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 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. The NCRO ontology is free and open to all users. (shrink)

Nonhuman primates represent the most significant extant species for comparative studies of cognition, including such complex phenomena as numerical competence, among others. Studies of numerical skills in monkeys and apes have a long, though somewhat sparse history, although questions for current empirical studies remain of great interest to several fields, including comparative, developmental, and cognitive psychology; anthropology; ethology; and philosophy, to name a few. In addition to demonstrated similarities in complex information processing, empirical studies of a variety of potential cognitive (...) limitations or constraints have provided insights into similarities and differences across the primate order, and continue to offer theoretical and pragmatic directions for future research. An historical overview of primate numerical studies is presented, as well as a summary of the 17‐year research history, including recent findings, of the Comparative Cognition Project at The Ohio State University Chimpanzee Center. Overall, the archival literature on number‐related skills and counting in nonhuman primates offers important implications for revising our thinking about comparative neuroanatomy, cross‐species (human/ape) cognitive similarities and differences, and the evolution of cognition represented by the primate continuum. (shrink)

Essays, previously published in somewhat different form by Milkweed Editions, Minneapolis.

The invisibility of nursing work has been discussed in the international literature but not in relation to learning clinical skills. Evans and Guile's (Practice‐based education: Perspectives and strategies, Rotterdam: Sense, 2012) theory of recontextualisation is used to explore the ways in which invisible or unplanned and unrecognised learning takes place as newly qualified nurses learn to delegate to and supervise the work of the healthcare assistant. In the British context, delegation and supervision are thought of as skills which are learnt (...) “on the job.” We suggest that learning “on‐the‐job” is the invisible construction of knowledge in clinical practice and that delegation is a particularly telling area of nursing practice which illustrates invisible learning. Using an ethnographic case study approach in three hospital sites in England from 2011 to 2014, we undertook participant observation, interviews with newly qualified nurses, ward managers and healthcare assistants. We discuss the invisible ways newly qualified nurses learn in the practice environment and present the invisible steps to learning which encompass the embodied, affective and social, as much as the cognitive components to learning. We argue that there is a need for greater understanding of the “invisible learning” which occurs as newly qualified nurses learn to delegate and supervise. (shrink)

Emotion recognition skills and the ability to understand the mental states of others are crucial for normal social functioning. Conversely, delays and impairments in these processes can have a profound impact on capability to engage in, maintain, and effectively regulate social interactions. Therefore, this study aimed to compare the performance of 42 autistic children, 45 unaffected siblings, and 41 typically developing controls on the Affect Recognition and Theory of Mind subtests of the Developmental Neuropsychological Assessment Battery. There were no significant (...) differences between siblings and TD controls. Autistic children showed significantly poorer performance on AR when compared to TD controls and on TOM when compared to both TD controls and unaffected siblings. An additional comparison of ASD, unaffected sibling and TD control subsamples, matched on full-scale IQ, revealed no group differences for either AR or TOM. AR and TOM processes have received less research attention in siblings of autistic children and remain less well characterized. Therefore, despite limitations, findings reported here contribute to our growing understanding of AR and TOM abilities in siblings of autistic children and highlight important future research directions. (shrink)

