Transcript of an Interview on the podcast: Irreverend: Faith and Current Affairs.

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

Simon Blackburn has not shied away from the use of vivid imagery in developing, over a long and prolific career, a large-scale philosophical vision. Here one might think, for instance, of ‘Practical Tortoise Raising’ or ‘Ramsey's Ladder’ or ‘Frege's Abyss’. Blackburn develops a ‘quasi-realist’ account of many of our philosophical and everyday commitments, both theoretical (e.g., modality and causation) and practical (e.g., moral judgement and normative reasons). Quasi-realism aims to provide a naturalistic treatment of its targeted phenomena while earning the (...) right to deploy all of the ‘trappings’ of realism—i.e., while eschewing any idea that our normal thought and talk about such phenomena are pervasively in error. The quasi-realist project is that of explaining how (as Huw Price puts it here) ‘the folk come to “talk the realist talk” without committing ourselves—us theorists, as it were—to “walking the metaphysical walk”’ (p. 136). Quasi-realism, too, can speak of truth, facts, properties, belief, knowledge, and so on. The imagery in this collection also abounds, though, in capturing a different view of quasi-realism: No fewer than three of the contributors picture Blackburn as wanting to have his cake and eat it too (Louise Antony asking, in addition, ‘Who doesn't? It's cake’ [p. 19]). (shrink)

In reference to the philosophical theology of medieval Islamic theologian Ibn Taymiyya, this paper outlines a parallel between Taymiyyan thought and Alvin Plantinga’s thesis of ‘Reformed Epistemology’. In critiquing a previous attempt to build an account of ‘Islamic externalism’, the Taymiyyan model offers an account that can be seen as wholly ‘Plantingan’.

In this chapter, I describe my “post-diagnosis” experiences as the parent of an autistic child, those years in which I tried, but failed, to make sense of the overwhelming and often nonsensical information I received about autism. I argue that immediately after being given an autism diagnosis, parents are pressured into making what amounts to a life-long commitment to a therapy program that (they are told) will not only dramatically change their child, but their family’s financial situation and even their (...) entire mode of existence. Moreover, despite information overload, many treatment programs for autism rely on empty jargon and make completely unrealistic promises, so parents are left feeling overwhelmed and panicked. Even well respected therapy programs encourage parents to spend liberally. Indeed, autistic therapists, who help construct what I refer to as the Culture of Autism, advise parents to commit to a minimum of 35 to 45 hours of intensive therapy every week. The implications are clear: for a parent who works full-time, their autistic child becomes a second full-time job. Autism is big business right now, and therapists are pushing parents to the brink of desperation. So it is not too surprising that there is a desperate cry for a more permanent solution—which is why researchers seek to cure autism. But there are two ways to conceptualize cure. A Therapeutic Cure model (TC) conceives of a cure as a beneficial treatment for the patient that eliminates or ameliorates the harms of the disease or condition. But the notion of a therapeutic cure for autism is highly implausible, given the complexities of autism. Indeed, at this point, the vast majority of researchers have come to the conclusion that the idea of a therapeutic cure for autism is simply a non-starter. Therefore the bulk of research seeking a cure for autism focuses instead on a second approach, which I refer to as the Negative Eugenics Cure model (NEC). With this model, the intention is to eliminate the disease or condition without regard for the health or well-being of the organism carrying the disease or condition. So, with regard to autism, researchers are focusing on identifying genetic markers for autism that can be detected in utero, or in embryos, so that autistic fetuses can be eliminated and autism eradicated by preventing the existence of autistic individuals. I review both models and argue that both fail to provide convincing arguments that the “solution” either offers is desirable. Both rest on the assumption that autism renders a life not worth living which, all things considered, is false. Instead of pushing to cure autism, an idea pervasive in this Culture of Autism, I contend that autistics are individuals with lives worth living. Moreover, rather than expend millions on research to search for the means to eliminate autism, we should instead expend our resources to ensure autistic individuals have access to support they may need. If the phenomenology of autism were better understood and appreciated, the panicked demand for a cure for autism might abate and perhaps autism could be seen as having value in and of its own right. (shrink)

