Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

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.

Robotization is an increasingly pervasive feature of our lives. Robots with high degrees of autonomy may cause harm, yet in sufciently complex systems neither the robots nor the human developers may be candidates for moral blame. John Danaher has recently argued that this may lead to a retribution gap, where the human desire for retribution faces a lack of appropriate subjects for retributive blame. The potential social and moral implications of a retribution gap are considerable. I argue that the retributive (...) intuitions that feed into retribution gaps are best understood as deontological intuitions. I apply a debunking argument for deontological intuitions in order to show that retributive intuitions cannot be used to justify retributive punishment in cases of robot harm without clear candidates for blame. The fundamental moral question thus becomes what we ought to do with these retributive intuitions, given that they do not justify retribution. I draw a parallel from recent work on implicit biases to make a case for taking moral responsibility for retributive intuitions. In the same way that we can exert some form of control over our unwanted implicit biases, we can and should do so for unjustifed retributive intuitions in cases of robot harm. (shrink)

Governments around the world have faced the challenge of how to respond to the recent outbreak of a novel coronavirus disease. Some have reacted by greatly restricting the freedom of citizens, while others have opted for less drastic policies. In this paper, I draw a parallel with vaccination ethics to conceptualize two distinct approaches to COVID-19 that I call altruistic and lockdown. Given that the individual measures necessary to limit the spread of the virus can in principle be achieved voluntarily (...) as well as through enforcement, the question arises of how much freedom governments ought to give citizens to adopt the required measures. I argue that an altruistic approach is preferable on moral grounds: it preserves important citizen freedoms, avoids a number of potential injustices, and gives people a much-needed sense of meaning in precarious times. (shrink)

Bioethics, Volume 36, Issue 6, Page 687-698, July 2022.

Moralization is a social-psychological process through which morally neutral issues take on moral significance. Often linked to health and disease, moralization may sometimes lead to good outcomes; yet moralization is often detrimental to individuals and to society as a whole. It is therefore important to be able to identify when moralization is inappropriate. In this paper, we offer a systematic normative approach to the evaluation of moralization. We introduce and develop the concept of ‘mismoralization’, which is when moralization is metaethically (...) unjustified. In order to identify mismoralization, we argue that one must engage in metaethical analysis of moralization processes while paying close attention to the relevant facts. We briefly discuss one historical example and two contemporary cases related to COVID-19 that we contend to have been mismoralized in public health. We propose a remedy of de-moralization that begins by identifying mismoralization and that proceeds by neutralizing inapt moral content. De-moralization calls for epistemic and moral humility. It should lead us to pull away from our tendency to moralize—as individuals and as social groups—whenever and wherever moralization is unjustified. (shrink)

Experimental philosophy is a relatively recent discipline that employs experimental methods to investigate the intuitions, concepts, and assumptions behind traditional philosophical arguments, problems, and theories. While experimental philosophy initially served to interrogate the role that intuitions play in philosophy, it has since branched out to bring empirical methods to bear on problems within a variety of traditional areas of philosophy—including metaphysics, philosophy of language, philosophy of mind, and epistemology. To date, no connection has been made between developments in experimental philosophy (...) and philosophy of technology. In this paper, I develop and defend a research program for an experimental philosophy of technology. (shrink)

Preventive vaccination can protect not just vaccinated individuals, but also others, which is often a central point in discussions about vaccination. To date, there has been no systematic study of self- and other-directed motives behind vaccination. This article has two major goals: first, to examine and distinguish between self- and other-directed motives behind vaccination, especially with regard to vaccinating for the sake of third parties, and second, to explore some ways in which this approach can help to clarify and guide (...) vaccination debates and policy. I propose conceiving of vaccination in terms of three basic elements: the vaccination decision-maker, the vaccine recipient and the primary beneficiary. I develop a taxonomy based on the relations between these elements to distinguish four kinds of vaccination: self-protective, paternalistic, altruistic and indirect. I finally discuss the case of human papillomavirus vaccine regulation for men and women to show how each kind of vaccination is associated with and raises specific ethical questions. (shrink)

