Bilimi ve bilimsel bilgiyi kültür, değer ve öznel yargılardan izole ederek nesnel bir şekilde ortaya koyabilmeye yönelik hararetli tartışmaların yaşandığı yirminci yüzyıl bilim anlayışının temel gayesi, deney ve gözleme tabi olabilecek fiziki dünyadaki olguları, mantıksal çözümlemeye tabi tutarak birleştirilmiş bilime ulaşmaktır. Bu amaca giden yolda olgulara dayanmayan ve sınanamayan her türlü metafizik öge yok sayılır. Bilimsel bilginin sadece deney ve gözleme tabi olana, diğer bir deyişle olgu verilerine dayandığı iddiasını taşıyan bu düşünce sistemi, özellikle Viyana Çevresi üyeleri tarafından benimsenmiştir. Bu (...) bakımdan Çevre üyelerinin bilimsellik anlayışındaki temel ölçüt olgulara dayanan önermelerin ya da yargıların doğrulanabilmesidir. Bilimsel bilginin sadece olgusal dünyanın gözlemlenmesi ve bu gözlem sonucunda ortaya konulan önermelerin ya da ifadelerin doğrulanmasıyla sağlandığını düşünen Çevre üyelerinin bu savlarındaki amacı bilimi ve onun bilgisini her türlü kültür ve değer alanından uzaklaştırarak metafiziksel unsurlardan arındırılmış nesnel bilgiye ulaşmaktır. Çevre üyelerinin birçoğu bilim alanı içerisinde tartışmaya yol açan meselelerin aslında metafiziksel içerikli ve dolayısıyla bunların görünüşte problemler olduğunu belirterek bu tartışmaların bilimsel bilginin gelişimi önünde bir engel oluşturacağı kanaatindedir (Hızır, 1965, s. 254). Söz gelimi, Carnap’a göre, metafizik ögeler olgusal içeriğe sahip olmadığı ve sınanabilir nitelikte olmadıkları için bilim alanı içerisinde değerlendirilemez. Bu nedenle, metafizik ögeler hem doğrulanması mümkün olmadığı hem de dilin mantıksal dizimine genellikle uymadığı gerekçesiyle anlamsızdır (Öztürk, 2011, s. 155). Bu bakımdan Çevre üyelerine göre, olgulara dayanmayan ve bilimde yanılsamalara yol açan metafizik söylemler bilimden ayıklanmalı ve bilimsel bilgi ancak olgu ve deneye dayanan önermeler üzerinden yürütülmelidir. Öte yandan Çevre düşünürleri mantıksal çözümleme yoluyla olgulara dayanan önermelerin metafiziksel unsurlar içeren önermelerden ayırt edilebileceğini ifade etmiştir. Bu bağlamda metafizik önermeleri, metafizik olmayan önermelerden ayırt edecek ölçütün doğrulanabilirlik olduğunu savunurlar. Çevre üyelerinin bu tutumları bir bakıma bilim ve sözde bilim arasında ayrım yapma ve metafiziği bilimin dışında tutma çabası olarak da değerlendirilebilir (Kabadayı, 2011, s. 39-40). Yirminci yüzyıl bilim anlayışında bilimsel etkinlikte gözlemin ve gözlemi yürüten bilim insanlarının dolaysız öznel duyu verileriyle ilişkili olduğu bu nedenle gözlem verilerinin psikolojizmin etkisinde olduğu fikri ortaya atılır. Başta Neurath olmak üzere dönemin bilim felsefecileri bilimsel bilginin kültür, değer ve psikoloji gibi öznel unsurlardan uzaklaştığı sürece değerli olduğu kanısında olduğu için bu fikre karşı çıkmaktadır (Gillies, 2018, s. 123). Görüldüğü üzere, Çevre üyelerinin temel amacı metafizik önermelerden arındırılmış, olgulara dayanan bir bilime ulaşmaktır. Bu amacın gerçekleşmesine olanak sağlayacak yöntem ise mantıksal çözümlemedir. Bu bağlamda Çevre üyeleri olgulara dayanan ve doğrulanabilen önermelerin, söz dizimi (sentaks) ve anlamsal (semantik) açıdan incelemeye tabi tutulması gerektiğini düşünmektedir (Yardımcı, 2018, s. 13-15). Özellikle Carnap (1935, s. 9-10) doğrulamanın ancak öne sürülen önermenin mantıksal analize tabi tutularak yapılması gerektiğini iddia etmiştir (Irzık, 1962, s. 65). Bununla birlikte, felsefenin işlevi, önermeleri mantıksal analize tabi tutarak yalın hale getirmektir. İşte felsefenin bu yönü Neurath’da bilimin birliği, Carnap’ta ise bilimin sentaksı, yani bilimin mantığı üzerine çalışma anlamına gelir (Hızır, 1965, s. 252). Bilimi, bilim olmayandan ayırma yöntemi olarak kullanılan doğrulama işlemi, teorik bir söylem ve gözlem önermesi arasında yapılan bir işlem olması bakımından mantıksal ve dilsel bir özellik taşır. Buradaki temel sorun ise teorik bir önermenin gözlem önermelerine indirgenebilir nitelikte olması ve gözlem önermelerinin, gözlem ile nasıl ilişki kurduğunu saptamaktır. İşte Viyana Çevresi üyeleri bu ilişkinin protokol önermeleri ile kurulduğu kanaatindedir (Ural, 2012, s. 105-107) çünkü onlara göre; öznelerarası bir bilimin sağlanması için yansız ve anlam karmaşasından arındırılmış bir dil gereklidir (Serin, 2015, s. 55). Bu dil de ancak protokol önermeler aracılığıyla kurulabilir. Bu bağlamda Çevre üyelerinin, metafiziksel ifadeler barındıran önermelerin anlamsızlığı ve bilimleri ortak bir paydada birleştiren fiziksel bir dil oluşturma olmak üzere iki temel hedefinin olduğu söylenebilir (Godfrey-Smith, 2003, s. 25; Salgar, 2012, s. 187). (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...) situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