The problem of religious disagreement between epistemic peers is a potential threat to the epistemic justification of one’s theistic belief. In this paper, I develop a response to this problem which draws on the central epistemological thesis of skeptical theism concerning our inability to make proper judgements about God’s reasons for permitting evil. I suggest that this thesis may extend over to our judgements about God’s reasons for self-revealing, and that when it does so, it can enable theists to remain (...) steadfast amid disagreement with epistemic peers who hold a contrary theistic belief (i.e., atheistic belief). For if we’re unable to make proper judgements about God’s reasons for self-revealing, then for all we know, God has some reason for not revealing Himself to our apparent epistemic peer. Thus, their epistemic credentials needn’t provide reason to reduce one’s confidence to such a degree as to no longer uphold one’s theistic belief. (shrink)

The extent to which individuals with a variety of cultural backgrounds differ in empathic responsiveness is unknown. This article describes the differences in trait empathy in one independent and one interdependent society (i.e., the US and Iran, respectively). The analysis of data collected from self-reported questionnaires answered by 326 adults indicated a significant difference in the cognitive component of empathy concerning participants’ affiliation to either egocentric or socio-centric society: Iranian participants with interdependent cultural norms, reported higher cognitive empathy compared to (...) American participants who share independent cultural norms. In line with previous studies, gender differences were observed in all subscales of questionnaires, except the Empathy Quotient (EQ). Female participants demonstrated more empathy than males in both samples. Implications for understanding the cross-cultural differences of various components of empathy are discussed. (shrink)

In this article, I consider how the epistemic problem of religious disagreement has been viewed within the Islamic tradition. Specifically, I consider two religious epistemological trends within the tradition: Islamic Rationalism and Islamic Traditionalism. In examining the approaches of both trends toward addressing the epistemic problem, I suggest that neither is wholly adequate. Nonetheless, I argue that both approaches offer insights that might be relevant to building a more adequate response. So, I attempt to combine insights from both by drawing (...) a distinction between inferential and noninferential reflective responsibility. Given this distinction, I argue that it may be possible for a theist to remain steadfast in upholding their tradition-specific theistic belief, without having to hold that belief by way of inference; but nevertheless, having to be sufficiently reflectively responsible in forming their theistic belief noninferentially. (shrink)

This article aims to draw on the ‘Qur'anic Rationalism’ of Taqī al-Dīn Ibn Taymiyya (1263–1328) in elucidating an Islamic epistemology of theistic natural signs, in the lens of contemporary philosophy of religion. In articulating what Ibn Taymiyya coins ‘God's method of proof through signs (istidlāluhu taʿālā bi'l-āyāt)’, it seeks aid in particular from the work of C. Stephen Evans and other contemporary philosophers of religion, in an attempt to understand the relevance and force of this alternative to natural theology within (...) the Islamic tradition. In doing so, it aims to respond to existing criticisms of Ibn Taymiyya's perspective in the literature, and to consider the implications of a Taymiyyan reading of theistic natural signs, on the epistemic function of Qur'anic āyāt as theistic evidence. (shrink)

Unjustifiable assumptions about sex and gender roles, the untamable potency of maleness, and gynophobic notions about women's bodies inform and influence a broad range of policy-making institutions in this society. In December 2004, the U.S. Court of Appeals for the Sixth Circuit continued this ignoble cultural pastime when they decided Everson v. Michigan Department of Corrections. In this decision, the Everson Court accepted the Michigan Department of Correction's claim that “the very manhood” of male prison guards both threatens the safety (...) of female inmates and violates the women's “special sense of privacy in their genitals” and declared that sex-specific employment policies for prison guards is not impermissibly discriminatory. I believe that the Court's decision relies on unacceptable stereotypes about sex, gender and sexuality and it significantly undermines Title VII's power to end discriminatory employment practices. (shrink)

