The “puzzle” of emotional plasticity concerns making sense of two conflicting bodies of evidence: evidence that emotions often appear modular in key respects, and evidence that our emotions also often appear to transcend this modularity. In this paper, I argue a developmentalist approach to emotion, which builds on Karmiloff-Smith’s (1986, 1992, 1994, 2015) work on cognitive development, can help us dissolve this puzzle.

The slides of a talk given at the Cavendish Laboratory in 2001, relating brain function to concepts such as hyperstructure theory (Baas), Memory Evolutive Systems (Ehresmann), and representational redescription (A Karmiloff-Smith).

The problem of variability concerns the fact that empirical data does not support the existence of a coordinated set of biological markers, either in the body or the brain, which correspond to our folk emotion categories; categories like anger, happiness, sadness, disgust and fear. Barrett (2006a, b, 2013, 2016, 2017a, b) employs this fact to argue (i) against the faculty psychology approach to emotion, e.g. emotions are the products of emotion-specific mechanisms, or “modules”, and (ii) for the view that emotions (...) are constructed from domain-general “core systems” with the aid of our folk concepts. The conjunction of (i) and (ii), she argues, heralds a paradigm shift in our understanding of emotion: emotions aren’t triggered but made. In this paper, I argue such a shift is premature for a faculty psychology framework can accommodate the neurobiological variability of emotion. This can be done by treating emotions as developmental modules: non-innate systems which behave like modules, but form as a product of ontogenetic development. (shrink)

The essay is critically examines the conceptual problems with the influential modularity model of mind. We shall see that one of the essential characters of modules, namely informational encapsulation, is not only inessential, it ties a knot at a crucial place blocking the solution to the problem of understanding the formation of concepts from percepts (nodes of procedural knowledge). Subsequently I propose that concept formation takes place by modulation of modules leading to cross-representations, which were otherwise prevented by encapsulation. It (...) must be noted that the argument is not against modular architecture, but a variety of an architecture that prevents interaction among modules. This is followed by a brief argument demonstrating that module without modularization, i.e. without developmental history, is impossible. Finally the emerging picture of cognitive development is drawn in the form of the layers in the fabric of mind, with a brief statement of the possible implications. (shrink)

It is becoming more common that the decision-makers in private and public institutions are predictive algorithmic systems, not humans. This article argues that relying on algorithmic systems is procedurally unjust in contexts involving background conditions of structural injustice. Under such nonideal conditions, algorithmic systems, if left to their own devices, cannot meet a necessary condition of procedural justice, because they fail to provide a sufficiently nuanced model of which cases count as relevantly similar. Resolving this problem requires deliberative capacities uniquely (...) available to human agents. After exploring the limitations of existing formal algorithmic fairness strategies, the article argues that procedural justice requires that human agents relying wholly or in part on algorithmic systems proceed with caution: by avoiding doxastic negligence about algorithmic outputs, by exercising deliberative capacities when making similarity judgments, and by suspending belief and gathering additional information in light of higher-order uncertainty. (shrink)

In this paper, I identify a theoretical and political role for ‘white ignorance’, present three alternative accounts of white ignorance, and assess how well each fulfils this role. On the Willful Ignorance View, white ignorance refers to white individuals’ willful ignorance about racial injustice. On the Cognitivist View, white ignorance refers to ignorance resulting from social practices that distribute faulty cognitive resources. On the Structuralist View, white ignorance refers to ignorance that (1) results as part of a social process that (...) systematically gives rise to racial injustice, and (2) is an active player in the process. I argue that, because of its greater power and flexibility, the Structuralist View better explains the patterns of ignorance that we observe, better illuminates the connection to white racial domination, and is overall better suited to the project of ameliorating racial injustice. As such, the Structuralist View should be preferred. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (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)

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)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