John Rawls thinks republicanism is compatible with his political liberalism. Philip Pettit insists that the two conflict in important ways. In this paper, I make sense of this dispute by employing David Chalmers’s method of elimination to reveal the meaning underlying key terms in Rawls’s political liberalism and Pettit’s republicanism. This procedure of disambiguating terms will show how the two theories defend the same institutional arrangement on the same grounds. The procedure thus vindicates Rawls’s view of the two theories being (...) compatible. The reason for this compatibility is that both theories are politicized—that is, they are constructed to attract the compliance of all reasonable members of a modern, pluralistic society. (shrink)

The predominant account of the etiology of moral injuries among Veterans and military personnel in the clinical psychological and psychiatric literature construes morality as inherent in belief structures. This supports the conceptualization of moral injuries as intrapsychic phenomena resulting from exposure to high-stakes events in which fixed beliefs are contravened in ways that result in psychological harms, including maladaptive beliefs and distress. We identify several problems with this formulation and offer suggestions for modification, including greater focus on: 1) experiences rather (...) than events in identifying circumstances in which moral injuries occur, and 2) degradation of relevant relationships rather than conflicts with and among moral contents. These shifts in framing could have epidemiological salience, facilitating more robust case characterization and enabling a variety of approaches to reestablishing the moral conditions that support life affirmation. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Every day, thousands of polls, surveys, and rating scales are employed to elicit the attitudes of humankind. Given the ubiquitous use of these instruments, it seems we ought to have firm answers to what is measured by them, but unfortunately we do not. To help remedy this situation, we present a novel approach to investigate the nature of attitudes. We created a self-transforming paper survey of moral opinions, covering both foundational principles, and current dilemmas hotly debated in the media. This (...) survey used a magic trick to expose participants to a reversal of their previously stated attitudes, allowing us to record whether they were prepared to endorse and argue for the opposite view of what they had stated only moments ago. The result showed that the majority of the reversals remained undetected, and a full 69% of the participants failed to detect at least one of two changes. In addition, participants often constructed coherent and unequivocal arguments supporting the opposite of their original position. These results suggest a dramatic potential for flexibility in our moral attitudes, and indicates a clear role for self-attribution and post-hoc rationalization in attitude formation and change. (shrink)