This chapter aims to draw on the critical threads of those vibrant theological conversations within the formative years of Islamic thought in considering the different theological models of the Divine within the broader Islamic tradition under the purview of classical theism as it is understood today in the contemporary philosophy of religion. In doing so, it makes reference to the major strands within the theological (‘ilm al- kalām & atharī scripturalism) and philosophical (falsafa) schools of the Islamic tradition. It aims (...) to consider how these different trends, schools, and thinkers construct a model of God in light of the classical and neo-classical theistic model of God. (shrink)

Abstract: Sign language recognition is one of the most rapidly expanding fields of study today. Many new technologies have been developed in recent years in the fields of artificial intelligence the sign language-based communication is valuable to not only deaf and dumb community, but also beneficial for individuals suffering from Autism, downs Syndrome, Apraxia of Speech for correspondence. The biggest problem faced by people with hearing disabilities is the people's lack of understanding of their requirements. In this paper we try (...) to fill this gap. By trying to translate sign language using artificial intelligence algorithms, we focused in this paper using transfer learning technique based on deep learning by utilizing a MobileNet algorithm and compared it with the previous paper results[10a], where we get in the Mobilenet algorithm on the degree of Accuracy 93,48% but the VGG16 the accuracy was 100% For the same number of images (43500 in the dataset in size 64*64 pixel ) and the same data split training data into training dataset (70%) and validation dataset(15%) and testing dataset(15%) and 20 epoch . (shrink)

Sign Language Recognition (SLR) aims to translate sign language into text or speech in order to improve communication between deaf-mute people and the general public. This task has a large social impact, but it is still difficult due to the complexity and wide range of hand actions. We present a novel 3D convolutional neural network (CNN) that extracts discriminative spatial-temporal features from photo datasets. This article is about classification of sign languages are not universal and are usually not mutually intelligible (...) although there are also similarities among different sign languages. They are the foundation of local Deaf cultures and have evolved into effective means of communication. Although signing is primarily used by the deaf and hard of hearing, hearing people also use it when they are unable to speak, when they have difficulty speaking due to a health condition or disability (augmentative and alternative communication), or when they have deaf family members, such as children of deaf adults. In this article we use the 43500 image in the dataset in size 64*64 pixel by use CNN Architecture and achieved 100% accuracy. (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)

This paper sets out a research agenda for a political theory of climate displacement, by critically examining one prominent proposal—the idea of a normative status for ‘climate refugees’—and by proposing an alternative. Drawing on empirical work on climate displacement, I show that the concept of the climate refugee obscures the complexity and heterogeneity of climate displacement. I argue that, because of this complexity and heterogeneity, approaches to climate displacement that put the concept of the climate refugee at their centre will (...) fail to treat like cases alike and relevantly different cases differently. In response to these failings, I outline an alternative—the pluralist theory of climate displacement—which confronts the specific challenges that climate displacement poses in different practical and institutional contexts, whilst also treating climate displacement as a unified phenomenon at the second-order level of burden-sharing. (shrink)

This article reviews three books written by Larry May concerning the foundations of international criminal law: Crimes Against Humanity: A Normative Account (2005), War Crimes and Just War (2007), and Aggression and Crimes Against Peace (2008).

. This article seeks to outline how a Muslim believer can deflect a defeater for Islamic belief put forward by Erik Baldwin and Tyler McNabb. In doing so, it aims to reject the suggestion that an Islamic religious epistemology is somehow antithetical to a model of Reformed epistemology which is not fully compatible with Plantingian. Taken together with previous work on Islam and RE, the article not only aims to provide reason to think that Baldwin and McNabb’s proposed epistemic defeater (...) for Islamic belief isn’t problematic, it also seeks to show how the concerns raised by Baldwin and McNabb over a Plantingian model of RE in Islamic milieu, are no longer tenable. (shrink)

This article responds to Nir Eisikovits’ recent book Sympathizing with the Enemy: Reconciliation, Transitional Justice, Negotiation (Martinus Nijhoff Publishers, 2010).

