This book is co-written in a lively, engaging form by Karen Carr, from the discipline of religious studies and Philip Ivanhoe, whose background is in the disciplines of religious studies and Asian languages and philosophy. Unlike typical co-authorship, these two authors write separate pieces about Zhuangzi and Soren Kierkegaard and then together offer a combined vision. Refreshingly, the emphasis is on contrast of exemplars of two different and irreconcilable ways instead of comparison between similar thinkers. The two authors are (...) to be congratulated for this in-depth interchange both with each other and with these two iconoclastic thinkers. It is hoped that this innovative genre-a study of contrasts that partially crosses disciplines, maintains the integrity of each coauthor, and yet attempts a comprehensive vision-will provide inspiration for comparative studies in the future. (shrink)

I argue for the Wittgensteinian thesis that mathematical statements are expressions of norms, rather than descriptions of the world. An expression of a norm is a statement like a promise or a New Year's resolution, which says that someone is committed or entitled to a certain line of action. A expression of a norm is not a mere description of a regularity of human behavior, nor is it merely a descriptive statement which happens to entail a norms. The view can (...) be thought of as a sort of logicism for the logical expressivist---a person who believes that the purpose of logical language is to make explicit commitments and entitlements that are implicit in ordinary practice. The thesis that mathematical statements are expression of norms is a kind of logicism, not because it says that mathematics can be reduced to logic, but because it says that mathematical statements play the same role as logical statements. ;I contrast my position with two sets of views, an empiricist view, which says that mathematical knowledge is acquired and justified through experience, and a cluster of nativist and apriorist views, which say that mathematical knowledge is either hardwired into the human brain, or justified a priori, or both. To develop the empiricist view, I look at the work of Kitcher and Mill, arguing that although their ideas can withstand the criticisms brought against empiricism by Frege and others, they cannot reply to a version of the critique brought by Wittgenstein in the Remarks on the Foundations of Mathematics. To develop the nativist and apriorist views, I look at the work of contemporary developmental psychologists, like Gelman and Gallistel and Karen Wynn, as well as the work of philosophers who advocate the existence of a mathematical intuition, such as Kant, Husserl, and Parsons. After clarifying the definitions of "innate" and "a priori," I argue that the mechanisms proposed by the nativists cannot bring knowledge, and the existence of the mechanisms proposed by the apriorists is not supported by the arguments they give. (shrink)

This paper draws attention to a divergence in approach to the social between Ken Gergen’s radical form of social constructionism and the more moderate constructionist approaches exemplified by the thinking of Shaun Gallagher, Jan Slaby and Karen Barad. Specifically, I argue that the latter stop just short of radical constructionism’s ontological and ethical implications. The ethical question for Gergen is not whether and how we achieve just relations but whether and how we deal with the struggle between competing goods, (...) how we manage to think beyond justice understood as singular traditions of the good, so that we can focus on enriching our traditions with alternative intelligibilities, thereby expanding the inclusiveness of our relational structures. Viewing the wayward person or group through Gergen’s lens of multi-being rather than the morality of blameful justice encourages us to strive for an ethics of responsibility without succumbing to a moralism of culpability. (shrink)

Loneliness is a near-universal experience. It is particularly common for individuals with (so-called) psychopathological conditions or disorders. In this paper, we explore the experiential character of loneliness, with a specific emphasis on how social goods are experienced as absent in ways that involve a diminished sense of agency and recognition. We explore the role and experience of loneliness in three case studies: depression, anorexia nervosa, and autism. We demonstrate that even though experiences of loneliness might be common to many psychopathologies, (...) these experiences nevertheless have distinctive profiles. Specifically, we suggest that: (i) loneliness is often a core characteristic of depressive experience; (ii) loneliness can drive, and even cement, disordered eating practices and anorectic identity in anorexia nervosa; iii) loneliness is neither a core characteristic of autism nor a driver but is rather commonly experienced as stemming from social worlds, environments, and norms that fail to accommodate autistic bodies and their distinctive forms of life. We aim to do justice to the pervasiveness of loneliness in many — if not all — psychopathologies, while also highlighting the need to attend to psychopathology-specific experiences of loneliness, agency, and (non-)recognition. (shrink)