This letter addresses the editorial decision to publish the article, “Research on group differences in intelligence: A defense of free inquiry” (Cofnas, 2020). Our letter points out several critical problems with Cofnas's article, which we believe should have either disqualified the manuscript upon submission or been addressed during the review process and resulted in substantial revisions.

Aggregating individuals’ consistent attitudes might produce inconsistent collective attitudes. Some groups therefore need the capacity to form attitudes that are irreducible to those of their members. Such groups, group-agent realists argue, are agents in control of their own attitude formation. In this paper, however, I show how group-agent realism overlooks the important fact that groups consist of strategically interacting agents. Only by eliminating group agency from our social explanations can we see how individuals vote strategically to gain control of their (...) groups and produce collective attitudes we cannot make sense of if we treat groups as agents. (shrink)

Purpose This systematic review aims to identify factors that influence parents’ decisions regarding pediatric diagnostic and predictive genetic testing (DT/PT). Factors are integrated into a conceptual model of decision-making. Implications for genetic counseling, research, and ethics are derived. Methods PubMed, PsychInfo, WebofScience and references of related reviews were searched for original publications between 2000 and 2023. Extracted factors were categorized into an existing model. Results Of 5843 publications, 56 met inclusion criteria. The included studies differentiate between DT, traditional, and expanded (...) PT and describe factors impacting parental decisions on both to have the child genetically tested and to be informed about additional findings. Factors included: 1. benefits/hopes, 2. worries/concerns, 3. values and beliefs, 4. individual circumstances, and 5. emotional states. Conclusion Our work extends an existing empirical decision model of family decisions about genome sequencing to genetic testing in pediatrics in general, adding the categories “individual circumstances” and “emotional states”. The factors can be further integrated into the Health Belief Model; the importance of emotional states is reflected in dual-process theories, such as Fuzzy Trace Theory. Research is required on emotional states, differences between DT and PT, parents’ decisions about result disclosure, and dyadic variables as decision-making predictors. (shrink)

Public reason liberals expect individuals to have justificatory reasons for their views of certain political issues. This paper considers how groups can, and whether they should, give collective public reasons for their political decisions. A problem is that aggregating individuals’ consistent judgments on reasons and a decision can produce inconsistent collective judgments. The group will then fail to give a reason for its decision. The paper considers various solutions to this problem and defends a deliberative procedure by showing how it (...) incentivizes information sharing and leads to outcomes most acceptable to the group members. (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)

Can a group be morally responsible instead of, or in addition to, its members? An influential defense of corporate responsibility is based on results in social choice theory suggesting that a group can form and act on attitudes held by few, or even none, of its members. The members therefore cannot be (fully) responsible for the group’s behavior; the group itself, as a corporate agent, must be responsible. In this paper, I reject this view of corporate responsibility by showing how (...) it pays insufficient attention to individual agency. By accounting for group members’ strategic behavior, we shall see how they control collective attitude formation and are therefore responsible for their group’s behavior. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

In the debate on how we ought to define political freedom, some definitions are criticized for implying that no one can ever be free to perform any action. In this paper, I show how the possibility of freedom depends on a definition that finds an appropriate balance between absence of interference and protection against interference. To assess the possibility of different conceptions of freedom, I consider the trade-offs they make between these two dimensions. I find that pure negative freedom is (...) clearly possible. Republican freedom might also be possible, though its protection requirement is too vague for a definitive verdict. Finally, the recently proposed ‘freedom as independence’ is impossible since it is an attempt to avoid the unavoidable trade-off. (shrink)

