is immortal. I conclude by arguing that Plato develops a view of reincarnation as the chief tool that (...) the gods have to ensure that virtue is victorious over vice throughout the whole cosmos. (shrink)

In this article, I argue that online echo chambers are in some cases and in some respects good. I do not attempt to refute arguments that they are harmful, but I argue that they are sometimes beneficial. In the first section, I argue that it is sometimes good to be insulated from views with which one disagrees. In the second section, I argue that the software-design principles that give rise to online echo chambers have a lot to recommend them. Further, (...) the opposing principle, serendipity, could give rise to serious harm, in light of the conclusion of the first section that sometimes we are better off being insulated from some content online. In the third section, I argue that polarization can be a useful tool for inculcating the appropriate attitudes in a person. (shrink)

In this article, I approach some phenomena seen predominantly on social-media sites that are grouped together as cancel culture with guidance from two major themes in Plato’s thought. In the first section, I argue that shame can play a constructive and valuable role in a person’s improvement, just as we see Socrates throughout Plato’s dialogues use shame to help his interlocutors improve. This insight can help us understand the value of shaming people online for, among other things, their morally reprehensible (...) views. In the second section, I argue that it is required for the proper functioning of democratic institutions that some views be excluded from the public sphere, which follows some Platonic ideas from the Laws. In neither case do I argue that this approach is good in an unqualified sense or even ultima facie good. However, I maintain that these important insights from Plato’s dialogues illuminate crucial aspects of how we should think about cancel culture. (shrink)

In this article, I make the case for the continued relevance of Plato’s Timaeus. I begin by sketching Allan Bloom’s picture of the natural sciences today in The Closing of the American Mind, according to which the natural sciences are, objectionably, increasingly specialized and have ejected humans qua humans from their purview. I argue that Plato’s Timaeus, despite the falsity of virtually all of its scientific claims, provides a model for how we can pursue scientific questions in a comprehensive way (...) that stresses their connections to other disciplines, including the humanities, and that puts humanity qua humanity back in the picture. I then argue that being led by Plato’s philosophy to return humanity conceptually to the natural world can improve our thinking regarding climate change and other important environmental crises. (shrink)

With an eye on the future of global ethics, I argue that social-media technologies are not morally neutral tools but are, for all intents and purposes, a kind of agent. They nudge us to do things that are bad for us. Moreover, I argue that we have a duty to quit using social-media platforms, not just on account of possible duties to preserve our own well-being but because users are akin to test subjects on whom developers are testing new nudges, (...) and we ought to deprive them of their test subjects. (shrink)

This paper concerns Plato’s characterization of the body as the soul’s tool. I take perception as an example of the body’s usefulness. I explore the Timaeus’ view that perception provides us with models of orderliness. Then, I argue that perception of confusing sensible objects is necessary for our cognitive development too. Lastly, I consider the instrumentality relationship more generally and its place in Plato’s teleological worldview.

I argue that Plato thinks that the soul has location, surface, depth, and extension, and that the Timaeus’ composition of the soul out of eight circles is intended literally. A novel contribution is the development of an account of corporeality that denies the entailment that the soul is corporeal. I conclude by examining Aristotle’s objection to the Timaeus’ psychology and then the intellectual history of this reading of Plato.

This is an impressive and important book about perception in Plato’s Timaeus, but most of its readers will probably be researchers who are interested in much broader questions about the dialogue. There is nothing deficient or lacking about this treatment of perception, but this book should be put alongside Thomas Johansen’s Plato’s Natural Philosophy and Sarah Broadie’s Nature and Divinity in the sense that this is, for all intents and purposes, a monograph about the whole Timaeus, even though it is (...) pitched as being focused on perception. There are only a few topics missing, such as the nature of the cosmic receptacle and psychic diseases. Virtually everything else, including the status of Timaeus’ so-called likely story, the generation of the lower gods, and the nature of bone, is discussed at length. (shrink)

The editors have put together an interesting and important collection of twelve essays that trace the development of explanations of the human body that appeal to machines and other technological artefacts. Although the focus of the book is ancient authors, with the oldest being Homer and Pindar, the last essay reaches into the eighteenth century, at which point there are no longer mere analogies between human bodies and machines but a conception of the human body as something mechanized. The essays (...) are put together in such a way that emphasizes the early-modern conception as the terminus of the ancient mode of inquiry. (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)

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

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

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)

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)

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)

