A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

This paper describes an undergraduate course in metaphilosophy for philosophy majors and argues that there are four potential benefits to students; namely that doing metaphilosophy (1) allows students to draw their own conclusions about what philosophy is, (2) develops students’ metacognitive skills to promote learning, (3) establishes students as members of the philosophical community, and (4) disposes students to live lives that reflect their philosophical education. It describes issues of transparency of course design and the particulars of the course, including (...) course content, and provides excerpts of student work to demonstrate student learning outcomes. Finally, it will suggest that even if it is not possible to offer a stand-alone course in metaphilosophy, instructors should provide opportunities to reflect on metaphilosophical issues in their other philosophy courses. (shrink)

The most notable contributions to contemporary philosophy of mind have been written by philosophers of mind for philosophers of mind. Without a good understanding of the historical framework, the technical terminology, the philosophical methodology, and the nature of the philosophical problems themselves, not only do undergraduate students face a difficult challenge when taking a first course in philosophy of mind, but instructors lacking specialized knowledge in this field might be put off from teaching the course. This paper is intended to (...) provide a framework for instructors with little background in this area of philosophy to develop a course in philosophy of mind. This course, aimed at the advanced undergraduate student, provides students with the tools necessary for understanding some of the key readings in contemporary philosophy of mind and offers unique benefits to both majors and non-majors. The course described here focuses on just two of the main problems in philosophy of mind—the mind-body problem and the problem of phenomenal consciousness—and briefly touches on other issues one might address. Finally, several solutions to common challenges that arise in an advanced philosophy course are discussed. (shrink)

The novelty in Smith’s way of looking at the economy is the discovery of a social character of wealth, something new in comparison with its definition in physical terms by the Physiocrats. The possibility of carrying out such an idealization was a result of the adoption of a Newtonian, as opposed to a Cartesian, epistemology, where an intermediate and provisional character of theoretical entities is explicitly accepted, dropping Cartesian strong epistemological realism.