Political candidates often believe they must focus their campaign efforts on a small number of swing voters open for ideological change. Based on the wisdom of opinion polls, this might seem like a good idea. But do most voters really hold their political attitudes so firmly that they are unreceptive to persuasion? We tested this premise during the most recent general election in Sweden, in which a left- and a right-wing coalition were locked in a close race. We asked our (...) participants to state their voter intention, and presented them with a political survey of wedge issues between the two coalitions. Using a sleight-of-hand we then altered their replies to place them in the opposite political camp, and invited them to reason about their attitudes on the manipulated issues. Finally, we summarized their survey score, and asked for their voter intention again. The results showed that no more than 22% of the manipulated replies were detected, and that a full 92% of the participants accepted and endorsed our altered political survey score. Furthermore, the final voter intention question indicated that as many as 48% (69.2%) were willing to consider a left-right coalition shift. This can be contrasted with the established polls tracking the Swedish election, which registered maximally 10% voters open for a swing. Our results indicate that political attitudes and partisan divisions can be far more flexible than what is assumed by the polls, and that people can reason about the factual issues of the campaign with considerable openness to change. (shrink)

The revival of republicanism was meant to challenge the hegemony of liberalism in contemporary political theory on the grounds that liberals show insufficient concern with institutional protection against political misrule. This article challenges this view by showing how neorepublicanism, particularly on Philip Pettit’s formulation, demands no greater institutional protection than does political liberalism. By identifying neutrality between conceptions of the good as the constraint on institutional requirements that forces neorepublicanism into the liberal framework, the article shows that neutrality is what (...) neorepublicans must jettison to offer a tenable critique of liberalism. Only then can neorepublicans ensure greater protection against misrule by demanding that citizens participate more actively in politics. They can then also criticize liberalism for failing to appreciate the importance of such protection. (shrink)

The debate on ideal theory focuses mainly on whether it can provide a long-term target and a metric for assessing the justice of different institutional arrangements in non-ideal theory. Both critics and defenders of ideal theory typically overlook the role it plays in a model of fairness that can restrict the range of permissible arrangements under non-ideal conditions. In this paper, I explain ideal theory’s fairness role and its part in ensuring an institutional structure that benefits everyone in a society. (...) Critics of ideal theory therefore cannot reject it as simply useless. But I consider how they can question the attractiveness of an ideal-theory-based fairness constraint on non-ideal theory. (shrink)

Can groups really be agents or is group agency just a fiction? Christian List and Philip Pettit argue influentially for group-agent realism by showing how certain groups form and act on attitudes in ways they take to be unexplainable at the level of the individual agents constituting them. Group agency is therefore considered not a fiction or a metaphor but a reality we must account for in explanations of certain social phenomena. In this paper, I challenge this defence of group-agent (...) realism by showing how it is undermined by individual-level analysis of how individuals interact within groups. While group agency can be a useful fiction, real agents are at the individual level, not the collective level. (shrink)

Institutions promoting republican freedom as non-domination are commonly believed to differ significantly from institutions promoting negative freedom as non-interference. Philip Pettit, the most prominent contemporary defender of this view, also maintains that these republican institutions are neutral between the different conceptions of the good that characterise a modern society. This paper shows why these two views are incompatible. By analysing the institutional requirements Pettit takes as constitutive of republican freedom, I show how they also promote negative freedom by reducing overall (...) interference. To avoid this result, republican institutions must be more restrictive and require that citizens conform to a life of political engagement. But then republican freedom will not be a neutral ideal. Rejecting negative freedom therefore means sacrificing neutrality. (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 are addressing this letter to the editors of Philosophical Psychology after reading an article they decided to publish in the recent vol. 33, issue 1. The article is by Nathan Cofnas and is entitled “Research on group differences in intelligence: A defense of free inquiry” (2020). The purpose of our letter is not to invite Cofnas’s contribution into a broader dialogue, but to respectfully voice our concerns about the decision to publish the manuscript, which, in our opinion, fails to (...) meet a range of academic quality standards usually expected of academic publications. (shrink)