I am grateful to Donald Ainslie, Lisa Austin, Michael Blake, Abraham Drassinower, David Dyzenhaus, George Fletcher, Robert Gibbs, Louis-Philippe Hodgson, Sari Kisilevsky, Dennis Klimchuk, Christopher Morris, Scott Shapiro, Horacio Spector, Sergio Tenenbaum, Malcolm Thorburn, Ernest Weinrib, Karen Weisman, and the Editors of Philosophy & Public Affairs for comments, and audiences in the UCLA Philosophy Department and Columbia Law School for their questions.

In addiction, apparently causally significant phenomena occur at a huge number of levels; addiction is affected by biomedical, neurological, pharmacological, clinical, social, and politico-legal factors, among many others. In such a complex, multifaceted field of inquiry, it seems very unlikely that all the many layers of explanation will prove amenable to any simple or straightforward, reductive analysis; if we are to unify the many different sciences of addiction while respecting their causal autonomy, then, what we are likely to need is (...) an integrative framework. In this paper, we propose the theory of “Externalist” or “4E” – for extended, embodied, embedded, and enactive – cognition, which focuses on the empirical and conceptual centrality of the wider extra-neural environment to cognitive and mental processes, as a candidate for such a framework. We begin in Section 2 by outlining how such a perspective might apply to psychiatry more generally, before turning to some of the ways it can illuminate addiction in particular: Section 3 points to a way of dissolving the classic dichotomy between the “choice model” and “disease model” in the addiction literature; Section 4 shows how 4E concepts can clarify the interplay between the addict’s brain and her environment; and Section 5 considers how these insights help to explain the success of some recovery strategies, and may help to inform the development of new ones. (shrink)

As technology improves, artificial systems are increasingly able to behave in human-like ways: holding a conversation; providing information, advice, and support; or taking on the role of therapist, teacher, or counsellor. This enhanced behavioural complexity, we argue, encourages deeper forms of affective engagement on the part of the human user, with the artificial agent helping to stabilise, subdue, prolong, or intensify a person’s emotional condition. Here, we defend a fictionalist account of human/AI interaction, according to which these encounters involve an (...) elaborate practise of imaginative pretence: a make-believe in which the artificial agent is attributed a life of its own. We attend, specifically, to the temporal characteristics of these fictions, and to what we imagine artificial agents are doing when we are not looking at them. (shrink)

Why is gauge symmetry so important in modern physics, given that one must eliminate it when interpreting what the theory represents? In this paper we discuss the sense in which gauge symmetry can be fruitfully applied to constrain the space of possible dynamical models in such a way that forces and charges are appropriately coupled. We review the most well-known application of this kind, known as the 'gauge argument' or 'gauge principle', discuss its difficulties, and then reconstruct the gauge argument (...) as a valid theorem in quantum theory. We then present what we take to be a better and more general gauge argument, based on Noether's second theorem in classical Lagrangian field theory, and argue that this provides a more appropriate framework for understanding how gauge symmetry helps to constrain the dynamics of physical theories. (shrink)

We present experimental evidence that an interpretation was accurate. Current wisdom notwithstanding, we could interpret from the text alone because its information is redundant: repetition provides internal checks. Knowing neither dreamer nor their associations we made falsifiable predictions that we tested by subsequently gathering information about the dreamer. Predictions were supported. Results were repeated with seven additional dreams. Each dream was tightly crafted, used humor, drama or hyperbole to penetrate the dreamer’s defenses, and furthered the emergence of personality. Our experiment (...) compliments fMRI and statistics because it studies a whole text as a unique narrative: one iteration identified healing steps during therapy; another confirmed the psychological meaning of a myth. Our experiment might generate a body of objective knowledge about interpretation and make interpretation itself more accurate. In the US 20% live with mental illness. Our experiment supports talk therapy against pressure from the drug and insurance industries. (shrink)