INTRODUÇÃO Para compreender como a Sociologia nasceu e se desenvolveu, é essencial analisar as transformações que ocorreram a partir do século XIV, na Europa ocidental, marcando a passagem da sociedade feudal para a sociedade capitalista, ou a passagem da sociedade medieval para a sociedade moderna. Para isso, é necessário realizar uma pequena viagem histórica, já que, para entender as ideias de um autor e de determinada época, é fundamental contextualizá-las historicamente. Em cada sociedade, em todos os tempos, os seres humanos (...) elaboraram explicações religiosas, míticas, culturais, étnicas etc. para as situações em que vivem. No século XIX, a busca por outro tipo de explicação para os fenômenos da sociedade – a explicação científica – deu origem à Sociologia. Para demonstrar como o pensamento social organizou-se historicamente e como a Sociologia estruturou o saber sobre a sociedade humana, este trabalho terá como objetivo estudar alguns autores que se sobressaíram no processo de desenvolvimento dessa ciência. PREMISSA A Sociologia surgiu como um corpo de ideias a respeito do processo de constituição, consolidação e desenvolvimento da sociedade moderna. É fruto da Revolução Industrial e, nesse sentido, é denominada “ciência da crise”, porque, com base nela, procurou-se dar respostas às questões sociais desencadeadas pelo processo revolucionário que, num primeiro momento, alterou a sociedade europeia e, depois, a maior parte do mundo. Como todas as ciências, a Sociologia não despontou de repente ou da reflexão de algum autor iluminado. Constituiu-se com base em conhecimentos sobre a natureza e a sociedade que se desenvolveram a partir do século XIV, acompanhando as mudanças que marcaram a transformação da sociedade feudal e a constituição da sociedade capitalista. Entre essas mudanças, a expansão marítima europeia e a ampliação do comércio ultramarino, a Reforma protestante e o desenvolvimento científico e tecnológico podem destacados. São o pano de fundo do movimento intelectual que alterou profundamente as formas de explicar a natureza e a sociedade. Essas mudanças estão todas vinculadas e não podem ser entendidas como eventos isolados. 1 A EXPANSÃO MARÍTIMA Com a circum-navegação da África e o descobrimento da rota para as Índias e para a América, a concepção de mundo dos europeus foi consideravelmente ampliada. A definição de um mundo territorialmente bem mais vasto, com outros povos, outras culturas e outros modos de explicar as coisas, requereu a reformulação da maneira de ver e de pensar dos europeus. Assim, ao mesmo tempo que conheciam novos povos e novas culturas, os europeus instalavam colônias na África, na Ásia e na América. Em razão disso, expandiu-se o comércio de mercadorias (sedas, especiarias e produtos tropicais, como açúcar, milho, tabaco e café) entre as metrópoles e as colônias, bem como entre os países europeus. Surgiu a possibilidade de um mercado muito mais amplo e com características mundiais. Este seria o primeiro grande movimento de globalização. A exploração de metais preciosos, principalmente na América, e o tráfico de escravos para suprir a mão de obra nas colônias deram grande impulso ao comércio, que não mais ficou restrito aos mercadores das cidades-repúblicas (Veneza, Florença ou Flandres), passando também para as mãos de grandes comerciantes e de soberanos dos Estados nacionais em formação na Europa. Toda essa expansão territorial e comercial acelerou o desenvolvimento da economia monetária, com a acumulação de capitais pela burguesia comercial, que, mais tarde, teve importância decisiva na gestação do processo de industrialização da Europa. 2 A REFORMA PROTESTANTE No século XVI, assistiu-se também ao movimento que ficaria conhecido como Reforma protestante. Os reformistas questionavam as condutas do clero, a estrutura da Igreja católica e a autoridade do Papa. Os líderes do movimento promoviam a valorização do indivíduo ao pregar a livre leitura das Escrituras Sagradas e dispensar a intermediação dos ministros da Igreja nas práticas religiosas e nos assuntos relativos à fé. A Reforma contribuiu, assim, para alimentar um movimento de resistência à autoridade e à tradição que desembocaria na Ilustração. Entre seus principais líderes figuram Martinho Lutero (1483-1546) e João Calvino (1509-1564). 3 O DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO A nova maneira de se relacionar com as coisas sagradas foi acompanhada de uma nova forma de analisar o universo e a vida em sociedade. A razão passou a ser considerada essencial para conhecer o mundo; com base nela, as pessoas se consideraram livres para julgar, avaliar, pensar e emitir opiniões sem se submeter a nenhuma autoridade transcendente ou divina. A análise do universo e da vida em sociedade com base no conhecimento racional, fundado na observação e na experimentação, difundiu-se de maneira lenta, entre os séculos XV e XVII. Os pensadores que adotaram essa forma de análise enfrentaram o dogmatismo e a autoridade da Igreja. Por meio do Concílio de Trento (1545-1563) e dos processos da Inquisição, por exemplo, os membros do clero procuraram impedir toda e qualquer manifestação que pudesse pôr em dúvida a autoridade eclesiástica, fosse no campo da fé, fosse no das explicações que se propunham para a sociedade e a natureza. Os principais representantes do pensamento racional nos séculos XV a XVII foram Nicolau Maquiavel (1469-1527), Erasmo de Roterdã (1466-1536), Nicolau Copérnico (1473- 1543), Galileu Galilei (1564 -1642), Thomas Hobbes (1588 -1679), Francis Bacon (1561- 1626), René Descartes (1596 -1650) e Baruch Spinoza (1632 -1677). Os conhecimentos desses precursores alimentaram outros pensadores, como John Locke (1632-1704), Gottfried Leibniz (1646-1716) e Isaac Newton (1643-1727), que propuseram novos princípios para a compreensão da sociedade e da natureza. Vale salientar, por fim, que os pensadores europeus dos séculos XV a XVII buscaram compreender os fenômenos da natureza e da sociedade por meio da observação e da experimentação. 4 AS TRANSFORMAÇÕES NO SÉCULO XVIII No final do século XVIII, na maioria dos países europeus, a burguesia comercial, formada basicamente por comerciantes e banqueiros, constituía uma classe poderosa, em razão, na maior parte das vezes, das ligações econômicas que mantinha com as monarquias. Além de sustentar o comércio entre os países europeus, a burguesia europeia lançava seus tentáculos a vários pontos do mundo, até onde pudesse chegar, comprando e vendendo mercadorias. O capital mercantil estendia-se também a outro ramo de atividade: gradativamente se organizava a produção manufatureira. A compra de matérias-primas e a organização da produção, por meio do trabalho domiciliar ou do trabalho em oficinas, levavam ao desenvolvimento de um novo processo produtivo em contraposição ao das corporações de ofício. Os organizadores das manufaturas passaram a se interessar cada vez mais pelo aperfeiçoamento das técnicas de produção, a fim de produzir mais com menos gente e aumentar significativamente seus lucros. Para tanto, procuraram financiar a invenção de máquinas que pudessem ser utilizadas no processo produtivo. Com a invenção das máquinas de tecer e de descaroçar algodão, e a aplicação industrial da máquina a vapor e de outros tantos inventos destinados a aumentar a produtividade do trabalho, desenvolveu-se o fenômeno que veio a ser chamado de maquinofatura. O trabalho que as pessoas faziam com as mãos ou com ferramentas passava, a partir de então, a ser realizado por máquinas, elevando muito o volume da produção de mercadorias. A utilização da máquina a vapor, que podia mover outras tantas, impulsionou a indústria construtora de máquinas e, consequentemente, a indústria voltada para a produção de ferro e, posteriormente, de aço. Nesse contexto de profundas alterações no processo produtivo, no qual a utilização do trabalho mecânico era cada vez mais frequente, o trabalho artesanal continuou a existir. A maquinofatura se completou com o trabalho assalariado, no qual eram utilizadas, numa escala crescente, a mão de obra feminina e a infantil. Longe da Europa, explorava-se ouro no Brasil, prata no México e algodão nos Estados Unidos da América e na Índia. A maioria dessas atividades era realizada com a utilização do trabalho escravo ou servil. Esses elementos, conjugados, asseguraram as bases do processo de acumulação necessária para a expansão da indústria na Europa. Essas mudanças, somadas à herança cultural e intelectual do século XVII, definiram o século XVIII como explosivo. Se no século anterior a Revolução Inglesa determinou novas formas de organização política, no século XVIII a Revolução Americana e a Francesa alteraram o quadro político ocidental e serviram de exemplo e parâmetro para as revoluções políticas posteriores. As transformações na esfera da produção, a emergência de novas formas de organização política e a exigência da representação popular conferiram características muito específicas a esse século, em que pensadores como Charles de Montesquieu (1689 -1755), Voltaire (1694 - 1778), Denis Diderot (1713 -1784), Jean le Rond d’Alembert (1717 -1783), David Hume (1711 -1776), Jean-Jacques Rousseau (1712 -1778), Adam Smith (1723 -1790) e Immanuel Kant (1724 -1804) procuraram, por caminhos às vezes divergentes, refletir sobre a realidade, na tentativa de explicá-la. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