Broadening access to both computational and educational resources is crit- ical to diffusing machine learning (ML) innovation. However, today, most ML resources and experts are siloed in a few countries and organizations. In this article, we describe our pedagogical approach to increasing access to applied ML through a massive open online course (MOOC) on Tiny Machine Learning (TinyML). We suggest that TinyML, applied ML on resource-constrained embedded devices, is an attractive means to widen access because TinyML leverages low-cost and globally (...) accessible hardware and encourages the development of complete, self-contained applications, from data collection to deployment. To this end, a collaboration between academia and industry produced a four part MOOC that provides application-oriented instruction on how to develop solutions using TinyML. The series is openly available on the edX MOOC platform, has no prerequisites beyond basic programming, and is designed for global learners from a variety of backgrounds. It introduces real-world applications, ML algorithms, data-set engineering, and the ethi- cal considerations of these technologies through hands-on programming and deployment of TinyML applications in both the cloud and on their own microcontrollers. To facili- tate continued learning, community building, and collaboration beyond the courses, we launched a standalone website, a forum, a chat, and an optional course-project com- petition. We also open-sourced the course materials, hoping they will inspire the next generation of ML practitioners and educators and further broaden access to cutting-edge ML technologies. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...) to other types of military and nonmilitary unmanned vehicle operations. (shrink)

The article argues that the doctrine of Gorgias of Leontinoi, as expressed in his "Encomion of Helen", is not a rhetorical technique but a practice of moral education. The medium of this "ethical speech practice" is perceptual forms, its basic mode being the practice of showing or epideictic speech. The crucial standard of this practice is "epideictic rightness", which is identical to Gorgias’ conception of "truth.". According to this conception, speech is true if it exemplifies morally right conduct and moral (...) beauty. True speech in this sense must also be effective speech, since it will promote right behaviour in the future. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

The full compliance assumption has been the focus of much recent criticism of ideal theory. Making this assumption, critics argue, is to ignore the important issue of how to actually make individuals compliant. In this article, I show why this criticism is misguided by identifying the key role full compliance plays in modelling fairness. But I then redirect the criticism by showing how it becomes appropriate when Rawls and other ideal theorists expect their model of fairness to guide real-world political (...) practice. Attempts to establish institutions conforming to this ideal could have undesirable consequences and might even undermine fairness itself. (shrink)

Principles of justice, David Estlund argues, cannot be falsified by people’s unwillingness to satisfy them. In his Utopophobia, Estlund rejects the view that justice must bend to human motivation to deliver practical implications for how institutions ought to function. In this paper, I argue that a substantive argument against such bending of justice principles must challenge the reasons for making these principles sensitive to motivational limitations. Estlund, however, provides no such challenge. His dispute with benders of justice is therefore a (...) verbal one over the true meaning of justice, which need not worry those with the intuition that justice should perform a function that requires bending. By focusing on John Rawls’s reasons for bending his justice principles, I point towards a substantive critique of bent justice. (shrink)

According to group-agent realism, treating groups as agents with their own intentional states, irreducible to those of the group members, helps us explain and predict the groups’ behavior. This paper challenges this view. When groups judge logically interconnected propositions, group members often have incentives to misrepresent their beliefs of propositions they care less about in order to increase the probability of their groups adopting their view of propositions they consider more important. Aggregating such untruthful judgments may lead to the group (...) forming false beliefs. Treating groups as agents will then not help us explain or predict their behavior. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