(NOTE: This is a transcript of the class. FOR THE FULL PAPER please click on "Maxson J McDowell" above.) An edited transcript of an experiment performed within a class on dream interpretation. Knowing only the dreamer’s age and gender, we interpreted his dream from its text. Our interpretation included predictions about the dreamer's psychological issues, and about his defenses. It also identified a series of jokes within the dream which would tend to penetrate the dreamer's defenses. When we had finished (...) our 'blind' interpretation, the bringer of the dream gave us more information about the dreamer against which we tested the accuracy of our predictions. A paper on this experiment has been submitted for publication. (shrink)

In an online, participatory class, we interpreted The Dream of Mercury knowing nothing of the dreamer and having none of the dreamer’s associations. Our interpretation included a series of falsifiable predictions about the dreamer. When it was complete, we asked the bringer of the dream (who had until then been silent and was not visible to us) to give us more information about the dreamer. The dreamer is instructed to confront a friendship he had abandoned and, when he does so, (...) is frightened by the inner life he discovers. This record is another iteration of an experiment that will be described more fully in the paper 'The Dream of the Six-Legged Dog: An Experimental System to Test Meaning,' soon to be published. This iteration repeats and confirms the evidence given in that paper. AN AUDIO-RECORD OF COMPLETE CLASS: link is given on first page of the paper you download here. (shrink)

In an online, participatory class, we interpreted The Dream of the Tabby Cats knowing nothing of the dreamer beyond age and gender, and having none of the dreamer’s associations. Our interpretation included a series of predictions about the dreamer. When it was complete, we asked the bringer of the dream (who had until then been silent and was not visible to us) to give us more information about the dreamer. Later the dreamer herself gave us more information. Of six predictions (...) four were confirmed. The dreamer’s apartment is repeatedly disturbed and, each time, a new cat appears. This record is another iteration of an experiment that will be described more fully in the paper The Dream of the Six-Legged Dog: An Experimental System to Test Meaning, soon to be published. This iteration repeats and confirms the evidence given in that paper. AUDIO RECORD OF CLASS AVAILABLE: link is on first page of the paper you download from this page. (shrink)

(NOTE: This is a transcript of the class. FOR THE FULL PAPER, please click on "Maxson J. McDowell".) A complete transcript of an experiment performed within a class on dream interpretation. Knowing only the dreamers age and gender, we interpreted his dream from its text. Our interpretation included predictions about the dreamer's psychological issues, and about his defenses. It also identified a series of jokes within the dream which would tend to penetrate the dreamer's defenses. When we had finished our (...) 'blind' interpretation, the bringer of the dream gave us more information about the dreamer against which we tested the accuracy of our predictions. A paper on this experiment has been submitted for publication. A link to an AUDIO-RECORDING of this class is given on the first page of this transcript. (shrink)

In an online, participatory class, we interpreted The Dream of the Flaming Sword knowing nothing of the dreamer beyond age and gender, and having none of the dreamer’s associations. Our interpretation included a series of predictions about the dreamer. When it was complete, we asked the bringer of the dream (who had until then been silent and who also gave no visual feedback to our discussion) to give us more information about the dreamer. Eight months later the bringer gave us (...) further information from the dreamer. Our predictions were mostly confirmed. In the dream, the dreamer’s identity is repeatedly questioned. -/- This record is another iteration of an experiment that is described more fully in the paper The Dream of the Six-Legged Dog, soon to be published. This iteration repeats and confirms the evidence given in that paper. -/- AUDIO RECORD OF THE CLASS ABOUT THE FLAMING SWORD: link is on the title page of the paper you can download here. (shrink)

In an online, participatory class, we interpreted 'The Dream of Geese Nesting in Trees' knowing nothing of the dreamer beyond age and gender, and having none of the dreamer’s associations. Our interpretation included predictions about the dreamer. When it was complete, we asked the bringer of the dream (who had until then been mostly silent and who also gave no visual feedback to our discussion) to give us more information about the dreamer. Our main predictions were confirmed. Goslings are falling (...) on the dreamer’s head. This record is another iteration of an experiment that will be described more fully in the paper, 'The Dream of the Six-Legged Dog: An Experimental System that Tests Meaning,' soon to be published. This iteration repeats and confirms the evidence given in that paper. AUDIO RECORD OF COMPLETE CLASS: link is at top of paper you can download from this page. (shrink)