Introduction Research supports the efficacy of both a remedial consent procedure ) and a motivational consent procedure for improving recall of informed consent to research. Although these strategies were statistically superior to standard consent, effects were modest and not clinically significant. This study examines a combined incentivised consent and CF procedure that simplifies the cognitive task and increases motivation to learn consent information.Methods We randomly assigned 104 individuals consenting to an unrelated host study to a consent as usual condition or (...) an incentivised CF condition . All participants were told they would be quizzed on their consent recall following their baseline assessment and at 4 monthly follow-ups. ICF participants were also informed that they would earn $5 for each correct answer and receive CF as needed.Results Quiz scores in the two conditions did not differ at the first administration ; however, ICF scores were significantly higher at each subsequent administration .Conclusions The ICF procedure increased consent recall from 72% to 83%, compared with the CAU condition in which recall decreased from 69% to 59%. This supports the statistical and clinical utility of a combined remedial and motivational consent procedure for enhancing recall of study information and human research protections. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:“Normalizing” Intersex Didn’t Feel Normal or Honest to Me.Karen A. WalshI am an intersex woman with Complete Androgen Insensitivity Syndrome (CAIS). My 57–year history with this has its own trajectory—mostly driven by medical events, and how I and my parents reacted. Most of my treatment by physicians has not been positive. It didn’t make me “normal” at all. I was born normal and didn’t require medical interventions. And (...) by the way, I’ve never been confused about who or what I am.Truthful disclosure didn’t come to me about my biology and what was done to me as an infant until I was 33, when I forced the issue by removing my medical records from my endocrinologist’s office. I learned that there was never full disclosure to my [End Page 119] parents either, and therefore there was no informed consent for the “corrective” surgeries performed on me as an infant. My parents were only told that their little girl would get cancer and would not have a normal development as a girl unless her “deformed ovaries” were removed, and that they should never discuss these problems with me. Thus, after having presented with an inguinal hernia and having exploratory surgery at age 16 months, my intra–abdominal testes were removed in a second surgery two months later. I was pronounced a “male pseudohermaphrodite,” a diagnosis that was shared neither with my parents nor with me.Years later, I discovered an article my surgeon published in 1960 in the Delaware Medical Journal about me and another intersex person he operated on (whom he labeled a “true hermaphrodite”). The article gives a very detailed pathology report of my gonads, but only two sentences regarding my welfare and the rationale for performing those surgeries. Dr. J. F. Kustrup wrote in this article, “These [two cases] emphasize the need for early diagnosis and treatment in order to avoid the possibility of malignant change and to permit these individuals to follow a normal psychosexual pattern.” And: “Hermaphroditism and pseudohermaphroditism are conditions in which early diagnosis and treatment are essential to avoid malignant degeneration and to allow the child some chance toward normal pyschic [sic] development.” I was grateful to find this article because it revealed the unfounded assumptions underpinning the recommendations for treatment, much of which continues today. Worse even than the sort of social prejudice that shapes treatment is the absence of evidence for what doctors treat as “necessary” interventions. For my syndrome, CAIS, there never was—and still is not—data to support the cancer scare, or the opinion that I’d be confused and not have a normal life.From about the age of four, I can remember being different and being stonewalled by my doctor and prevented by my parents from talking about it. The feelings and fears I tried to express were shushed away, and I could tell that my questions were upsetting everyone. Even if I had wanted to be complicit with their lame diversions and nonsensical explanations, the massive abdominal scars were there as a daily reminder and hinted at a very different story.The Road to Hell is Paved with Good IntentionsGrowing up, I was treated like a fascinoma and a lab rat at a major teaching hospital on the East Coast. All I learned from those doctors as a young kid was what it feels like to be ogled, photographed and probed by a roomful of white–coated male doctors. Dissociation made itself my friend, and helped me to cope through the annual genital and anal exams and probing. I thought I was a freak and I felt completely powerless to protect myself from them and their “care”.At my annual appointment at age 12, with my mom present, three doctors told me I was infertile. Learning that I couldn’t have kids really saddened and shocked me, but there was no opportunity to talk about my feelings—either that day, or any time afterward. I was told to stop crying. I remember them telling me that there was no one else like me and that this was a random genetic anomaly, thereby reinforcing the freakishness... (shrink)