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

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

This is the third draft of a paper that aims to clarify the apparent contradictions in the views presented in certain standards and other specifications of health informatics systems, contradictions which come to light when the latter are evaluated from the perspective of realist philosophy. One of the origins of this document was Klein’s discussion paper of 2005-07-02 entitled “Conceptology vs Reality” and the responses from Smith, as well as the several hours of discussions during the 2005 MIE meeting (...) in Geneva. (shrink)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

The problem of moral disagreement has been presented as an objection to contextualist semantics for ‘ought’, since it is not clear that contextualism can accommodate or give a convincing gloss of such disagreement. I argue that independently of our semantics, disagreements over ‘ought’ in non-cooperative contexts are best understood as indirect metalinguistic disputes, which is easily accommodated by contextualism. If this is correct, then rather than posing a problem for contextualism, the data from moral disagreements provides some reason to adopt (...) a semantics that allows contextual variance in the meanings of ‘ought’. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

I argue that the offense generation pattern of slurring terms parallels that of impoliteness behaviors, and is best explained by appeal to similar purely pragmatic mechanisms. In choosing to use a slurring term rather than its neutral counterpart, the speaker signals that she endorses the term. Such an endorsement warrants offense, and consequently slurs generate offense whenever a speaker's use demonstrates a contrastive preference for the slurring term. Since this explanation comes at low theoretical cost and imposes few constraints on (...) an account of the semantics of slurs, this suggests that we should not require semantic accounts to provide an independent explanation of the offense profile. (shrink)