This paper integrates symbolic thought and experimental research. We hypothesized that symbolic narratives provide homeostasis for the complex adaptive system that is personality. Our interpretation of a dream was based, in part, on this hypothesis. We found that the dream retold the myth of Saturn. When, by direct experiment, we tried to falsify our interpretation, our results supported our interpretation and thereby supported our hypothesis. Previously, evidence for this hypothesis had been only anecdotal. __________________________________________ For an audio-record of entire class: (...) link is given on 1st page of the text you download from this page. (shrink)

In an online, participatory class, we interpreted The Dream of the White House knowing nothing of the dreamer and having none of the dreamer’s associations. Our interpretation included a series of falsifiable predictions about the dreamer. When it was complete, we asked the bringer of the dream (who had until then been silent and was not visible to us) to give us more information about the dreamer. Of 17 predictions 15 were confirmed. The dreamer suffers dislocation and loss until she (...) asks a female manager for help. This record is another iteration of an experiment that will be described more fully in the paper 'The Dream of the Six-Legged Dog: An Experimental System to Test Meaning,' soon to be published. This iteration repeats and confirms the evidence given in that paper. More than any of the other iterations, it details how talk therapy promotes personality reorganization. It then supports these observations with experimental evidence. Because it demonstrates how talk therapy works, this iteration supports talk therapy against pressure from the drug and insurance corporations. AUDIO-RECORDING OF WHOLE CLASS: link provided on first page of the paper you download here. (shrink)

Arguably the biggest challenge in analyzing English tense is to account for the double access interpretation, which arises when a present tensed verb is embedded under a past attitude—e.g., "John said that Mary is pregnant". Present-under-past does not always result in a felicitous utterance, however—cf. "John believed that Mary is pregnant". While such oddity has been noted, the contrast has never been explained. In fact, English grammars and manuals generally prohibit present-under-past. Work on double access, on the other hand, has (...) either disregarded the oddity (e.g., Abusch 1997: 39) or treated it as a reflex of a particular dialect (e.g., Kratzer 1998: 14). The goal of the paper is to argue—based on a corpus study—that a present-under-past sentence is grammatical, but modulated by two, interacting pragmatic phenomena: cessation and parentheticality. (shrink)

Research on the ethics of algorithms has grown substantially over the past decade. Alongside the exponential development and application of machine learning algorithms, new ethical problems and solutions relating to their ubiquitous use in society have been proposed. This article builds on a review of the ethics of algorithms published in 2016, 2016). The goals are to contribute to the debate on the identification and analysis of the ethical implications of algorithms, to provide an updated analysis of epistemic and normative (...) concerns, and to offer actionable guidance for the governance of the design, development and deployment of algorithms. (shrink)

Public discussions of political and social issues are often characterized by deep and persistent polarization. In social psychology, it’s standard to treat belief polarization as the product of epistemic irrationality. In contrast, we argue that the persistent disagreement that grounds political and social polarization can be produced by epistemically rational agents, when those agents have limited cognitive resources. Using an agent-based model of group deliberation, we show that groups of deliberating agents using coherence-based strategies for managing their limited resources tend (...) to polarize into different subgroups. We argue that using that strategy is epistemically rational for limited agents. So even though group polarization looks like it must be the product of human irrationality, polarization can be the result of fully rational deliberation with natural human limitations. (shrink)

The empirical phenomenon at the center of this paper is projection, which we define (uncontroversially) as follows: (1) Definition of projection An implication projects if and only if it survives as an utterance implication when the expression that triggers the implication occurs under the syntactic scope of an entailment-cancelling operator. Projection is observed, for example, with utterances containing aspectual verbs like stop, as shown in (2) and (3) with examples from English and Paraguayan Guaraní (Paraguay, Tupí-Guaraní).1 The Guaraní example in (...) (2) and its English translation have at least the following implications: (i) Carla has previously smoked, and (ii) Carla stopped smoking. The first but not the second of these implications is also conveyed by the question version of sentence (2), as in (3a), or when (2) is embedded under entailment-cancelling sentential operators, such as negation, as in (3b), the antecedent of a conditional, as in (3c), or an epistemic modal, as in (3d). Hence, by the definition in (14), the first but not the second implication of (2) projects. (shrink)