Vaccination can protect vaccinated individuals and often also prevent them from spreading disease to other people. This opens up the possibility of getting vaccinated for the sake of others. In fact, altruistic vaccination has recently been conceptualized as a kind of vaccination that is undertaken primary for the benefit of others. In order to better understand the potential role of altruistic motives in people’s vaccination decisions, we conducted two focus group studies with a total of 37 participants. Study 1 included (...) three focus groups on the subject of HPV vaccination for boys. Study 2 included three focus groups on the subject of pertussis and measles vaccination for childcare workers. We found substantial evidence of other-regarding motives across all focus groups, which suggests that altruistic motives could be an important factor when it comes to people’s vaccination decisions. We address the significance of these findings for vaccination policy surrounding HPV vaccination for boys and vaccination for childcare workers. We also extend the findings to normative work on vaccination for the sake of others more generally. (shrink)

Should people get vaccinated for the sake of others? What could ground—and limit—the normative claim that people ought to do so? In this paper, we propose a reasons-based consequentialist account of vaccination for the benefit of others. We outline eight harm-based and probabilistic factors that, we argue, give people moral reasons to get vaccinated. Instead of understanding other-directed vaccination in terms of binary moral duties (i.e., where people either have or do not have a moral duty to get vaccinated), we (...) develop a scalar approach according to which people can have stronger or weaker moral reasons to get vaccinated in view of the moral good of vaccination. One advantage of our approach is that it can capture why a person might have strong moral reasons to get vaccinated with Vaccine A, but only weak moral reasons to get vaccinated with Vaccine B. We discuss theoretical strengths of our approach and provide a case study of vaccination against COVID-19 to demonstrate its practical significance. (shrink)

The potential for vaccines to prevent the spread of infectious diseases is crucial for vaccination policy and ethics. In this paper, I discuss recent evidence that the current COVID-19 vaccines have only a modest and short-lived effect on reducing SARS-CoV-2 transmission and argue that this has at least four important ethical implications. First, getting vaccinated against COVID-19 should be seen primarily as a self-protective choice for individuals. Second, moral condemnation of unvaccinated people for causing direct harm to others is unjustified. (...) Third, the case for a harm-based moral obligation to get vaccinated against COVID-19 is weak. Finally, and perhaps most significantly, coercive COVID-19 vaccination policies (e.g., measures that exclude unvaccinated people from society) cannot be directly justified by the harm principle. (shrink)

Type 1 diabetes (T1D) is a chronic illness that requires intensive lifelong management of blood glucose concentrations by means of external insulin administration. There have been substantial developments in the ways of measuring glucose levels, which is crucial to T1D self-management. Recently, continuous glucose monitoring (CGM) has allowed people with T1D to keep track of their blood glucose levels in near real-time. These devices have alarms that warn users about potentially dangerous blood glucose trends, which can often be shared with (...) ther people. CGM is consistently associated with improved glycemic control and reduced hypoglycemia and is currently recommended by doctors. However, due to the costs of CGM, only those who qualify for hospital provision or those who can personally afford it are able to use it, which excludes many people. In this paper, I argue that unequal access to CGM results in: (1) unjust health inequalities, (2) relational injustice, (3) injustice with regard to agency and autonomy, and (4) epistemic injustice. These considerations provide prima facie moral reasons why all people with T1D should have access to CGM technology. I discuss the specific case of CGM policy in the Netherlands, which currently only provides coverage for a small group of people with T1D, and argue that, especially with additional considerations of cost-effectiveness, the Dutch government ought to include CGM in basic health care insurance for all people with T1D. (shrink)

This dissertation explores the idea and ethics of vaccination for the sake of others. It conceptually distinguishes four different kinds of vaccination—self-protective, paternalistic, altruistic, and indirect—based on who receives the primary benefits of vaccination and who ultimately makes the vaccination decision. It describes the results of focus group studies that were conducted to investigate what people who might get vaccinated altruistically think of this idea. It also applies the different kinds of vaccination to ethical issues surrounding COVID-19, such as lockdown (...) measures, routine or mandatory vaccination of healthy children, and the ethical justification of restrictive measures for unvaccinated people. A more general philosophical account of vaccination ethics is ultimately developed, which is based not on moral duties, but on the moral reasons that people may have to get vaccinated for the sake of others. It is argued that such reasons may be stronger or weaker, depending on various factors related to the vaccines in question and the specific epidemiological circumstances. (shrink)