The most public-facing forms of contemporary Darwinism happily promote its worldview ambitions. Popular works, by the likes of Richard Dawkins, deflect associations with eugenics and social Darwinism, but also extend the reach of Darwinism beyond biology into social policy, politics, and ethics. Critics of the enterprise fall into two categories. Advocates of Intelligent Design and secular philosophers (like Mary Midgley and Thomas Nagel) recognise it as a worldview and argue against its implications. Scholars in the rhetoric of science or science (...) communication, however, typically take the view that Darwinism isn't a worldview, but a scientific theory, which has been improperly embellished by some; they uphold the distinction between is and ought and argue that science is restricted to the former. This prompts an is–ought problem on another level. I catalogue the ways in which Darwinism plainly is a worldview and why commentators' beliefs that it ought not to be distorts their analysis. Hence, it is their own worldview that precludes them from accepting Darwinism's worldview implications. (shrink)

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

Past work has demonstrated that people’s moral judgments can influence their judgments in a number of domains that might seem to involve straightforward matters of fact, including judgments about freedom, causation, the doing/allowing distinction, and intentional action. The present studies explore whether the effect of morality in these four domains can be explained by changes in the relevance of alternative possibilities. More precisely, we propose that moral judgment influences the degree to which people regard certain alternative possibilities as relevant, which (...) in turn impacts intuitions about freedom, causation, doing/allowing, and intentional action. Employing the stimuli used in previous research, Studies 1a, 2a, 3a, and 4a show that the relevance of alternatives is influenced by moral judgments and mediates the impact of morality on non-moral judgments. Studies 1b, 2b, 3b, and 4b then provide direct empirical evidence for the link between the relevance of alternatives and judgments in these four domains by manipulating (rather than measuring) the relevance of alternative possibilities. Lastly, Study 5 demonstrates that the critical mechanism is not whether alternative possibilities are considered, but whether they are regarded as relevant. These studies support a unified framework for understanding the impact of morality across these very different kinds of judgments. (shrink)

This book examines autism from the tradition of analytic philosophy, working from the premise that Autism Spectrum Disorders raise interesting philosophical questions that need to be and can be addressed in a manner that is clear, jargon-free, and accessible. The goal of the original essays in this book is to provide a philosophically rich analysis of issues raised by autism and to afford dignity and respect to those impacted by autism by placing it at the center of the discussion.

Chapter: WHITE PRIVILEGE AND THE COLOR OF FEAR This chapter focuses on the role that power, innocence and ignorance play in maintaining the position of white privilege. There are times when white people use their privilege in ways that overtly attempt to put and keep people of color in their places, but more often white privilege is less obvious. White privilege does not stand out in white peoples’ behavior at all times. When white behavior is normalized, it is masked. At (...) these times, white privilege and power hide behind the masks of innocence and the masks of ignorance. White people can mask from themselves and others their location with relations to power. In the film, The Color of Fear, David C. hides his power. As he hides his power, he keeps his privilege invisible, that is, behind a mask. In this chapter, we focus on the masking and unmasking of innocence and ignorance to get a better look at how the process of normalization of these masks makes whiteness powerful and consequently hides white privilege. The logic of power and privilege is reflected in the following relationship: -/- innocence + ignorance = Invisibility (of White Privilege) -/- . (shrink)

Whiteness theorists argue that whiteness has two essential features. First, whiteness colonizes, appropriates and controls the Other. Whiteness is, then, racist.Second, whiteness is constructed unwittingly. Whites are, it is claimed, unaware of the harms they inflict on a genocidal scale because whiteness, like the air we breathe, is “invisible” to those who construct it and are constructed by it. Whiteness is, then, innocent. I think defining whiteness as innocent racism is troubling for two reasons. First, it leaves whites unaccountable for (...) the acts of racism they perpetuate. Second, I think that the claim that whiteness is invisible “like the air we breathe,” while a powerful and fascinating metaphor, is mistaken. I will argue that whiteness is closeted; and while the closet makes the acknowledgement of whiteness difficult, it does not make it impossible. Thus, though closeted, whites are morally accountable for the acts of racism they commit. (shrink)