Law-enforcement agencies are increasingly able to leverage crime statistics to make risk predictions for particular individuals, employing a form of inference that some condemn as violating the right to be “treated as an individual.” I suggest that the right encodes agents’ entitlement to a fair distribution of the burdens and benefits of the rule of law. Rather than precluding statistical prediction, it requires that citizens be able to anticipate which variables will be used as predictors and act intentionally to avoid (...) them. Furthermore, it condemns reliance on various indexes of distributive injustice, or unchosen properties, as evidence of law-breaking. (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)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

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

The Joint Battle Management Language (JBML) is an XML-based language designed to allow Command and Control (C2) systems to interface easily with Modeling and Simulation (M&S) systems. While some of the XML-tags defined in this language correspond to types of entities that exist in reality, others are mere syntactic artifacts used to structure the messages themselves. Because these two kinds of tags are not formally distinguishable, JBML messages in effect confuse data with what the data represent. In this paper we (...) show how a realism-based ontology combined with a rule language can be used to make these distinctions explicit. The approach allows storage of the contents of JBML messages in a Referent Tracking System in a format that mimics the structure of reality thereby providing an aid to message validation. (shrink)

Some, but not all, of the mistakes a person makes when acting in apparently necessary self-defense are reasonable: we take them not to violate the rights of the apparent aggressor. I argue that this is explained by duties grounded in agents' entitlements to a fair distribution of the risk of suffering unjust harm. I suggest that the content of these duties is filled in by a social signaling norm, and offer some moral constraints on the form such a norm can (...) take. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

In addition to protecting agents’ autonomy, consent plays a crucial social role: it enables agents to secure partners in valuable interactions that would be prohibitively morally risk otherwise. To do this, consent must be observable: agents must be able to track the facts about whether they have received a consent-based permission. I argue that this morally justifies a consent-practice on which communicating that one consents is sufficient for consent, but also generates robust constraints on what sorts of behaviors can be (...) taken as consent- communicating. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

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

Sometimes speakers within a linguistic community use a term that they do not conceptualize as a slur, but which other members of that community do. Sometimes these speakers are ignorant or naïve, but not always. This article explores a puzzle raised when some speakers stubbornly maintain that a contested term t is not derogatory. Because the semantic content of a term depends on the language, to say that their use of t is semantically derogatory despite their claims and intentions, we (...) must individuate languages in a way that counts them as speaking our language L, assigns t a determinately derogatory content in L, and still accommodates the other features of slurs’ linguistic profile. Given the difficulty of doing this, there is some reason to give a non-semantic analysis of the derogatory aspect of slurs. The author suggests that rather than dismissing the stubborn as semantically incompetent, we would do better to appeal to expected uptake as moral reasons for the stubborn to adjust their linguistic practices. (shrink)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

In some cases, there appears to be an asymmetry in the evidential value of statistical and more individualized evidence. For example, while I may accept that Alex is guilty based on eyewitness testimony that is 80% likely to be accurate, it does not seem permissible to do so based on the fact that 80% of a group that Alex is a member of are guilty. In this paper I suggest that rather than reflecting a deep defect in statistical evidence, this (...) asymmetry might arise from a general constraint on rational inquiry. Plausibly the degree of evidential support needed to justify taking a proposition to be true depends on the stakes of error. While relying on statistical evidence plausibly raises the stakes by introducing new kinds of risk to members of the reference class, paradigmatically `individualized' evidence---evidence tracing back to A's voluntary behavior---can lower the stakes. The net result explains the apparent evidential asymmetry without positing a deep difference in the brute justificatory power of different types of evidence. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

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

​I evaluate a suggestion, floated by Kimberly Ferzan (this volume), that the twitter hashtag campaign #BelieveWomen is best accommodated by non-reductionist views of testimonial justification. I argue that the issue is ultimately one about the ethical obligation to trust women, rather than a question of what grounds testimonial justification. I also suggest that the hashtag campaign does not simply assert that ‘we should trust women’, but also militates against a pernicious striking-property generic (roughly: ‘women make false sexual assault accusations’), that (...) distorts our evaluation of women’s testimony concerning sexual assault. I conclude #BelieveWomen does not demand that we believe against the evidence, or uncritically, or be more trusting than we have evidential justification to be. Rather, it aims to bring our trust closer to what is merited by the base-rate of reliable testimony from women concerning sexual assault. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

