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)

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)

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)

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)

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)

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)

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)

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)

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)

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.

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)

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)

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 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 firstorder 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)

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)

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)

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)

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)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

This article discusses the ‘nature’ of our contemporary fascination with wildness, in light of the popular documentary “Grizzly Man.”Taking as its central point of departure the film’s central protagonist Timothy Treadwell’s fascination with wild grizzlies and director Werner Herzog’s condemnation of it as gross anthropomorphism, this paper will explore the context and basis of our contemporary fascination with wildness in terms of the current debate raging within environmental philosophy between the social constructivist or postmodern position as exemplified by Martin (...) Drenthen and the feral humanist position as articulated by Paul Shepard.The former argues that this fascination with wildness is reflective of certain historical and cultural trends within contemporary western society, while the latter argues that it is reflective of our primordial human heritage. (shrink)

Dialogue between feminist and mainstream philosophy of science has been limited in recent years, although feminist and mainstream traditions each have engaged in rich debates about key concepts and their efficacy. Noteworthy criticisms of concepts like objectivity, consensus, justification, and discovery can be found in the work of philosophers of science including Philip Kitcher, Helen Longino, Peter Galison, Alison Wylie, Lorraine Daston, and Sandra Harding. As a graduate student in philosophy of science who worked in both literatures, I was often (...) left with the feeling that I had joined a broken family with two warring factions. This is apparent in the number of anthologies that have emerged on both sides in the aftermath of the “Science Wars” (Gross, Paul R., Norman Levitt, and Martin W. Lewis, eds. 1996; Koertge, Noretta, ed. 1998; Sokal, Alan and Jean Bricmont. 1998; etc.) Depending on one’s perspective on the Science Wars, the breadth of illustrative cases and examples found in Science and Other Cultures can either give more ammunition for the battle, or grounding for a much needed treaty of accord. The most important feature of this book is that it does not merely claim that science is only political, and it does not merely dismiss science as a social phenomenon to be deconstructed using the standard postmodern conceptual tools. Instead, the collection illustrates ways in which postcolonial analysis and multicultural examples can enrich our understanding of “good” science and ethics. Here, the concept of “strong objectivity” from Harding’s earlier books is fleshed out through a variety of cases. The anthology is the culmination of a series of research activities funded by a National Science Foundation grant to the American Philosophical Association. The grant, under the auspices of the NSF Ethics and Values Program, sponsored fourteen summer research projects and thirty-six presentations at four regional APA meetings. (shrink)

La categoría ‘arte conceptual’ se aplica a una gran cantidad de obras de arte contemporáneo. El artista Sol LeWitt introdujo el término en la jerga del arte al describir obras de arte donde “la idea o el concepto es el aspecto más importante de la obra” (LeWitt 1967: 79, traducción mía). Inicialmente, el término se utilizó para referirse a obras producidas entre finales de los años sesenta y principios de los setenta por artistas como Sol LeWitt, Robert Barry, Lawrence (...) Weiner, On Kawara, Joseph Kosuth, John Baldessari, el grupo Art & Language y otros (véase Lippard 1973). En España fueron relevantes el Grup de Treball, Zaj o Esther Ferrer entre otros. Más tarde se hizo evidente no solo que obras como Fuente (1917) de Marcel Duchamp – un urinario de porcelana, que fue firmado “R. Mutt” y presentado para una exposición de la Sociedad de Artistas Independientes – tenían mucho en común con aquellas producidas a finales de la década de 1960 y principios de la de 1970, sino también que obras de arte conceptual continuaron siendo producidas a lo largo de la década de 1970 y las décadas siguientes, hasta el punto de que podría argumentarse que gran parte del arte contemporáneo es, en cierta medida, conceptual. -/- Es característico de los primeros autores conceptuales el uso del lenguaje natural en obras que son en principio visuales o plásticas, como las frases de Weiner, las definiciones de Kosuth o los ensayos de Art&Language. Se trata de un interés por el significado y el lenguaje heredado de la semiótica y la filosofía analítica de la época. También señala el énfasis (a menudo exclusivo) de todas las obras de arte conceptual en el elemento conceptual, como ocurre en los dibujos y pinturas murales de LeWitt, donde el artista produjo las instrucciones para su ejecución, luego las realizó en colaboración con otros, o transfirió completamente a otros esta tarea. Otra característica de las primeras obras de arte conceptual es que los artistas no manipularon ningún material para producir un objeto (como en Fuente de Duchamp) o usaron materiales excéntricos como el lenguaje natural, su propio cuerpo -como en I am the locus (# 1) (1975) de Adrian Piper, una performance en la que la artista se pegó un bigote en la cara, se puso una peluca Afro y anteojos redondos con montura de alambre y caminó en las calles actuando como un hombre-, o el chocolate con el que Anya Gallaccio revistió las paredes de un viejo edificio agrícola en Stroke (2004), dejando que el público las tocara y que el chocolate se pudriese. -/- Debido a sus características inusuales, el arte conceptual plantea muchas preguntas filosóficas: sobre la definición de arte, sobre la ontología y los medios de las obras de arte y sobre nuestra experiencia apreciativa de ellas. En lo que sigue, presentaré brevemente cada uno de estos temas. (shrink)