After stating "I am gay" Navy Lieutenant Paul G. Thomasson was honorably discharged from the military. In Thomasson v. Perry (1996), the United States Court of Appeals for the Fourth District affirmed Thomasson's discharge. Thomasson is now considered the leading case evaluating the U.S. military's "don't ask, don't tell" policy. In this paper, I show that the court's analysis of the Department of Defense policy rests of two unarticulated and undefended assumptions about sexuality. The first is that an act of (...) sex is essentially defined in terms of the sexual orientation of the persons engaging in that act. The second is that whether or not a person is an open homosexual determines the essential nature of the homosexual acts of others. I conclude that both assumptions are untenable, therefore the "don't ask, don't tell" policy is indefensible. (shrink)

What is so striking about Breaking Bad is how centrally impairment and disability feature in the lives of the characters of this series. It is unusual for a television series to cast characters with visible or invisible impairments. On the rare occasions that television shows do have characters with impairments, these characters serve no purpose other than to contribute to their ‘Otherness.’ Breaking Bad not only centralizes impairment, but impairment drives and sustains the story lines. I use three interrelated themes (...) from Disability Scholarship to analyze Breaking Bad. The first theme, Bodily Control, is that good bodies are controlled bodies and that uncontrolled, messy bodies are frightening, bad bodies. Indeed, the messiness of impairment and disability is so bad, that impaired and disabled individuals are excluded or shut out or excluded from many areas of public life. The second theme, Normalcy, is that the effect of hiding away impairment, of attempting to conceal disability, is that society becomes defined by, and structured around, the concept of normalcy. Normalcy, being normal, attaining and maintaining normalcy, is the preoccupation of most in society. To fail to be normal, or to fall from what is considered to be normal, is a source of tremendous anxiety for most people. These two themes, Bodily Control and Normalcy are conceptually connected: impairment, disease and dying are so feared because they are socially invisible and, therefore unknown and unknowable. They are the undiscussable taboos. The third theme, Bodily Realism, is that having a realistic view of the body, which would at minimum require accepting the fact that human bodies are fragile things, prone to disease and accident and are ultimately destined to die, makes one more at ease in the world, and able to live better lives and live as a better person. Indeed, so the argument goes, our lives would be richer, more rewarding—emotionally and morally—if we cared less about normalcy because of a dread of abnormalcy, but instead learned to accept if not positively value the physical variability of human existence. (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 National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

If one can judge a society by how it treats its prisoners, one can surely judge a society by how it treats cognitively- and learning-impaired children. In the United States children with physical and cognitive impairments are subjected to higher rates of corporal punishment than are non-disabled children. Children with disabilities make up just over 13% of the student population in the U.S. yet make up over 18% of those children who receive corporal punishment. Autistic children are among the most (...) likely to receive corporal punishment. -/- Although they may deny or redescribe particular instances of corporal punishment or their use of restraints, educators defend such actions as legitimate punishment. In this paper, I assess the logic underlying the use of restraints and corporal punishment on autistic children by educators. The rationalizations for the corporal punishment or restraint of autistics stems from the educator’s desire to control the autistic children so as to end typical autistic behaviors such as rocking, repetitive verbalizations, or “flapping” but also the autistic child’s non-affective responses such as not appearing to feel remorse or shame or the absence of a verbal acknowledgement of remorse or shame. The educators assume that the autistic’s failure to exhibit the desired responses is evidence of the autistic’s moral incorrigibility and is, therefore, evidence of the appropriateness of corporal punishment. But this assumption of the incorrigibility of the autistic child is questionable. -/- Indeed accepting this incorrigibility assumption reveals two important problems. First, instructors using physical punishment on autistic children do not understand autism. Second, they are not working with a tenable conception of punishment. Any action undertaken to induce socially acceptable behaviors (whether it be the end of autistic acts or responses such as remorse) is to fail to understand what the legitimate punishment of children is about. (shrink)

Although typical arguments for knitting are that it is useful, therapeutic or the latest trend, I argue that knitting can play a life-changing part in the creation of a person’s self. Knitting can be a genuinely powerful activity, one worthy of respect and admiration.