Recently, Joshua Greene has argued that we need a metamorality to solve moral problems for which evolution has not prepared us. The metamorality that he proposes is a utilitarian account that he calls deep pragmatism. Deep pragmatism is supposed to arbitrate when the values espoused by different groups clash. To date, no systematic appraisal of this argument for a metamorality exists. We reconstruct Greene’s case for deep pragmatism as a metamorality and consider three lines of objection to it. We argue (...) that, in the end, only one of these objections seriously threatens Greene’s position. Greene has to commit to the nonexistence of moral truth in order for his argument for the need of a metamorality to get off the ground. This, however, leads to a tension in his overall argument for deep pragmatism: ultimately, it casts his rejection of antiutilitarian moral intuitions into doubt. (shrink)

Onychectomy involves the surgical amputation of a cat's claws. Tendonectomy entails surgically cutting tendons to prevent the extension and full use of a cat's claws. Both surgeries practically declaw cats and are not only painful but also associated with high complication rates. While feline declawing surgeries have been banned in various places around the world, they are still elective in many countries and U.S. states. This article provides an ethical analysis of declawing cats. It discusses the harms posed by feline (...) declawing surgeries, like pain and complications, which are not offset by any benefits to cats. Drawing on Martha Nussbaum's capabilities approach, it also offers an additional and broader ethical argument against declawing, namely that removing cats' claws is unjust because it thwarts important capabilities for feline flourishing (e.g., play, bodily integrity, control over one's environment). It concludes that declawing cats for non-medical purposes is unethical and must be opposed. (shrink)

For Albert Camus, plague was both a fact of life and a powerful metaphor for the human condition. Camus engaged most explicitly and extensively with the subject of plague in his 1947 novel, The Plague (La peste), which chronicles an outbreak of what is presumably cholera in the French-Algerian city of Oran. I often thought of this novel—and what it might teach us—during the recent COVID-19 pandemic. In this article, I discuss seven important insights from The Plague about epidemics, public (...) health and morality. (shrink)

The rapid expansion of Big Tech companies into various societal domains (e.g., health, education, and agriculture) over the past decade has led to increasing concerns among governments, regulators, scholars, and civil society. While existing theoretical frameworks—often revolving around privacy and data protection, or market and platform power—have shed light on important aspects of Big Tech expansionism, there are other risks that these frameworks cannot fully capture. In response, this editorial proposes an alternative theoretical framework based on the notion of sphere (...) transgressions, which draws on political philosopher Michael Walzer's theory of justice. The editorial not only introduces the sphere transgressions framework, but it also highlights its potential to generate novel research questions. Furthermore, this editorial introduces eight articles and one commentary from a group of interdisciplinary scholars that critically examine Big Tech expansionism by reflecting on this expansionism from the perspective of different societal spheres or by engaging with the sphere transgressions framework itself. (shrink)

COVID-19 vaccination of children has begun in various high-income countries with regulatory approval and general public support, but largely without careful ethical consideration. This trend is expected to extend to other COVID-19 vaccines and lower ages as clinical trials progress. This paper provides an ethical analysis of COVID-19 vaccination of healthy children. Specifically, we argue that it is currently unclear whether routine COVID-19 vaccination of healthy children is ethically justified in most contexts, given the minimal direct benefit that COVID-19 vaccination (...) provides to children, the potential for rare risks to outweigh these benefits and undermine vaccine confidence, and substantial evidence that COVID-19 vaccination confers adequate protection to risk groups, such as older adults, without the need to vaccinate healthy children. We conclude that child COVID-19 vaccination in wealthy communities before adults in poor communities worldwide is ethically unacceptable and consider how policy deliberations might evolve in light of future developments. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

Volume 19, Issue 9, September 2019, Page 64-66.

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

The replicability of a research claim is often positioned as an important step in establishing the credibility of scientific research. This expectation persists despite ongoing disagreements over how to characterise replication practices in various contexts. Rather than attempt to explain or resolve these disagreements, we propose that there is value in exploring the variable uses of the replicability concept. To this end, we treat the replicability concept as a goal-directed tool for studying scientific practices. This approach extends scholarship on the (...) goal-directed uses of concepts within investigative practices to explore the value of reflexively interrogating those concepts used to study the sciences as practiced. In doing so, we highlight the importance of considering how and when a given concept is an appropriate tool for a given goal when studying scientific practices. For instance, in the case of the replicability concept, our examination suggests that there is value in clarifying how a given characterisation of replicability is appropriate to a given context-specific analytic and/or evaluative goal. In addition, we hope to draw attention to how Metaresearch and HPS contexts provide complementary insights for those seeking to understand when and how replication practices can help in assessing a given research claim. (shrink)