The democratic boundary problem raises the question of who has democratic participation rights in a given polity and why. One possible solution to this problem is the all-affected principle, according to which a polity ought to enfranchise all persons whose interests are affected by the polity’s decisions in a morally significant way. While AAP offers a plausible principle of democratic enfranchisement, its supporters have so far not paid sufficient attention to economic participation rights. I argue that if one commits oneself (...) to AAP, one must also commit oneself to the view that political participation rights are not necessarily the only, and not necessarily the best, way to protect morally weighty interests. I also argue that economic participation rights raise important worries about democratic accountability, which is why their exercise must be constrained by a number of moral duties. (shrink)

There is a widespread consensus that a commodification of body parts is to be prevented. Numerous policy papers by international organizations extend this view to the blood supply and recommend a system of uncompensated volunteers in this area—often, however, without making the arguments for this view explicit. This situation seems to indicate that a relevant source of justified worry or unease about the blood supply system has to do with the issue of commodification. As a result, the current health minister (...) of Ontario is proposing a ban on compensation even for blood plasma—despite the fact that Canada can only generate 30 % of the plasma needed for fractionation into important plasma protein products and has to purchase the rest abroad. In the following, I am going to suggest a number of alternative perspectives on the debate in order to facilitate a less dogmatic and more differentiated debate about the matter. Especially in light of the often over-simplified notions of altruism and commodification, I conclude that the debate has not conclusively established that it would be morally objectionable to provide blood plasma donors with monetary compensation or with other forms of explicit social recognition as an incentive. This is especially true of donations for fractionation into medicinal products by profit-oriented pharmaceutical companies. (shrink)

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

In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed (...) partitions along three axes: (a) degree of correspondence between partition cells and objects in reality; (b) degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) degree of completeness and exhaustiveness with which a partition represents reality. This classification is used to characterize three types of partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain. (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)

Weyma Lübbe is one of the most resolute contemporary critics of interpersonal welfare aggregation, as it lies at the heart of most consequentialist ethical theories. Her latest book is a rich extension of her numerous articles on this matter. The main object of criticism is the often-presumed moral relevance of welfare efficiency, for instance in rescue conflicts as they occur in health care systems with limited resources. The central philosophical starting point of her discussion is the ‘numbers debate’ introduced by (...) Philippa Foot and John Taurek, which questions the moral relevance of numbers, as opposed to fairness, when it comes to rescue conflicts between groups of different sizes. In decidedly anti-consequentialist fashion, Lübbe argues that (a) interpersonal welfare efficiency cannot play any foundational role in normative ethics (ch. 3). She also tries to prove (b) the inconsistency of any attempt to supplement welfarist axiologies by fairness aspects, denying the possibility to assign independent moral relevance to both aspects (ch. 4 and 5). In the constructive part of the book (ch. 5 and 6), she presents (c) her own account of distributive ethics based on the principle of equal concern for persons (“Gleichachtung”). (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

There is a concern according to which analyzing crime scene DNA to determine biogeographic origin and skin color of suspects can lead to discrimination against minority populations. This article summarizes and explains some of those parts of the investigation process that can give rise to discrimination. The second part of the paper offers an analysis of the notion of discrimination and presents different accounts of the exact ground of its moral wrongness. As it will emerge, these different accounts lead to (...) different assessments of the use of DNA phenotype analyses in police investigations. -/- ----- Dieser Beitrag befasst sich mit der Befürchtung, dass eine Erweiterung der DNA-Analyse von Tatortspuren für Zwecke der Polizeiarbeit zu Diskriminierungen führen wird. Diese Erwartung bezieht sich insbesondere auf die Ermittlung der sogenannten biogeografischen Abstammung und der Hautschattierung. In dieser Untersuchung werden einige Stellen im Ermittlungsprozess, an denen auf Grundlage solcher Analysen Diskriminierungspotential auftreten könnte, zunächst gesammelt und dargelegt. Im zweiten Teil wird dann der Diskriminierungsbegriff genauer beleuchtet. Dabei wird sich zeigen, dass verschiedene Positionen zu der Frage, was genau eine Diskriminierung moralisch problematisch macht, zu unterschiedlichen Einschätzungen der DNA-Phänotypisierung in der Polizeiarbeit führen. (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)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