Attention Deficit Hyperactivity Disorder (ADHD) continues to be controversial with arguments for and against its veracity being waged by individuals representing a variety of disciplines from behavioral scientists to philosophers. Our perspective focuses on the epistemological underpinnings of what is now commonly known as ADHD. Its ignominious history and current disputes may stem from a "pessimistic" epistemology, meaning that truth is only the province of persons in authority and power. The authoritative organizations that govern the diagnostic labels and criteria are (...) the American Psychiatric Association and their Diagnostic and Statistical Manual and the World Health Organization that sponsors the International Classification of Disease. We contrast the pessimistic epistemology with criteria for truth from the scientific method. Although scientific scrutiny has been and is being applied subsequent to "authoritarian edicts" of the disorder, we opine that ADHD currently does not have status beyond that of the "hypothetical construct." Moreover, current brain-based causal models have failed to provide rigorous supporting data that comes from testing falsifiable hypotheses. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

In an online, participatory class, we interpreted 'The Dream of the Three Orcas' knowing nothing of the dreamer beyond age and gender, and having none of the dreamer’s associations. -/- Our interpretation included nine predictions about the dreamer. When it was complete, we asked the bringer of the dream (who had not been present before our interpretation was complete) to give us more information about the dreamer. Later the dreamer also gave us more information. Our predictions were mostly confirmed. The (...) dreamer is standing on beach when huge orca-like floats appear. -/- This record is another iteration of an experiment that is described more fully in the paper 'The Dream of the Six-Legged Dog: An Experimental System that Tests Symbolic Meaning,' soon to be published. This iteration repeats and confirms the evidence given in that paper. ONLINE AUDIO RECORD OF ENTIRE ORCAS' CLASS : link is on title page of the paper you can download here. (shrink)

The scope of this article is to propose a reflection about the concept of citizenship presented by Aristotle in his work “Politics”, and which people were considered citizens then in comparison to nowadays. There is no intention to make a deep historical assessment about the particularities of each period of time, but analyse the characteristics which kept some groups inside of the political life and as well kept other groups away from it, in order to demonstrate how strong is the (...) maintenance of the estrangement between people who achieve everything is possible to, whereas other groups cannot achieve even what is deemed to be worthy by law. Keywords: citizenship; citizen; state; law; minorities; achievement. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The purpose of this symposium is to explore the ways in which literature, broadly construed to include poetry and narrative in a variety of modes of representation, can change the world by providing interventions in justice. Our approach foregrounds the relationship between the activity demanded by some individual literary works and some categories of literary work on the one hand and the way in which those works can make a tangible difference to social reality on the other. We consider three (...) types of active literary engagement: doing philosophy, ideological critique, and necessary rather than contingent performance. Kate Kirkpatrick opens with Kamel Daoud’s The Meursault Investigation (2013), reading the narrator as not only a critic of colonial and postcolonial discourse but also a literary exemplar of the search for justice when it is difficult to know to what level of explanation to attribute its absence. Rafe McGregor demonstrates how the final season of Prime Video’s The Man in the High Castle (2015–19) makes a radical break from the previous three, exposing the misanthropy at the core of right-wing populism and calling for a fundamentally democratic response from the left. Finally, Karen Simecek argues that poetry in performance has a potentially reparative function for the ethically lonely – the vulnerable, the oppressed, and the persecuted – in society. (shrink)