This article is the lead piece in a special report that presents the results of a bioethical investigation into chimeric research, which involves the insertion of human cells into nonhuman animals and nonhuman animal embryos, including into their brains. Rapid scientific developments in this field may advance knowledge and could lead to new therapies for humans. They also reveal the conceptual, ethical, and procedural limitations of existing ethics guidance for human‐nonhuman chimeric research. Led by bioethics researchers working closely with an (...) interdisciplinary work group, the investigation focused on generating conceptual clarity and identifying improvements to governance approaches, with the goal of helping scholars, funders, scientists, institutional leaders, and oversight bodies (embryonic stem cell research oversight [ESCRO] committees and institutional animal care and use committees [IACUCs]) deliver principled and trustworthy oversight of this area of science. The article, which focuses on human‐nonhuman animal chimeric research that is stem cell based, identifies key ethical issues in and offers ten recommendations regarding the ethics and oversight of this research. Turning from bioethics’ previous focus on human‐centered questions about the ethics of “humanization” and this research's potential impact on concepts like human dignity, this article emphasizes the importance of nonhuman animal welfare concerns in chimeric research and argues for less‐siloed governance and oversight and more‐comprehensive public communication. (shrink)

The classic Lewis-Stalnaker semantics for counterfactuals captures that Sobel sequences are consistent sequences, for example: a.If Sophie had gone to the parade, she would have seen Pedro dance. b.But if Sophie had gone to the parade and been stuck behind someone tall, she would not have seen Pedro dance. But reverse a sequence like this one and it no longer sounds so good, which is surprising on the classic semantics. This observation motivated Kai von Fintel and Thony Gillies to propose (...) dynamic semantic accounts of counterfactual conditionals. Subsequently, Sarah Moss defended the classic semantics against the charge that it need be abandoned in the face of these order effects, arguing that the infelicity of the reverse sequences is pragmatic. I argue that both accounts are ultimately untenable, but each account has strengths. Seeing what works and what doesn't in each account points the way to the right positive view. With this in mind, I defend a contextualist account of counterfactuals that takes conversational relevance to play a central role. (shrink)

Unser globalisiertes Leben ist aufgrund der Fülle von vernetzten Daten derart komplex und undurchsichtig, dass zur Beherrschung allumfassende Detailkenntnisse notwendig wären. Es scheint nur zwei Möglichkeiten der Bewältigung zu geben: Reduktion auf Weniges oder aber, Komplexität mit Komplexität selbst zu begegnen. Im Unterschied zur meist praktischen Umgangsweise mit Komplexität im Alltag die erfolgreiche Verhaltensregeln parat hält will das vorliegende Buch keine praktische Anweisung geben. Es bietet vielmehr eine philosophische Analyse von Komplexität und Komplexitätsbewältigung auf der sinnlich-affektiven, der praktisch-pragmatischen und der (...) rationalen Ebene. Karen Gloy zeigt auf, dass Komplexität nicht einzufangen ist und es neben richtigen Lösungen stets auch Fehler gibt.--. (shrink)

This boy is Ignorance. This girl is Want. Beware them both, and all of their degree, but most of all beware this boy, for on his brow I see that written which is Doom... —Charles Dickens, A Christmas Carol.

One of the central questions of discourse dynamics is when an anaphoric pronoun is licensed. This paper addresses this question as it pertains to the complex data involving anaphora and negation. It is commonly held that negation blocks anaphoric potential, for example, we cannot say “Bill doesn’t have a car. It is black”. However, there are many exceptions to this generalization. This paper examines a variety of types of discourses in which anaphora on indefinites under the scope of negation is (...) felicitous. These cases are not just of intrinsic interest, but I argue present serious problems for the dynamic semantic framework, which builds the licensing facts into the semantics. I argue in favor of adopting a dynamic pragmatics, a theory that explains context change through general Gricean principles, and combining it with a static, d-type theory of anaphora, in which pronouns go proxy for definite descriptions. (shrink)

This case is part of a series of case studies used as an exercise within a program on research ethics education. The case involves research on genetic birth defects in a culturally distinct, closed religious community in which elders speak for the community. The case raises ethical issues of informed consent in such a setting; of collaboration with the community; of conflicts between the researchers’ responsibilities to the community as a whole and to individual subjects; of the impact of the (...) researcher’s findings on the practices and values of the community and issues regarding how the researchers share findings with subjects and how the findings are stored. (shrink)