In the TACITUS project for using commonsense knowledge in the understanding of texts about mechanical devices and their failures, we have been developing various commonsense theories that are needed to mediate between the way we talk about the behavior of such devices and causal models of their operation. Of central importance in this effort is the axiomatization of what might be called commonsense metaphysics. This includes a number of areas that figure in virtually every domain of discourse, such as granularity, (...) scales, time, space, material, physical objects, shape, causality, functionality, and force. Our effort has been to construct core theories of each of these areas, and then to define, or at least characterize, a large number of lexical items in terms provided by the core theories. In this paper we discuss our methodological principles and describe the key ideas in the various domains we are investigating. (shrink)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 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)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a banks computers, however, the formula fails, (...) because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (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)

Este artigo procura analisar algumas das principais ideias abordadas no encontro anual promovido pela “American Association for the Advancement of Sciencie” em Boston (EUA) em 1953. Parte do encontro foi para abordar sobre o estado atual da concepção operacional de significado desenvolvida por Percy W. Bridgman a partir de 1927. As principais ideias tratadas no encontro foram posteriormente publicadas pela revista “The Scientific Montly” em 1954-1955 e republicadas no capítulo 2 do livro “The validation of scientific theories” (1961), editado por (...) Philipp Frank. A obra de 1961 será utilizada aqui como referência para as citações. Os autores dos capítulos são Henry Margenau, Gustav Bergmann, Carl G. Hempel, R. B. Lindsay, Raymond J. Sieger, Adolf Gründbaun, além do artigo do próprio Percy Bridgman. Este debate surgiu a mais de 20 anos depois da publicação da primeira obra de Bridgman, a saber, “The Logic of Modern Physics” (1927), onde ele apresenta pela primeira vez sua concepção de significado dos conceitos científicos baseada em procedimentos operacionais. A obra de 1927 trouxe os debates sobre a importância da linguagem científica e da correspondência empírica, uma questão pertinente na filosofia da ciência da época inflacionada pela filosofia da ciência do empirismo lógico. Os debates do encontro tiveram como objetivo apresentar questionamentos e fazer exposições gerais sobre a forma como a concepção operacional pode ser interpretada por cientistas e filósofos da época, seja em seus elementos favoráveis na ciência, enquanto resolvendo questões pertinentes para cientistas e filósofos da ciência, seja por mostrar também as limitações da concepção operacional através dos questionamentos dirigidos a ela. Ressaltamos a importância deste debate na época e nos dias atuais. Temos aqui um material que pode servir de direcionamento histórico e de debate filosófico para algumas das questões pertinentes dos filósofos da ciência da época. (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)

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.

Trata-se de um ensaio sobre o conceito de "Akrasia" em Aristóteles, o qual é introduzido e argumentado em seu livro VII de Ética à Nicômaco, a partir de 1145a15. Tenta-se analisar o conceito de "akrasia" com base no lvro original supracitado e no artigo "Sobre a Akrasia em Aristóteles", de R. Robinson.

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)

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)

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)

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)

In this response to comments on my article, “The Chimera of Relativism,” in the same issue of *Common Knowledge* , by cognitive neuroscientist Andreas Roepstorff, classicist G. E. R. Lloyd, and anthropologist Martin Holbraad, I illustrate and reinforce Lloyd's cautions regarding the hazards of intercultural—here, Chinese-Western—comparisons in studies of culture and cognition. Examination of a foundational study in East-West cultural/cognitive differences cited by Roepstorff indicates extensive conceptual and methodological problems in that tradition of research. Although Holbraad champions a more radical (...) relativism than that offered in my work, the moves he urges have either been present in my work from the beginning or are both dubiously radical and otherwise undesirable. (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)

Adam Smith argued that the ideal moral judge is both well-informed and impartial. As non-ideal moral agents, we tend only to be truly well-informed about those with whom we frequently interact. These are also those with whom we tend to have the closest affective bonds. Hence, those who are well-informed, like our friends, tend to make for partial judges, while those who are impartial, like strangers, tend to make for ill-informed ones. Combining these two traits in one person seems (...) far from straightforward. Still, if becoming well-informed is, as Smith also claims, a matter of imaginative perspective-taking with the “person principally concerned”, it might be possible to become well-informed without the emotional entanglement that comes from any actual proximity to those we judge. Against this intuition, I use Construal Level Theory to show that the tension between being well-informed and impartial is likely to persist even if we take any actual proximity out of the equation. I end by discussing some implications of this, and suggest that we should consider revising the ideal to accommodate them. (shrink)