In the second edition Preface of Religion Within the Bounds of Bare Reason Kant responds to an anonymous review of the first edition. We present the first English translation of this obscure book review. Following our translation, we summarize the reviewer's main points and evaluate the adequacy of Kant's replies to five criticisms, including two replies that Kant provides in footnotes added in the second edition. A key issue is the reviewer's claim that Religion adopts an implied standpoint, described using (...) transcendental terminology. Kant could have avoided much confusion surrounding Religion, had he taken this review more seriously. We therefore respond to three objections that Kant failed to address: how the Wille–Willkür distinction enables the propensity to evil to be viewed as coexisting with freedom of choice; how moral improvement is possible, even though the propensity to evil is necessary and universal; and how a ‘deed’ can be regarded as ‘noumenal’.Send article to KindleTo send this article to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle. Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply. Find out more about the Kindle Personal Document Service.The Implied Standpoint of Kant's Religion: An Assessment of Kant's Reply to an Early Book Review of Religion Within the Bounds of Bare ReasonVolume 18, Issue 1Stephen R. Palmquist and Steven Otterman DOI: https://doi.org/10.1017/S1369415412000295Your Kindle email address Please provide your Kindle [email protected]@kindle.com Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Send article to Dropbox To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to Dropbox. The Implied Standpoint of Kant's Religion: An Assessment of Kant's Reply to an Early Book Review of Religion Within the Bounds of Bare ReasonVolume 18, Issue 1Stephen R. Palmquist and Steven Otterman DOI: https://doi.org/10.1017/S1369415412000295Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Send article to Google Drive To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to Google Drive. The Implied Standpoint of Kant's Religion: An Assessment of Kant's Reply to an Early Book Review of Religion Within the Bounds of Bare ReasonVolume 18, Issue 1Stephen R. Palmquist and Steven Otterman DOI: https://doi.org/10.1017/S1369415412000295Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Export citation. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptual Spaces framework work, (...) the similarity values between the contents of observations on the one hand and the properties of the entities observed on the other needs to be found. This paper shows how to exploit Dempster-Shafer theory to implement a statistical approach for finding these similarities values. This approach will allow a user to identify the uncertainty involved in similarity value data, which can later be propagated through the developed mathematical model in order for the user to know the overall uncertainty in the observation-to-concept mappings needed for space event characterization. (shrink)

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

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)

Although an inverse relationship between religion and deviance is empirically well-established in the western context, previous studies on Islam and deviance conducted in non-western countries are limited. To address this gap in deviance research, we hypothesized that individual religiosity would be inversely related to deviance with the inverse relationship being more likely for ascetic than anti-ascetic or secular deviance. To test this hypothesis, we applied ordinary least squares and logistic regression methods to analyze data collected from 2,005 survey participants of (...) a Turkish public university student population. Regression results provided partial support for the hypothesis, as we found that religiosity was inversely related to both ascetic and secular deviance. The observed inverse relationship is noteworthy in that it was found in an institutionally secular, Muslim country. Implications of our findings are discussed. (shrink)

This paper presents a preliminary analysis of the first participatory budgeting experiment in the United States, in Chicago's 49th Ward. There are two avenues of inquiry: First, does participatory budgeting result in different budgetary priorities than standard practices? Second, do projects meet normative social justice outcomes? It is clear that allowing citizens to determine municipal budget projects results in very different outcomes than standard procedures. Importantly, citizens in the 49th Ward consistently choose projects that the research literature classifies as low (...) priority. The results are mixed, however, when it comes to social justice outcomes. While there is no clear pattern in which projects are located only in affluent sections of the ward, there is evidence of geographic clustering. Select areas are awarded projects like community gardens, dog parks, and playgrounds, while others are limited to street resurfacing, sidewalk repairs, bike racks, and bike lanes. Based on our findings, we offer suggestions for future programmatic changes. (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)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Safe-by-Design (SBD) frameworks for the development of emerging technologies have become an ever more popular means by which scholars argue that transformative emerging technologies can safely incorporate human values. One such popular SBD methodology is called Value Sensitive Design (VSD). A central tenet of this design methodology is to investigate stakeholder values and design those values into technologies during early stage research and development (R&D). To accomplish this, the VSD framework mandates that designers consult the philosophical and ethical literature to (...) best determine how to weigh moral trade-offs. However, the VSD framework also concedes the universalism of moral values, particularly the values of freedom, autonomy, equality trust and privacy justice. This paper argues that the VSD methodology, particularly applied to nano-bio-info-cogno (NBIC) technologies, has an insufficient grounding for the determination of moral values. As such, an exploration of the value-investigations of VSD are deconstructed to illustrate both its strengths and weaknesses. This paper also provides possible modalities for the strengthening of the VSD methodology, particularly through the application of moral imagination and how moral imagination exceed the boundaries of moral intuitions in the development of novel technologies. (shrink)