The paper investigates whether it is plausible to hold the late stage demented criminally responsible for past actions. The concern is based on the fact that policy makers in the United States and in Britain are starting to wonder what to do with prison inmates in the later stages of dementia who do not remember their crimes anymore. The problem has to be expected to become more urgent as the population ages and the number of dementia patients increases. This paper (...) argues that the late-stage demented should not be punished for past crimes. Applicable theories of punishment, especially theories with an appropriate expressivist, or communicative element, fail to justify the imprisonment of the late-stage demented. Further imprisonment would require a capacity for comprehension on the part of the punished, and, under certain narrowly specified conditions, even a capacity to be at least in principle capable of recalling the crime again. (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)

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)

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)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Many countries have adopted new triage recommendations for use in the event that intensive care beds become scarce during the COVID‐19 pandemic. In addition to establishing the exact criteria regarding whether treatment for a newly arriving patient shows a sufficient likelihood of success, it is also necessary to ask whether patients already undergoing treatment whose prospects are low should be moved into palliative care if new patients with better prospects arrive. This question has led to divergent ethical guidelines. This paper (...) explores the distinction between withholding and withdrawing medical treatment during times of scarcity. As a first central point, the paper argues that a revival of the ethical distinction between doing and allowing would have a revisionary impact on cases of voluntary treatment withdrawal. A second systematic focus lies in the concern that withdrawal due to scarcity might be considered a physical transgression and therefore more problematic than not treating someone in the first place. In light of the persistent disagreement, especially concerning the second issue, the paper concludes with two pragmatic proposals for how to handle the ethical uncertainty: (1) triage protocols should explicitly require that intensive care attempts are designed as time‐limited trials based on specified treatment goals, and this intent should be documented very clearly at the beginning of each treatment; and (2) lower survival prospects can be accepted for treatments that have already begun, compared with the respective triage rules for the initial access of patients to intensive care. (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.

Lockheed Martin Corp. has funded research to generate a framework and methodology for developing semantic reasoning applications to support the discipline oflntelligence Analysis. This chapter outlines that framework, discusses how it may be used to advance the information sharing and integrated analytic needs of the Intelligence Community, and suggests a system I software architecture for such applications.

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Bettina Schöne-Seifert and Marco Stier present a host of detailed and intriguing arguments to the effect that potentiality arguments have to be viewed as outdated due to developments in stem cell research, in particular the possibility of re-setting the development potential of differentiated cells, such as skin cells. However, their argument leaves them without an explanation of the intuitive difference between skin cells and human beings, which seems to be based on the assumption that a skin cell is merely part (...) of a human organism, while an embryo is at some point a human organism. An appropriately designed concept of the human organism can explain the difference, but also has the potential of re-dividing the argumentative landscape along familiar lines. (shrink)

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of terms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been little (...) effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. To address this requirement, we are developing an Emotion Ontology (EMO). (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

The most well-known goal of non-invasive prenatal testing (NIPT) is still to determine whether or not a fetus has trisomy 21. Since women often terminate the pregnancy upon a positive result, there is concern that the use of NIPT contributes to discrimination against persons with disabilities. If this concern is justified, it could have an impact on the wider social acceptability of existing testing practices and their potential further expansion. This paper demonstrates four different versions of the discrimination worry, indicates (...) how international policy papers have reacted to them, and identifies the ethically most relevant feature of the concern. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

Michael Quante’s book Person offers a systematic and argumentative assessment of the question what a person is and accounts for the multiple aspects that play a role in our everyday understanding of the term. Quante is skeptical about the possibility of constructing a purely psychological account of the person and proposes to base the diachronic unity conditions of persons on the human organism. At the same time he acknowledges that psychological considerations, including the notion of a person’s personality, are important (...) for practical purposes. However, one may wonder why he proposes the human organism as the remedy for the alleged shortcomings of the psychological approach, rather than introducing an additional physical continuity requirement of the cerebrum or other parts of the brain. (shrink)

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)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