An influential view in the ethics of self-defence is that causal responsibility for an unjust threat is a necessary requirement for liability to defensive harm. In this article, I argue against this view by providing intuitive counterexamples and by revealing weaknesses in the arguments offered in its favour. In response, adherents of the causal view have advanced the idea that although causally inefficacious agents are not liable to defensive harm, the fact that they may deserve harm can justify harming them (...) in the course of defending oneself. I argue that this strategy is ad hoc and leads to more problems than it solves. Once we allow normative facts outside our account of liability to affect a person's moral protection against harm, the lieability verdicts cannot tell us whether there is a relevant moral asymmetry between the victim and the target of defence. In conclusion, the causal view is wrong and causal responsibility for an unjust threat is not a necessary requirement for liability to defensive harm. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Abstract Criteria of scientific value are of different kinds. This paper concerns ultimate criteria, i.e. the axiology of science. Most ultimate criteria are multi?dimensional. This gives rise to an aggregation problem, which cannot be adequately solved with reference to attitudes and behaviour within the scientific community. Therefore, in many cases, there is no fact of the matter as to whether one theory is better than another. This, in turn, creates problems for methodology.

In this article I argue for an empiricist view on laws. Some laws are fundamental in the sense that they are the result of inductive generalisations of observed regularities and at the same time in their formulation contain a new theoretical predicate. The inductive generalisations simul- taneously function as implicit definitions of these new predicates. Other laws are either explicit definitions or consequences of other previously established laws. I discuss the laws of classical mechanics, relativity theory and electromagnetism in detail. (...) Laws are necessary, whereas acciden- tal generalisations are not. But necessity here is not a modal concept, but rather interpreted as short for the semantic predicate “... is necessarily true”. Thus no modal logic is needed. The neces- sity attributed to law sentences is in turn interpreted as “necessary condition for the rest of the the- ory”, which is true since fundamental laws are implicit definitions of theoretical predicates use in the theory. (shrink)

In Reason, Truth and History and certain related writings, Hilary Putnam attacked the fact-value distinction. This paper criticizes his arguments and defends the distinction. Putnam claims that factual statements presuppose values, that “the empirical world depends upon our criteria of rational acceptability,” and that “we must have criteria of rational acceptability to even have an empirical world.” The present paper argues that these claims are mistaken.

In the visual representation of ontologies, in particular of part-whole relationships, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...) Basic Formal Ontology. But it can be used also for more general applications, particularly in the biomedical domain. (shrink)

In the graphical representation of ontologies, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of mereotopological relationships between the entities.

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude with a description of how the (...) body fluids ontology initiative may provide support to basic and translational science. (shrink)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a (...) standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

There are different ways of dividing psychology into subdisciplines. The purpose of the present paper is to explore one specific meta-perspective on psychological science, seen as having three main branches: person psychology, population psychology, and mechanism psychology, linked to three different levels of research. Person-level research focuses on psychological phenomena as experienced and enacted by individual persons in their interaction with other persons and other parts of the environment, and in their development over time. Population-level research focuses on populations of (...) individuals, frequencies of various psychological phenomena in a population, risk factors, and population-level effects of various psychological interventions. Mechanism-level research focuses on psychological func-tioning as explained in terms of neurophysiological mechanisms and information processes at a sub-personal level. It is argued that the failure to differentiate clearly between research questions at these three levels lead to questionable research practices. Most notably, a failure to differentiate clearly between the population level and the person level leads to problem-method mismatches in the form of re-searchers trying to answer questions about persons by research on populations. Also, because of a failure to differentiate between the person level and the mechanism level, explanations in terms of sub-personal mechanisms are too often seen as providing answers about what occurs at the person level, thereby failing to study persons as intentional agents in interaction with other persons and other parts of the environment. It is argued that a clear differentiation between three levels of psychological science – population, person, and mechanism – may contribute to an increased clarity in these matters and may thereby contribute to the development and maturation of psychological science. (shrink)