Actualists routinely characterize their view by means of the slogan, “Everything is actual.” They say that there aren’t any things that exist but do not actually exist—there aren’t any “mere possibilia.” If there are any things that deserve the label ‘possible world’, they are just actually existing entities of some kind—maximally consistent sets of sentences, or maximal uninstantiated properties, or maximal possible states of affairs, or something along those lines. Possibilists, in contrast, do think that there are mere possibilia, that (...) there are things that are not actual. They think that more exists than what actually exists. All I have done so far, though, is rephrase the slogan in various ways. To say that everything is actual is precisely to say that there are no things that do not actually exist, which is precisely to say that there are no mere possibilia, and which is also precisely to say that we cannot sep- arately quantify over what exists and what is actual. These claims all amount to the same thing. But what is that, exactly? What on earth does it mean to say that everything is actual, that there are no mere possibilia, and so on? What does the actualist slogan really come to? I think the literature is far from clear on this point, and that people work themselves into unnecessary muddles because of it. Indeed, certain confusions that I shall discuss in the first half of this article seem to be on the rise. It is high time to lay out the issues and the choice points as clearly as possible. There are two primary choices to be made; there are two axes along which versions of actualism can vary. One choice has to do with how to treat claims about things that merely could exist. The other choice has to do with the modal status of the view and of how we should think about the “actual” in actualism. I make no claim that the positions I will eventually endorse are star- tlingly new. I think that most people will agree with the decisions I make at both choice points and will in fact find some bits of this essay obvious. But not everyone agrees with my decisions, and it has been my experience that people differ remarkably about which bits they find obvious—a fact I find rather telling. My goal, then, is to show that the two axes are there and to clarify the consequences of the choices. (shrink)

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life (...) and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life? A schematic of the process of building a unified tree of life. Inputs are published phylogenetic estimates and a unified taxonomy. These inputs are combined into a summary supertree containing ≈2 million taxa. The relationships among any subset of taxa may easily be accessed and used in downstream analyses. (shrink)

In this study we explore how a selection of Norwegian women account for their decision to undergo weight loss surgery. We argue that women’s descriptions of their experiences leading up to this choice of action illuminate issues regarding social norms of bodily appearance and personal responsibility. The starting point is women’s own experiences within a cultural context in which opting for WLS often attracts moral scrutiny. Inspired by Merleau-Ponty’s notion of consciousness as embodied and de Beauvoir’s ideas concerning women’s situation, (...) we argue that bodily as well as socio-cultural aspects intertwine with women’s choice of surgery as a means of losing weight. Although society’s stigmatization of women with obesity has been well challenged by scholars in the field of critical fat studies, women with obesity still experience the bodily hindrances associated with being overweight in an intense and subjective way. The findings suggest that women confronting the option of WLS do so in a context of pain, dysfunction and social stigma, a combination which illuminates the intricate ambiguity of the obese body as both subject and object. (shrink)

Bernard Linsky and Edward Zalta have recently proposed a new form of actualism. I characterize the general form of their view and the motivations behind it. I argue that it is not quite new – it bears interesting similarities to Alvin Plantinga’s view – and that it definitely isn’t actualist.

Much previous study has been done on the degree spectra of prime models of a complete atomic decidable theory. Here we study the analogous questions for homogeneous models. We say a countable model A has a d-basis if the types realized in A are all computable and the Turing degree d can list $\Delta _{0}^{0}$ -indices for all types realized in A. We say A has a d-decidable copy if there exists a model B ≅ A such that the elementary (...) diagram of B is d-computable. Goncharov, Millar, and Peretyat'kin independently showed there exists a homogeneous A with a 0-basis but no decidable copy. We prove that any homogeneous A with a 0'-basis has a low decidable copy. This implies Csima's analogous result for prime models. In the case where all types of the theory T are computable and A is a homogeneous model with a 0-basis, we show A has copies decidable in every nonzero degree. A degree d is 0-homogeneous bounding if any automorphically nontrivial homogeneous A with a 0-basis has a d-decidable copy. We show that the nonlow₂ $\Delta _{2}^{0}$ degrees are 0-homogeneous bounding. (shrink)