This article aims to describe the last 10 years of the collaborative scientific endeavors on polarization in particular and collective problem-solving in general by our multidisciplinary research team. We describe the team’s disciplinary composition—social psychology, political science, social philosophy/epistemology, and complex systems science— highlighting the shared and unique skill sets of our group members and how each discipline contributes to studying polarization and collective problem-solving. With an eye to the literature on team dynamics, we describe team logistics and processes that (...) we believe make our multidisciplinary team persistent and productive. We emphasize challenges and difficulties caused by disciplinary differences in terms of terminology, units/levels of analysis, methodology, and theoretical assumptions. We then explain how work disambiguating the concepts of polarization and developing an integrative theoretical and methodological framework with complex systems perspectives has helped us overcome these challenges. We summarize the major findings that our research has produced over the past decade, and describe our current research and future directions. Last, we discuss lessons we have learned, including difficulties in a “three models” project and how we addressed them, with suggestions for effective multidisciplinary team research. (shrink)

Despite the frequency of stillbirths, the subsequent implications are overlooked and underappreciated. We present findings from comprehensive, systematic literature reviews, and new analyses of published and unpublished data, to establish the effect of stillbirth on parents, families, health-care providers, and societies worldwide. Data for direct costs of this event are sparse but suggest that a stillbirth needs more resources than a livebirth, both in the perinatal period and in additional surveillance during subsequent pregnancies. Indirect and intangible costs of stillbirth are (...) extensive and are usually met by families alone. This issue is particularly onerous for those with few resources. Negative effects, particularly on parental mental health, might be moderated by empathic attitudes of care providers and tailored interventions. The value of the baby, as well as the associated costs for parents, families, care providers, communities, and society, should be considered to prevent stillbirths and reduce associated morbidity. (shrink)

Extant theoretical work on the political resource curse implies that dependence on resource revenues should decrease autocracies’ likelihood of democratizing but not necessarily affect democracies’ chances of survival. Yet most previous empirical studies estimate models that are ill-suited to address this claim. We improve upon earlier studies, estimating a dynamic logit model that interacts a continuous measure of resource dependence with an indicator of regime type using data from 166 countries, covering the period from 1816-2006. We find that an increase (...) in resource dependence at time t - 1 increases the likelihood of autocratic persistence at t, but has no appreciable effect on democratic survival. We go beyond existing empirical studies to show that increases in resource dependence have persistent and substantial cumulative effects on autocracies' likelihood of becoming democratic over the long-term, showing that the total effect of resource dependence on regime type is much larger than the short-term (one period) effect indicates. (shrink)

When interpreting the meanings of visual features in information visualizations, observers have expectations about how visual features map onto concepts (inferred mappings.) In this study, we examined whether aspects of inferred mappings that have been previously identified for colormap data visualizations generalize to a different type of visualization, Venn diagrams. Venn diagrams offer an interesting test case because empirical evidence about the nature of inferred mappings for colormaps suggests that established conventions for Venn diagrams are counterintuitive. Venn diagrams represent classes (...) using overlapping circles and express logical relationships between those classes by shading out regions to encode the concept of non-existence, or none. We propose that people do not simply expect shading to signify non-existence, but rather they expect regions that appear as holes to signify non-existence (the hole hypothesis.) The appearance of a hole depends on perceptual properties in the diagram in relation to its background. Across three experiments, results supported the hole hypothesis, underscoring the importance of configural processing for interpreting the meanings of visual features in information visualizations. (shrink)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: -/- The main aim of this review will be to assess the effects of changing practitioner empathy or patient expectations for all conditions. The main objective is to conduct a systematic review of randomised trials where the intervention involves manipulating either (a) practitioner empathy or (b) patient expectations, or (c) both.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (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)

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)

Nosotres, biólogues, ecologistas y otres profesionales dedicados a proteger la vida, les escribimos con una solicitud urgente. Les pedimos muy comedidamente que su organización o institución emita un comunicado oficial condenando la crisis en curso y abordando los impactos ambientales y humanitarios en Palestina.

This paper summarizes (in German) recent tendencies in the philosophy of the life sciences.