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

How can researchers use race, as they do now, to conduct health-care studies when its very definition is in question? The belief that race is a social construct without “biological authenticity” though widely shared across disciplines in social science is not subscribed to by traditional science. Yet with an interdisciplinary approach, the two horns of the social construct/genetics dilemma of race are not mutually exclusive. We can use traditional science to provide a rigorous framework and use a social-science approach so (...) that “invisible” factors are used to adjust the design of studies on an as-needed basis. One approach is to first observe health-care outcomes and then categorize the outcomes, thus removing genetic differences as racial proxies from the design of the study. From the outcomes, we can then determine if there is a pattern of conceivable racial categories. If needed, we can apply dynamic notions of race to acknowledge bias without prejudice. We can use them constructively to improve outcomes and reduce racial disparities. Another approach is nearly identical but considers race not at all: While analyzing outcomes, we can determine if there are biological differences significant enough to identify classifications of humans. That is, we look for genetic patterns in the outcomes and classify only those patterns. There is no attempt to link those patterns to race. (shrink)

Abstract -/- “The Obvious Invisibility of the Relationship Between Technology and Social Values” -/- We all too often assume that technology is the product of objective scientific research. And, we assume that technology’s moral value lies in only the moral character of its user. Yet, in order to objectify technology in a manner that removes it from a moral realm, we rely on the assumption that technology is value neutral, i.e., it is independent of all contexts other than the context (...) in which it is used morally or immorally by someone. However, there is a power to technology. At the very least, technology should be seen as reflecting the values that it rises from: a developmental context. Consequently, we can make the invisible moral realm visible as we investigate the relationship between culture and technology. Pragmatically, we can trace how cultural values inform what counts as a scientific question. When we look at the 1980s epidemiological model for AIDS we see how the presuppositions within a culture frame the type of question asked, i.e. What population do we see AIDS occurring in? This question initially leads scientific research away from actual individual behaviors until a different question is asked that leads the question towards behavioral epidemiological models rather than population models. Secondly, we can make visible the circumstance that depicts that what constitutes a scientific problem has a direct relationship to the types of technologies that are developed. We can more clearly see this circular relationship between culture and technology by looking at clinical research and practice regarding heart disease. Men who were dying of diagnosed heart disease were showing symptoms of problems in large arteries of the heart. Women were also dying of heart disease, but since their large arteries were not overwhelmingly compromised they were not being properly diagnosed until recently. Different technologies and protocol were needed to “see” different symptoms in the smaller vessels of women. Thirdly, I show how the types of technology developed, in turn, can create new values or enhance preexisting values within a culture. DNA research can be used to investigate long, unanswered questions about qualitative dimensions of life in quantitative manners. Yet, long held unanswered questions about a biological basis of race or intelligence are themselves rarely challenged as uninteresting or misguided even when they are tied to prejudicial qualitative assumptions if the chance of a “scientific” answer is possible. When existing technologies or modifications of existing technologies can be used they seem to direct human reactions and behaviors in predictable ways. The technologies themselves may be said to direct culture in ethically valenced manners. (shrink)

I argue that, if doxastic involuntarism is true, then we should reconceive what are traditionally called reasons for belief. The truth of doxastic involuntarism would rule out a certain understanding of reasons for belief according to which they are reasons to form, alter, or relinquish beliefs. Thus, reconceiving reasons for belief would require reconceiving doxastic obligations. I argue that, in fact, a reconception of reasons for belief warrants abandoning the notion of doxastic obligations, understood as obligations to perform acts of (...) belief formation, alteration, or relinquishment. Instead, the only sorts of obligations we would have that concern our doxastic states would be aretaic or practical. (shrink)