This paper surveys some philosophical issues with the language surrounding mental illness, but is especially focused on pejoratives relating to mental illness. I argue that though 'crazy' and similar mental illness-based epithets (MI-epithets) are not best understood as slurs, they do function to isolate, exclude, and marginalize members of the targeted group in ways similar to the harmfulness of slurs more generally. While they do not generally express the hate/contempt characteristic of weaponized uses of slurs, MI-epithets perpetuate epistemic injustice by (...) portraying sufferers of mental illness as deserving minimal credibility. After outlining the ways in which these epithets can cause harm, I examine available legal and social remedies, and suggest that the best path going forward is to pursue a reclamation project rather than aiming to censure the use of MI-epithets. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

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

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Recently, an increasing number of scholars have been showing interest in old-fashioned racism again. While recent studies on old-fashioned racism apparently increase our knowledge of this psychological theory of racism, the studies actually shed light on a different type of racism, namely offensive racism. The aim of this text is to argue that psychological theories of racism, like old-fashioned racism and modern racism, depend on societies’ social norms. I will show that questionnaires are highly sensitive to social norms, and if (...) there is change in social norms, the original measurement object alters. The theory of old-fashioned racism implicitly assumes agents that follow (or conform to) the social norm to behave prejudiced. Today, however, this social norm does not exist in Western societies. If agents express the same prejudices today, they indicate their willingness to breach the social norm to behave unprejudiced. Thereby, classic old-fashioned racism measures reflect a new kind of racism today. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

A popular informal argument suggests that statistics about the preponderance of criminal involvement among particular demographic groups partially justify others in making defensive mistakes against members of the group. One could worry that evidence-relative accounts of moral rights vindicate this argument. After constructing the strongest form of this objection, I offer several replies: most demographic statistics face an unmet challenge from reference class problems, even those that meet it fail to ground non-negligible conditional probabilities, even if they did, they introduce (...) new costs likely to cancel out any justificatory contribution of the statistic, but even if they didn’t, demographic facts are the wrong sort to make a moral difference to agents’ negative rights. I conclude that the popular argument should be rejected, and evidence-relative theories do not have the worrisome implication. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

Research on research ethics—regarding both the governance and practice of the ethical review of human subjects research—has a tumultuous history in North America and Europe. Much of the academic literature focuses on issues to do with regulating the conduct and quality of ethics review of research protocols by ethics committees (research ethics boards (REBs) in Canada and institutional review boards (IRBs) in the United States). In addition, some of the literature attends to issues particular to the review of qualitative research, (...) and still other literature addresses the challenges posed by and the need for research on REBs/IRBs. It is this third group of literature within which our article is situated. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

Richard Wollheim famously argued that figurative pictures depict their scenes, in part, in virtue of their ability to elicit a unique type of visual experience in their viewers, which he called seeing-in. According to Wollheim, experiences of seeing-in are necessarily twofold, that is, they involve two aspects of visual awareness: when a viewer sees a scene in a picture, she is simultaneously aware of certain visible features of the picture surface, the picture’s design, and the scene depicted by the picture. (...) Even though Wollheim’s notion of twofoldness has been very influential, a number of philosophers have put forward powerful arguments against it. In this paper, I defend the claim that some pictorial experiences are twofold in Wollheim’s sense. My argument has two parts. In the first part, I provide a phenomenal contrast argument in favor of twofoldness. In the second part, I respond to what I take to be the most important objections against twofoldness. I believe that both parts together provide strong support for the claim that some pictorial experiences are twofold in Wollheim’s sense. (shrink)

There has been recent discussion of a puzzle posed by emotions that are backward looking. Though our emotions commonly diminish over time, how can they diminish fittingly if they are an accurate appraisal of an event that is situated in the past? Agnes Callard (2017) has offered a solution by providing an account of anger in which anger is both backwards looking and resolvable, yet her account depends upon contrition to explain anger’s fitting diminishment. My aim is to explain how (...) anger can fittingly diminish even when there is lack of contrition. I propose a permissivism about fittingness by showing that both anger and compassion are fitting responses to blameworthy behaviour. I argue that anger is rendered fitting because it accurately appraises the behaviour, whereas compassion becomes fitting as a valuational response to what the behaviour reveals about the lived experience of the offender. I then respond to some worries my account raises, and I clarify details of my account to show that it is not unrealistic to the way some of our anger actually does diminish. I end with a proposal that our anger can fittingly diminish through the act of forgiveness when compassion is not a forthcoming affective response. (shrink)