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

The aim of this workshop was to ask potential end-users of the citizens’ information pack on legal and ethical issues around ICTs the following questions: What is your knowledge of the EU’s General Data Protection Regulation, and what actions have you taken in response to these regulations? What challenges are you experiencing in ensuring the protection and security of your project data, and compliance with the GDPR, within existing data management processes/systems? What information/tools/resources do you need to overcome these challenges? (...) What are the best formats/channels for receiving, sharing and acting upon this information? What is the most appropriate structure/format for the citizens’ information pack? (shrink)

ICTs, personal data, digital rights, the GDPR, data privacy, online security… these terms, and the concepts behind them, are increasingly common in our lives. Some of us may be familiar with them, but others are less aware of the growing role of ICTs and data in our lives - and the potential risks this creates. These risks are even more pronounced for vulnerable groups in society. People can be vulnerable in different, often overlapping, ways, which place them at a disadvantage (...) to the majority of citizens; Table 3 in this guide presents some of the many forms and causes of vulnerability. As a result, vulnerable people need greater support to navigate the digital world, and to ensure that they are able to exercise their rights. This guide explains where such support can be found, and also answers the following questions: - What are the main ethical and legal issues around ICTs for vulnerable citizens? - Who is vulnerable in Europe? - How do issues around ICTs affect vulnerable people in particular? This guide is a resource for members of vulnerable groups, people who work with vulnerable groups, and citizens more broadly. It is also useful for data controllers1 who collect data about vulnerable citizens. While focused on citizens in Europe, it may be of interest to people in other parts of the world. It forms part of the Citizens’ Information Pack produced by the PANELFIT project, and is available in English, French, German, Italian and Spanish. You are welcome to translate this guide into other languages. Please send us a link to online versions in other languages, so that we can add them to the project website. (shrink)

In this paper I describe and defend an account of virtuous motivation that differs from what we might call ordinary moral motivation. It is possible to be morally motivated without being virtuously motivated. In the first half of the essay, I explore different senses of moral motivation and the philosophical puzzles and problems it poses. In the second half, I give an account of virtuous motivation that, unlike ordinary moral motivation, requires the motivational structure characteristic of a fully virtuous person. (...) I draw on Aristotle's account of virtuous action to argue that a fully virtuous agent's judgment reflects a robust form of moral knowledge about what features of an action render it virtuous and hence, choiceworthy. Virtuously motivated actions are chosen in light of those features and are accompanied by the affective state appropriate to the overall moral landscape in which the judgment is made. (shrink)

The theories of pre-existence and epigenesis are typically taken to be opposing theories of generation in the seventeenth and eighteenth centuries. One can be a pre-existence theorist only if one does not espouse epigenesis and vice versa. It has also been recognized, however, that the line between pre-existence and epigenesis in the nineteenth century, at least, is considerably less sharp and clear than it was in earlier centuries. The debate (1759-1777) between Albrecht von Haller and Caspar Friedrich Wolff on their (...) theories of generation is usually taken to be a debate between a pre-existence theorist and an epigeneticist, and the supposed fact that these two theories of generation are mutually exclusive explains (so the story goes) the divide between Haller and Wolff. However, it’s not clear that Haller endorsed an especially robust form of pre-existence, and nor is it clear that Wolff’s theory of generation -- once he considered it carefully -- is clear epigenetic. Rather, Haller’s theory of generation is marked by traces of epigensis and Wolff’s theory has elements of pre-existence theory. This is not to say that their theories of generation are basically the same, but the debate between the two ought not to be framed in terms of pre-existence versus epigenesis. Their points of difference must be explained in some other way. In this way, their controversy bears characteristics of similar disputes over generation in the nineteenth century more than it resembles those in the seventeenth century. In this paper, I argue that (a) Haller’s and Wolff’s theories both blend elements from pre-existence and epigenesis; (b) but there are still deeply-rooted differences between the two generation theories; (c) one source of these differences is that Haller and Wolff have divergent conceptions of what an adequate explanation is; (d) we can see that they have different conceptions of what constitutes an adequate explanation by paying heed to their evaluations of Descartes’ epistemology and methodology in his theory of generation (such as it is); and (e) this shows that one of the main differences between Haller’s generation theory and that of Wolff is the degree to which each thinks we need to (and indeed can) explain the nature of the causes -- both efficient and final -- at play during the formation of organic beings. (shrink)