Autobiographical survey of interactions between the author and Barry Smith, especially as concerns the background and influence of the Seminar for Austro-German Philosophy and work on the relevance of Adolf Reinach, Roman Ingarden and other Central-European thinkers to contemporary analytic philosophy.

Nick Shea’s Representation in Cognitive Science commits him to representations in perceptual processing that are about probabilities. This commentary concerns how to adjudicate between this view and an alternative that locates the probabilities rather in the representational states’ associated “attitudes”. As background and motivation, evidence for probabilistic representations in perceptual processing is adduced, and it is shown how, on either conception, one can address a specific challenge Ned Block has raised to this evidence.

Zenon Pylyshyn argues that cognitively driven attentional effects do not amount to cognitive penetration of early vision because such effects occur either before or after early vision. Critics object that in fact such effects occur at all levels of perceptual processing. We argue that Pylyshyn’s claim is correct—but not for the reason he emphasizes. Even if his critics are correct that attentional effects are not external to early vision, these effects do not satisfy Pylyshyn’s requirements that the effects be direct (...) and exhibit semantic coherence. In addition, we distinguish our defense from those found in recent work by Raftopoulos and by Firestone and Scholl, argue that attention should not be assimilated to expectation, and discuss alternative characterizations of cognitive penetrability, advocating a kind of pluralism. (shrink)

A survey of innateness in cognitive science, focusing on (1) what innateness might be, and (2) whether concepts might be innate.

Does perceptual consciousness require cognitive access? Ned Block argues that it does not. Central to his case are visual memory experiments that employ post-stimulus cueing—in particular, Sperling's classic partial report studies, change-detection work by Lamme and colleagues, and a recent paper by Bronfman and colleagues that exploits our perception of ‘gist’ properties. We argue contra Block that these experiments do not support his claim. Our reinterpretations differ from previous critics' in challenging as well a longstanding and common view of visual (...) memory as involving declining capacity across a series of stores. We conclude by discussing the relation of probabilistic perceptual representations and phenomenal consciousness. (shrink)

An overview of debates surrounding the use of meta-linguistic judgments in linguistics, including recent relevant empirical results.

Theories of consciousness divide over whether perceptual consciousness is rich or sparse in specific representational content and whether it requires cognitive access. These two issues are often treated in tandem because of a shared assumption that the representational capacity of cognitive access is fairly limited. Recent research on working memory challenges this shared assumption. This paper argues that abandoning the assumption undermines post-cue-based “overflow” arguments, according to which perceptual conscious is rich and does not require cognitive access. Abandoning it also (...) dissociates the rich/sparse debate from the access question. The paper then explores attempts to reformulate overflow theses in ways that don’t require the assumption of limited capacity. Finally, it discusses the problem of relating seemingly non-probabilistic perceptual consciousness to the probabilistic representations posited by the models that challenge conceptions of cognitive access as capacity-limited. (shrink)