In this contribution, I investigate the way in which our understanding of a dementia patient’s self holds relevance to issues of punishment and respon- sibility. This topic is motivated by the fact that some countries with particularly large prison populations—such as the United States—are starting to build special- ized prison tracts for inmates with dementia. In other countries that do not have such specialized facilities, authorities are trying to find the least badly-equipped facility for such patients, and they are turning (...) to ordinary retirement homes, forensic hospitals as well as ordinary psychiatric and geriatric hospital wards. The problem is expected to become increasingly urgent as the population ages and the number of dementia patients increases. I analyse the way in which justifications of legal (or private) punishment for offenders with dementia can depend on an account of relevant psychological features of the self. I argue that especially retributivist and expressivist justifications of punishment require the offender’s ability to comprehend that he or she is being punished for a particular action in the past and that it was him or herself who committed this action. In the second part of my paper, I distinguish between different accounts of responsibility and argue that accounts of relevant features of the self are also needed here to answer the question of whether offenders with dementia are still responsible for past or current inappropriate behavior. In the final part of the paper, I argue that potentially existing private punishment intuitions among care- takers as well as certain puzzles of responsibility interpretation can make it plausible to relieve certain caretakers from primary responsibility for offenders with dementia, especially caretakers who belong to a relevant former victim group of the offender. (shrink)

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the (...) relation between fetus and mother. (shrink)

The increasing number of dementia cases has led to renewed interest in philosophical theories of personal identity, because these patients seem to “drop out” of their own identities in some ways. Philosophical positions that try to account for the phenomenon of identity loss include numerical theories of identity which argue for a psychological or a biological continuity criterion, narrative theories of identity, as well as reflections about different forms of memory, some of which have had influence in modern psychology and (...) in the neurosciences. This special issue brings together current articles by experts in these areas. ------ Die zunehmende Verbreitung von Demenzerkrankungen hat zu einem erhöhten Interesse an philosophischen Theorien der personalen Identität geführt, da diese Patienten in manchen Hinsichten aus ihrer eigenen Identität „herauszufallen“ scheinen. Zu den philosophischen Ansätzen, die sich hiermit beschäftigen, gehören Theorien der numerischen Identität, wie etwa das psychologische oder das biologische Kontinuitätskriterium, narrative Theorien der Identität, aber auch Refl exionen über verschiedene Formen des Erinnerns, die sich zum Teil in der modernen Psychologie und in den Neurowissenschaften niederschlagen. Dieses Schwerpunktheft enthält aktuelle Beiträge von Experten aus den genannten Bereichen. ​The increasing number of dementia cases has led to renewed interest in philosophical theories of personal identity, because these patients seem to “drop out” of their own identities in some ways. Philosophical positions that try to account for the phenomenon of identity loss include numerical theories of identity which argue for a psychological or a biological continuity criterion, narrative theories of identity, as well as reflections about different forms of memory, some of which have had influence in modern psychology and in the neurosciences. This special issue brings together current articles by experts in these areas. (shrink)

This paper argues that Henry Sidgwick's theory of the good is a form of enlightened preference hedonism. In order to support this conclusion, the paper argues that the correct interpretation of his notorious passage about the 'ideal element' of the good should get tied to his views about weakness of the will. Sidgwick believes that reaching your own good requires overcoming weakness of the will. An applied section illustrates the practical significance of this finding. In cases in which shooting down (...) a passenger plane can save a greater number of people on the ground, and no other relevant considerations apply, the passengers should desire their own destruction-not only to promote the general good, but also in order to reach the only good they can still secure for themselves: giving their inevitable deaths a positive meaning. This utilitarian position regarding some one-versusthe-many cases has been overlooked in the German Supreme Court ruling on the destruction of 9/11 airplanes in 2006. (shrink)