In this paper, I argue that within Kantianism, widespread indifference of the global rich to the suffering of the global poor should be understood as resulting at least partly from vice. Kant had much more to say about vice than is often recognized, and it forms a crucial part of his moral anthropology. Kantians should thus attend to the ways in which vice functions as a practical obstacle to fulfilling duties of beneficence. In vice-fueled indifference, inclinations associated with self-love and (...) self-conceit work their way into our wills, interfering with our moral commitments by impeding our ability to recognize moral requirements and our motivation to act on them. Vice distorts our reasoning in ways that promote self-deception and rationalization about the extent to which we are fulfilling moral demands. Kantian vice also has social dimensions. I argue that widespread indifference exacerbates our individual vices through social norms and practices that legitimize ignoring the needs of others. I conclude by offering some potential remedies to indifference within the Kantian framework. (shrink)

I think that there is an awful lot wrong with the exclusion problem. So, it seems, does just about everybody else. But of course everyone disagrees about exactly _what_ is wrong with it, and I think there is more to be said about that. So I propose to say a few more words about why the exclusion problem is not really a problem after all—at least, not for the nonreductive physicalist. The genuine _dualist_ is still in trouble. Indeed, one of (...) my main points will be that the nonreductive physicalist is in a rather different position vis à vis the exclusion problem than the dualist is. Properly understanding nonreductive physicalism—and clearly recognizing that it is, after all, a form of _physicalism_—goes a long way toward solving the exclusion problem. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Relationships between current theories, and relationships between current theories and the sought theory of quantum gravity (QG), play an essential role in motivating the need for QG, aiding the search for QG, and defining what would count as QG. Correspondence is the broad class of inter-theory relationships intended to demonstrate the necessary compatibility of two theories whose domains of validity overlap, in the overlap regions. The variety of roles that correspondence plays in the search for QG are illustrated, using examples (...) from specific QG approaches. Reduction is argued to be a special case of correspondence, and to form part of the definition of QG. Finally, the appropriate account of emergence in the context of QG is presented, and compared to conceptions of emergence in the broader philosophy literature. It is argued that, while emergence is likely to hold between QG and general relativity, emergence is not part of the definition of QG, and nor can it serve usefully in the development and justification of the new theory. (shrink)

According to Margaret Cavendish the entire natural world is essentially rational such that everything thinks in some way or another. In this paper, I examine why Cavendish would believe that the natural world is ubiquitously rational, arguing against the usual account, which holds that she does so in order to account for the orderly production of very complex phenomena (e.g. living beings) given the limits of the mechanical philosophy. Rather, I argue, she attributes ubiquitous rationality to the natural world in (...) order to ground a theory of the ubiquitous freedom of nature, which in turn accounts for both the world's orderly and disorderly behavior. (shrink)

Between 1653 and 1655 Margaret Cavendish makes a radical transition in her theory of matter, rejecting her earlier atomism in favour of an infinitely-extended and infinitely-divisible material plenum, with matter being ubiquitously self-moving, sensing, and rational. It is unclear, however, if Cavendish can actually dispense of atomism. One of her arguments against atomism, for example, depends upon the created world being harmonious and orderly, a premise Cavendish herself repeatedly undermines by noting nature’s many disorders. I argue that her supposed difficulties (...) with atomism expose a deeper tension in her work between two fundamental metaphysical commitments each of which has substantial philosophical support: her monist theory of the material world (which maintains that there exists just one natural substance which is the single principal cause) and her occasional theory of causation (which requires multiple finite principal causes in nature -- causes that might be considered individual substances). Her monism undermines atomism while her theory of occasional cause seems to rest on a conception of nature that would be especially friendly to atomism. I argue further that we can solve this tension within a Cavendishian framework in such a way as to preserve her theory of causation and her monism, but that this solution depends upon our taking her monism in a particular (and weak) form. I finally note that we can best make sense of her unique and interesting form of monism by acknowledging her social-political motivations in addition to her motivations in natural philosophy. (shrink)