Fiona Macpherson (2012) argues that various experimental results provide strong evidence in favor of the cognitive penetration of perceptual color experience. Moreover, she proposes a mechanism for how such cognitive penetration occurs. We argue, first, that the results on which Macpherson relies do not provide strong grounds for her claim of cognitive penetrability; and, second, that, if the results do reflect cognitive penetrability, then time-course considerations raise worries for her proposed mechanism. We base our arguments in part on several of (...) our own experiments, reported herein. (shrink)

Is temporal representation constitutively necessary for perception? Tyler Burge (2010) argues that it is, in part because perception requires a form of memory sufficiently sophisticated as to require temporal representation. I critically discuss Burge’s argument, maintaining that it does not succeed. I conclude by reflecting on the consequences for the origins of temporal representation.

Linguistic intuitions are a central source of evidence across a variety of linguistic domains. They have also long been a source of controversy. This chapter aims to illuminate the etiology and evidential status of at least some linguistic intuitions by relating them to error signals of the sort posited by accounts of on-line monitoring of speech production and comprehension. The suggestion is framed as a novel reply to Michael Devitt’s claim that linguistic intuitions are theory-laden “central systems” responses, rather than (...) endorsed outputs of a modularized language faculty (the “Voice of Competence”). Along the way, it is argued that linguistic intuitions may not constitute a natural kind with a common etiology; and that, for a range of cases, the process by which intuitions used in linguistics are generated amounts to little more than comprehension. (shrink)

Can one combine Davidsonian semantics with a deflationary conception of truth? Williams argues, contra a common worry, that Davidsonian semantics does not require truth-talk to play an explanatory role. Horisk replies that, in any event, the expressive role of truth-talk that Williams emphasizes disqualifies deflationary accounts—at least extant varieties—from combination with Davidsonian semantics. She argues, in particular, that this is so for Quine's disquotationalism, Horwich's minimalism, and Brandom's prosententialism. I argue that Horisk fails to establish her claim in all three (...) cases. This involves clarifying Quine’s understanding of a purely referential occurrence; explaining how Davidsonians can avail themselves of a syntactic treatment of lexical ambiguity; and correcting a common misreading of Brandom (answering along the way an objection offered by Künne as well). (shrink)

A longish (12 page) discussion of Richard Sorabji's excellent book, with a further discussion of what it means for a theory of emotions to be a cognitive theory.

A reply to commentators -- Jake Beck, Nico Orlandi and Aaron Franklin, and Ian Phillips -- on our paper "Does perceptual consciousness overflow cognitive access?".

This chapter examines the “externalist” claim that semantics should include theorizing about representational relations among linguistic expressions and (purported) aspects of the world. After disentangling our main topic from other strands in the larger set of externalist-internalist debates, arguments both for and against this claim are discussed. It is argued, among other things, that the fortunes of this externalist claim are bound up with contentious issues concerning the semantics-pragmatics border.

Michael Devitt ([2006a], [2006b]) argues that, insofar as linguists possess better theories about language than non-linguists, their linguistic intuitions are more reliable. (Culbertson and Gross [2009]) presented empirical evidence contrary to this claim. Devitt ([2010]) replies that, in part because we overemphasize the distinction between acceptability and grammaticality, we misunderstand linguists' claims, fall into inconsistency, and fail to see how our empirical results can be squared with his position. We reply in this note. Inter alia we argue that Devitt's (...) focus on grammaticality intuitions, rather than acceptability intuitions, distances his discussion from actual linguistic practice. We close by questioning a demand that drives his discussion—viz., that, for linguistic intuitions to supply evidence for linguistic theorizing, a better account of why they are evidence is required. (shrink)

This paper motivates two bases for ascribing propositional semantic knowledge (or something knowledgelike): first, because it’s necessary to rationalize linguistic action; and, second, because it’s part of an empirical theory that would explain various aspects of linguistic behavior. The semantic knowledge ascribed on these two bases seems to differ in content, epistemic status, and cognitive role. This raises the question: how are they related, if at all? The bulk of the paper addresses this question. It distinguishes a variety of answers (...) and their varying philosophical and empirical commitments. (shrink)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies (...) of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