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

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

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

American Sign Language, or ASL as its acronym is commonly known, is a fascinating language, and many people outside of the Deaf community have begun to recognize its value and purpose. It is a visual language consisting of coordinated hand gestures, body movements, and facial expressions. Sign language is not a universal language; it varies by country and is heavily influenced by the native language and culture. The American Sign Language alphabet and the British Sign Language alphabet are completely contrary. (...) Fingerspelling is one-handed in ASL and two-handed in BSL, with the exception of the letter C. AI technologies, particularly deep learning, can play an important role in breaking down communication barriers between deaf or hearing-impaired people and other communities, significantly contributing to their social inclusion. Recent advances in sensing technologies and AI algorithms have paved the way for the development of a wide range of applications aimed at meeting the needs of the deaf and hearing-impaired communities. To that end, the purpose of this paper is By attempting to translate sign language using artificial intelligence algorithms, we focused in this paper on a transfer learning technique based on deep learning using a ResNet algorithm and compared it to previous papers in which we used VGG19[1]and mobileNet [2], where we get in the ResNet algorithm on the degree of Accuracy 93,48% e number of images (43500 in the dataset in size 64*64 pixel ) and the data split training data into training dataset (70%) and validation dataset(15%) and testing dataset(15%) and 20 epoch. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

there is a communication gap between hearing-impaired people and those with normal hearing, sign language is the main means of communication in the hearing-impaired population. Continuous sign language recognition, which can close the communication gap, is a difficult task since the ordered annotations are weakly supervised and there is no frame-level label. To solve this issue, we compare the accuracy of each model using two deep learning models, Inception and Xception . To that end, the purpose of this paper is (...) By attempting to translate sign language using deep learning models, we focused in this paper a comparing between Inception and Xception ¬¬¬¬¬ algorithm and compared it to previous papers in which we used VGG19[1], mobileNet [2], where we get in the Inception and Xception algorithm on the degree of Accuracy 99.32%, 99,43% respectively. number of images (29000 in the dataset in size 75*75 pixel ) and the data split training data into training dataset (70%) and validation dataset(15%) and testing dataset(15%) and 20 epoch. (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 desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (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)

This chapter aims to lay out a map of the diverse epistemological perspectives within the Islamic theological tradition, in the conceptual framework of contemporary analytic philosophy of religion. In order achieve that goal, it aims to consider epistemological views in light of their historic context, while at the same time seeking to “translate” those broadly medieval perspectives into contemporary philosophical language. In doing so, the chapter offers a succinct overview of the main epistemic trends within the Islamic theological tradition concerning (...) religious epistemology. The chapter is divided into two main sections designated for discussions of differing accounts found in distinct trends of the tradition, namely the Rationalist and Traditionalist trends. The discussion concerning the Rationalist trend focuses on the philosophical-theologians of the dominant Mu’tazilite, Ash’arite, and Maturidite schools. The section on Islamic Traditionalism focuses on the Atharite scripturalism of Ibn Qudāma, and in particular the thought of Ibn Taymiyya. In order to map out these historic positions in light of contemporary religious epistemology, reference is made to a threefold typology of current views in the literature: (1) theistic evidentialism, (2) reformed epistemology, and (3) fideism. As such, the remainder of the chapter will attempt to outline the different approaches toward religious epistemology in the Islamic theological tradition with this threefold typology in mind. (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.

In a recent paper in this journal Duncan Pritchard responds to an objection to the modal account of risk pressed by Ebert, Smith and Durbach ( 2020 ). In this paper, I expand upon the objection and argue that it still stands. I go on to consider a more general question raised by this exchange – whether risk is ‘objective’, or whether it is something that varies from one perspective to another.

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)

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)