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)

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

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)

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)

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)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (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)

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)

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)

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (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)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...) modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (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)

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 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)

This article seeks to describe in general terms what has become the standard way of conceptualizing moral injury in the clinical psychological and psychiatric literature, which is the key source for applications of the concept in other domains. What we call “the standard model” draws on certain assumptions about beliefs, mental states, and emotions as well as an implicit theory of causation about how various forms of harm arise from certain experiences or “events” that violate persons’ moral beliefs and systems. (...) Our analysis makes these assumptions more explicit and subjects them to critical scrutiny. In so doing, we survey the current literature and identify basic features of how moral injuries are defined, how they are thought to occur, and the forms of treatment or repair that appear to be indicated. We caution that it matters how moral experience is characterized and argue that an alternative understanding of what is the moral in moral injury is important for overcoming critical challenges to the standard model. Moreover, recently evolving approaches to moral repair could be more consistent with an alternative model. Our concluding suggestion is that a more robust account of the nature of moral experience and its relations to self-identity and social experience more generally could advance understanding of the etiology of moral injury and promote rehabilitation. (shrink)

In this paper I investigate whether there are any cases in which it is rational for a person to hold inconsistent beliefs and, if there are, just what implications this might have for the theory of epistemic justification. A number of issues will crop up along the way – including the relation between justification and rationality, the nature of defeat, the possibility of epistemic dilemmas, the importance of positive epistemic duties, and the distinction between transitional and terminal attitudes.

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)

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)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

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)

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)

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 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)

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)

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)

This book is a survey of the most important developments in Austrian philosophy in its classical period from the 1870s to the Anschluss in 1938. Thus it is intended as a contribution to the history of philosophy. But I hope that it will be seen also as a contribution to philosophy in its own right as an attempt to philosophize in the spirit of those, above all Roderick Chisholm, Rudolf Haller, Kevin Mulligan and Peter Simons, who have done so much (...) to demonstrate the continued fertility of the ideas and methods of the Austrian philosophers in our own day. For some time now, historians of philosophy have been gradually coming to terms with the idea that post-Kantian philosophy in the German-speaking world ought properly to be divided into two distinct traditions which we might refer to as the German and Austrian traditions, respectively. The main line of the first consists in a list of personages beginning with Kant, Fichte, Hegel and Schelling and ending with Heidegger, Adorno and Bloch. The main line of the second may be picked out similarly by means of a list beginning with Bolzano, Mach and Meinong, and ending with Wittgenstein, Neurath and Popper. As should be clear, it is the Austrian tradition that has contributed most to the contemporary mainstream of philosophical thinking in the Anglo-Saxon world. For while there are of course German thinkers who have made crucial contributions to the development of exact or analytic philosophy, such thinkers were outsiders when seen from the perspective of native German philosophical culture, and in fact a number of them found their philosophical home precisely in Vienna. When, in contrast, we examine the influence of the Austrian line, we encounter a whole series of familiar and unfamiliar links to the characteristic concerns of more recent philosophy of the analytic sort. As Michael Dummett points out in his Origins of Analytic Philosophy, the newly fashionable habit of referring to analytic philosophy as "Anglo-American" is in this light a "grave historical distortion". If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy "could at least as well be called "Anglo-Austrian" (1988, p. 7). Much valuable scholarly work has been done on the thinking of Husserl and Wittgenstein, Mach and the Vienna Circle. The central axis of Austrian philosophy, however, which as I hope to show in what follows is constituted by the work of Brentano and his school, is still rather poorly understood. Work on Meinong or Twardowski by contemporary philosophers still standardly rests upon simplified and often confused renderings of a few favoured theses taken out of context. Little attention is paid to original sources, and little effort is devoted to establishing what the problems were by which the Austrian philosophers in general were exercised -- in spite of the fact that many of these same problems have once more become important as a result of the contemporary burgeoning of interest on the part of philosophers in problems in the field of cognitive science. (shrink)

Introduction and translation of “The Four Phases of Philosophy” by Franz Brentano.

​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)

A type of argument occasionally made in metaethics, epistemology and philosophy of science notes that most ordinary uses of some expression fail to satisfy the strictest interpretation of the expression, and concludes that the ordinary assertions are false. This requires there to be a presumption in favour of a strict interpretation of expressions that admit of interpretations at different levels of strictness. We argue that this presumption is unmotivated, and thus the arguments fail.

According to a captivating picture, epistemic justification is essentially a matter of epistemic or evidential likelihood. While certain problems for this view are well known, it is motivated by a very natural thought—if justification can fall short of epistemic certainty, then what else could it possibly be? In this paper I shall develop an alternative way of thinking about epistemic justification. On this conception, the difference between justification and likelihood turns out to be akin to the more widely recognised difference (...) between ceteris paribus laws and brute statistical generalisations. I go on to discuss, in light of this suggestion, issues such as classical and lottery-driven scepticism as well as the lottery and preface paradoxes. (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)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (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)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (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)

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

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)

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)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

This is a revised version of the introductory essay in C. Eschenbach, C. Habel and B. Smith (eds.), Topological Foundations of Cognitive Science, Hamburg: Graduiertenkolleg Kognitionswissenschaft, 1994, the text of a talk delivered at the First International Summer Institute in Cognitive Science in Buffalo in July 1994.

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)

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)