Donald Davidson aims to illuminate the concept of meaning by asking: What knowledge would suffice to put one in a position to understand the speech of another, and what evidence sufficiently distant from the concepts to be illuminated could in principle ground such knowledge? Davidson answers: knowledge of an appropriate truth-theory for the speaker’s language, grounded in what sentences the speaker holds true, or prefers true, in what circumstances. In support of this answer, he both outlines such a truth-theory for (...) a substantial fragment of a natural language and sketches a procedure—radical interpretation—that, drawing on such evidence, could confirm such a theory. Bracketing refinements (e.g., those introduced to.. (shrink)

In this note, I clarify the point of my paper “The Nature of Semantics: On Jackendoff’s Arguments” (NS) in light of Ray Jackendoff’s comments in his “Linguistics in Cognitive Science: The State of the Art.” Along the way, I amplify my remarks on unification.

Stewart Shapiro’s book develops a contextualist approach to vagueness. It’s chock-full of ideas and arguments, laid out in wonderfully limpid prose. Anyone working on vagueness (or the other topics it touches on—see below) will want to read it. According to Shapiro, vague terms have borderline cases: there are objects to which the term neither determinately applies nor determinately does not apply. A term determinately applies in a context iff the term’s meaning and the non-linguistic facts determine that they do. The (...) non-linguistic facts include the “external” context: “comparison class, paradigm cases, contrasting cases, etc.” (33) But external-contextsensitivity is not what’s central to Shapiro’s contextualism. Even fixing external context, vague terms’ (anti-)extensions exhibit sensitivity to internal context: the decisions of competent speakers. According to Shapiro’s open texture thesis, for each borderline case, there is some circumstance in which a speaker, consistently with the term’s meaning and the non-linguistic facts, can judge it to fall into the term’s extension and some circumstance in which the speaker can judge it to fall into the term’s anti-extension: she can “go either way.” Moreover, borderline sentences are Euthyphronically judgment- dependent: a competent speaker’s judging a borderline to fall into a term’s (anti- )extension makes it so. For Shapiro, then, a sentence can be true but indeterminate: a case left unsettled by meaning and the non-linguistic facts (and thus indeterminate, or borderline) may be made true by a competent speaker’s judgment. Importantly, among the non-linguistic facts that constrain speakers’ judgments (at least in the cases Shapiro cares about) is a principle of tolerance: for all x and y, if x and y differ marginally in the relevant respect (henceforth, Mxy), then if one competently judges Bx, one cannot competently judge y in any other manner in the same (total) context.1 This does not require that one judge By: one might not consider the matter at all.. (shrink)

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

Revised version published as Barry Smith and Achille Varzi, “Fiat and Bona Fide Boundaries”, Philosophy and Phenomenological Research, 60: 2 (March 2000), 401–420.

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by philosophers, the (...) term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

This paper advances the somewhat unphilosophical thesis that “Trump is gross” to draw attention to the need to take matters of taste seriously in politics. I begin by exploring the slipperiness of distinctions between aesthetics, epistemology, and ethics, subsequently suggesting that we may need to pivot toward the aesthetic to understand and respond to the historical moment we inhabit. More specically, I suggest that, in order to understand how Donald Trump was elected President of the United States and in (...) order to stem the damage that preceded this and will ensue from it, we need to understand the power of political taste (and distaste, including disgust) as both a force of resistance and as a force of normalization. (shrink)

In 1890 Christian von Ehrenfels published his classic paper "Über 'Gestaltqualitäten'", the first systematic investigation of the philosophy and psychology of Gestalt. Ehrenfels thereby issued an important challenge to the psychological atomism that was still predominant in his day. His paper not only exerted a powerful influence on the philosophy of the Meinong school, it also marked the beginning of the Gestalt tradition in psychology, later associated with the work of Wertheimer, Köhler and Koffka in Berlin. Includes papers by C. (...) Von Ehrenfels, Kurt Grelling and Paul Oppenheim and contributions by K. Mulligan, P.M. Simons and Barry Smith. (shrink)