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

Adam Smith is respected as the father of contemporary economics for his work on systemizing classical economics as an independent field of study in The Wealth of Nations. But he was also a significant moral philosopher of the Scottish Enlightenment, with its characteristic concern for integrating sentiments and rationality. This article considers Adam Smith as a key moral philosopher of commercial society whose critical reflection upon the particular ethical challenges posed by the new pressures and possibilities of commercial (...) society remains relevant today. The discussion has three parts. First I address the artificial separation between self-interest and morality often attributed to Smith, in which his work on economics is stripped of its ethical context. Second I outline Smith’s ethical approach to economics, focusing on his vigorous but qualified defence of commercial society for its contributions to prosperity, justice, and freedom. Third I outline Smith’s moral philosophy proper as combining a naturalistic account of moral psychology with a virtue ethics based on propriety in commercial society. (shrink)

Atomically precise manufacturing (APM) is the assembly of materials with atomic precision. APM does not currently exist, and may not be feasible, but if it is feasible, then the societal impacts could be dramatic. This paper assesses the net societal impacts of APM across the full range of important APM sectors: general material wealth, environmental issues, military affairs, surveillance, artificial intelligence, and space travel. Positive effects were found for material wealth, the environment, military affairs (specifically nuclear disarmament), and space travel. (...) Negative effects were found for military affairs (specifically rogue actor violence and AI. The net effect for surveillance was ambiguous. The effects for the environment, military affairs, and AI appear to be the largest, with the environment perhaps being the largest of these, suggesting that APM would be net beneficial to society. However, these factors are not well quantified and no definitive conclusion can be made. One conclusion that can be reached is that if APM R&D is pursued, it should go hand-in-hand with effective governance strategies to increase the benefits and reduce the harms. (shrink)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a banks computers, however, the formula fails, (...) because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

Why be moral? Why, in the language of Adam Smith, act on what you think is praiseworthy even when it does not get you praise from other people? Because, answers Smith, you love praiseworthiness. But what is this love of praiseworthiness, and where does it come from? In this article, 1) I argue that we start to love praiseworthiness when we redirect our love of praise away from other people toward the ‘impartial spectator’-aspect of ourselves, and 2) show (...) how this fits with evidence that the rudimentary moral compass which guides us early in childhood needs correction through socialisation to develop into a mature moral conscience. (shrink)

Safe-by-Design (SBD) frameworks for the development of emerging technologies have become an ever more popular means by which scholars argue that transformative emerging technologies can safely incorporate human values. One such popular SBD methodology is called Value Sensitive Design (VSD). A central tenet of this design methodology is to investigate stakeholder values and design those values into technologies during early stage research and development (R&D). To accomplish this, the VSD framework mandates that designers consult the philosophical and ethical literature to (...) best determine how to weigh moral trade-offs. However, the VSD framework also concedes the universalism of moral values, particularly the values of freedom, autonomy, equality trust and privacy justice. This paper argues that the VSD methodology, particularly applied to nano-bio-info-cogno (NBIC) technologies, has an insufficient grounding for the determination of moral values. As such, an exploration of the value-investigations of VSD are deconstructed to illustrate both its strengths and weaknesses. This paper also provides possible modalities for the strengthening of the VSD methodology, particularly through the application of moral imagination and how moral imagination exceed the boundaries of moral intuitions in the development of novel technologies. (shrink)

There are two primary camps in which nanotechnology today can be categorized normal nanotechnology and speculative nanotechnology. The birth of nanotechnology proper was conceived through discourses of speculative nanotechnology. However, current nanotech-nology research has detracted from its speculative promises in favour of more attainable material products. Nonetheless, normal nanotechnology has leveraged the popular support and consequential funding it needs to conduct research and development (R&D) as a result of popular conceptions of speculative nanotechnology and its promises. Similarly, the scholarly literature (...) has shifted its focus away from speculative nanofutures towards normal nanotech-nology R&D. This paper shows that there is an incongruence between the representation of nanotechnology in the media, scholarly journals and industry. (shrink)