In this paper I defend a little noted claim of Kant’s — that we should “keep the shutters closed” on our flaws and failings. Kant’s own arguments for this claim aren’t fully satisfactorily, and they rest primarily on pragmatic considerations. My aim in this paper is to provide a more robust Kantian-inspired argument for the moral value of reserve. I argue that collaborating with others to keep the shutters closed on our individual and collective flaws aids in the difficult task (...) of building and maintaining moral community among morally frail and flawed human beings. The paper consists of three parts. In Part I, I examine what Kant himself says about reserve. In Part II, I present a Kantian-inspired argument for the moral value of reserve, drawing on sociologist Erving Goffman’s concept of a front. Moral fronts, I argue, contribute to the fulfillment of the Kantian duties of moral self-improvement and beneficence. To put it differently, they help us instantiate the kingdom of ends in a world of imperfect human beings. In Part III, I address three objections to my argument: that fronts are deceptive, that they actually interfere with moral self-improvement, and that they preclude morally valuable forms of intimacy. I argue that my account can accommodate these concerns. (shrink)

We examine recent work in cognitive neuroscience that investigates brain networks. Brain networks are characterized by the ways in which brain regions are functionally and anatomically connected to one another. Cognitive neuroscientists use various noninvasive techniques (e.g., fMRI) to investigate these networks. They represent them formally as graphs. And they use various graph theoretic techniques to analyze them further. We distinguish between knowledge of the graph theoretic structure of such networks (structural knowledge) and knowledge of what instantiates that structure (nonstructural (...) knowledge). And we argue that this work provides structural knowledge of brain networks. We explore the significance of this conclusion for the scientific realism debate. We argue that our conclusion should not be understood as an instance of a global structural realist claim regarding the structure of the unobservable part of the world, but instead, as a local structural realist attitude towards brain networks in particular. And we argue that various local approaches to the realism debate, i.e., approaches that restrict realist commitments to particular theories and/or entities, are problematic insofar as they don't allow for the possibility of such a local structural realist attitude. (shrink)

Many women today prepare for a big meeting by reading a stack of folders and applying lipstick. They order their male colleagues around, then wait for those same men to help them on with their coats. They have higher-status jobs than some of the men they date, yet they never call men socially or ask them out. What's going on? Why such seemingly contradictory behaviors? Have women completely failed feminism--or has feminism failed them? In The Lipstick Proviso , Karen (...) Lehrman--hailed by the New York Times as the "sharpest" of the new feminist thinkers--shows that women today are failing neither feminism nor themselves. Rather, they've entered a new stage of feminism, one in which the personal is not political, differences between the sexes need to be respected, and courtship, chivalry, and the nuclear family don't have to be jettisoned just because they existed before the sixties. Thirty years after the women's movement liberated women from narrowly defined roles, Lehrman argues, we are finally beginning to see which traditionally feminine behaviors are more deeply rooted in biology and which are more heavily influenced by culture. Lehrman asserts that the result--whatever it is--will not undermine feminism as long as women still retain equal rights, opportunities, and responsibilities. Dispensing with the outdated notion of sisterhood, Lehrman offers women a "lipstick proviso": women don't have to sacrifice their complex individuality in order to be equal. As the first book to move beyond a critique of orthodox feminism, The Lipstick Proviso sets a radically new course for the future of the women's movement. While there's still much political work to be done, Lehrman argues that women should now focus on the personal sides of their lives. Women can't rightly be called autonomous if they stay with abusive or even emotionally challenged lovers; say "yes" to sex when they really mean "no"; overeat or undereat to hide their sexuality. With wit and grace, Karen Lehrman offers in The Lipstick Proviso a way to complete the feminist revolution, and clearly establishes herself as the definitive voice of the next generation of feminism. (shrink)