A particularly significant criticism of utilitarian and consequentialist moral theories is that they are overly demanding. According to the epistemic variant of this critique, it is overly demanding to have to determine which of one's possible actions would promote the good in the best possible way. A particularly striking articulation of this concern was put forward by James Lenman, who argued that not only is it difficult to predict the consequences of actions, but it is often outright impossible. The reason, (...) according to Lenman, is that we are simply ignorant of what the consequences of an action will be—especially in the distant future, after long and highly complex causal chains. In From Value to Rightness, Vuko Andrić defends an act-consequentialism with a subjective decision criterion designed to avoid these objections. According to this position, agents should decide based on the outcomes they can reasonably expect to occur, rather than the outcomes that actually occur. -/- ----- Eine besonders einschlägige Kritik an utilitaristischen und konsequentialistischen Moraltheorien besagt, dass sie überfordernd sind. Der epistemischen Variante dieser Kritik zufolge ist es überfordernd, wenn man grundsätzlich herausfinden muss, welche der eigenen Handlungsmöglichkeiten das Gute auf die bestmögliche Weise befördern würde. Eine besonders einschlägige Zuspitzung dieser Sorge wurde von James Lenman vorgebracht, demzufolge es nicht nur schwierig ist, Handlungsfolgen abzuschätzen, sondern regelmäßig unmöglich. Der Grund dafür ist laut Lenman, dass wir schlicht ahnungslos sind, welche Folgen eine Handlung haben wird – besonders in der fernen Zukunft nach langen und sehr komplexen Kausalketten. In From Value to Rightness verteidigt Vuko Andrić einen Handlungskonsequentialismus mit subjektivem Entscheidungskriterium, der diesen Vorwürfen entgehen soll. Dieser Position zufolge sollen Handelnde auf Grundlage derjenigen Handlungsfolgen entscheiden, mit deren Eintreten sie vernünftigerweise rechnen können und nicht auf Grundlage der tatsächlich eintretenden Folgen. (shrink)

This paper addresses the so-called Taurek debate on whether or not to save the greater number of victims in rescue conflicts. In this controversy we take a consequentialist and aggregationist pro-numbers position and defend it against various objections. In particular, we consider it to be compatible with the principle of equal concern. Given that the pro-numbers position hinges to a significant extent on the acceptance of the person-neutral value of personal well-being, we offer a coherentist justification for this value claim. (...) Systematically though, we argue that neither pure welfare aggregationism nor its strict rejection are convincing. Rather, rejoining the two ethical dimensions of individual claims and collective well-being requires a hybrid position. Identifying three possible ways of constructing such a position, we briefly defend them against a recent version of the charge that they cannot be coherently expressed in a rational choice framework. -/- ----- Im Rahmen der sogenannten Taurek-Debatte wird die Frage diskutiert, ob in Rettungskonflikten die größere Anzahl an Opfern gerettet werden sollte oder nicht. Wir beziehen in dieser Kontroverse eine konsequentialistische und aggregationistische Pro-Anzahl-Position und verteidigen diese gegen verschiedene Einwände. Insbesondere halten wir die Position für kompatibel mit dem Prinzip gleicher Achtung. Angesichts des Umstandes, dass die Pro-Anzahl-Position in maßgeblicher Weise von der Annahme eines personenneutralen Wertes persönlichen Wohlergehens abhängt, bieten wir eine kohärentistische Rechtfertigung für diese Wertbehauptung. Systematisch argumentieren wir, dass weder ein reiner Wohlergehensaggregationismus noch seine komplette Zurückweisung überzeugend sein können. Die Vereinigung der beiden ethischen Dimensionen individueller Ansprüche und kollektiven Wohlergehens erfordert stattdessen eine hybride Position. Wir identifizieren drei mögliche Wege für die Konstruktion einer solchen Hybridposition und verteidigen diese abschließend kurz gegen einen aktuellen Vorwurf, demzufolge diese nicht auf kohärente Weise im Rahmen der rationalen Entscheidungstheorie abgebildet werden können. (shrink)

Most theorists working on moral obligations to refugees conceive of western states as innocent bystanders with duties to aid refugees if they can do so at little cost to themselves. This paper challenges this dominant theoretical framing of global displacement by highlighting for the first time certain practices of western states in response to refugee flows such as border violence, detention, encampment and containment which may make us question whether states who engage in such practices are indeed innocent. This paper (...) provides the first normative analysis of these practices by seeking to classify them as either doing or allowing harm and invoking the fundamental moral imperative central to core common moral commitments - not to harm innocent people - to suggest that certain western states are not merely failing to aid refugees and allowing harm to come to them, but are instead responding to their calls for aid by harming them. (shrink)