Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to (...) genomic features and that support numerous user-defined statistical tests. To summarize integration site data from human gene therapy samples, we developed a reproducible report format that catalogs sample population structure, longitudinal dynamics, and integration frequency near cancer-associated genes. We also introduce a novel summary statistic, the UC50, which provides a single number summarizing possible clonal expansion. Using these tools, we characterize ongoing longitudinal characterization of a patient from the first trial to treat severe combined immunodeficiency-X1, showing successful reconstitution for 15 years accompanied by persistence of a cell clone with an integration site near the cancer-associated gene CCND2. Software is available at https://github.com/BushmanLab/INSPIIRED. (shrink)

In The Ethics of Food, Gregory E. Pence brings together a collection of voices who share the view that the ethics of genetically modified food is among the most pressing societal questions of our time. This comprehensive collection addresses a broad range of subjects, including the meaning of food, moral analyses of vegetarianism and starvation, the safety and environmental risks of genetically modified food, issues of global food politics and the food industry, and the relationships among food, evolution, and human (...) history. (shrink)

We agree with Archer that human sex differences in aggression are well explained by sexual selection, but note that explanations of human behaviors are not logically mutually exclusive from explanations and therefore should not be framed as such. We discuss why this type of framing hinders the development of both social learning and evolutionary theories of human behavior.

We present a one per cent measurement of the cosmic distance scale from the detections of the baryon acoustic oscillations in the clustering of galaxies from the Baryon Oscillation Spectroscopic Survey, which is part of the Sloan Digital Sky Survey III. Our results come from the Data Release 11 sample, containing nearly one million galaxies and covering approximately 8500 square degrees and the redshift range 0.2 < z < 0.7. We also compare these results with those from the publicly released (...) DR9 and DR10 samples. Assuming a concordance Λ cold dark matter cosmological model, the DR11 sample covers a volume of 13 Gpc3 and is the largest region of the Universe ever surveyed at this density. We measure the correlation function and power spectrum, including density-field reconstruction of the BAO feature. The acoustic features are detected at a significance of over 7σ in both the correlation function and power spectrum. Fitting for the position of the acoustic features measures the distance relative to the sound horizon at the drag epoch, rd, which has a value of rd,fid = 149.28 Mpc in our fiducial cosmology. We find DV = at z = 0.32 and DV = at z = 0.57. At 1.0 per cent, this latter measure is the most precise distance constraint ever obtained from a galaxy survey. Separating the clustering along and transverse to the line of sight yields measurements at z = 0.57 of DA = and H =. Our measurements of the distance scale are in good agreement with previous BAO measurements and with the predictions from cosmic microwave background data for a spatially flat CDM model with a cosmological constant. © 2014 The Author Published by Oxford University Press on behalf of the Royal Astronomical Society. (shrink)

© 2017. The American Astronomical Society. All rights reserved.We present new observations of the low-mass companion to HD 984 taken with the Gemini Planet Imager as a part of the GPI Exoplanet Survey campaign. Images of HD 984 B were obtained in the J and H bands. Combined with archival epochs from 2012 and 2014, we fit the first orbit to the companion to find an 18 au orbit with a 68% confidence interval between 14 and 28 au, an eccentricity (...) of 0.18 with a 68% confidence interval between 0.05 and 0.47, and an inclination of 119°with a 68% confidence interval between 114°and 125°. To address the considerable spectral covariance in both spectra, we present a method of splitting the spectra into low and high frequencies to analyze the spectral structure at different spatial frequencies with the proper spectral noise correlation. Using the split spectra, we compare them to known spectral types using field brown dwarf and low-mass star spectra and find a best-fit match of a field gravity M6.5 ±1.5 spectral type with a corresponding temperature of K. Photometry of the companion yields a luminosity of log=2.88 ± 0.07 dex with DUSTY models. Mass estimates, again from DUSTY models, find an age-dependent mass of 34 ±1 to 95 ±4 M Jup. These results are consistent with previous measurements of the object. (shrink)

The Black Mirror episode “Arkangel” tells a disturbing story of over-parenting driven by technology. The single mother Marie’s adoption of the Arkangel system has invited overwhelmingly negative moral evaluation from philosophers. But what accounts for the moral failure of a loving and concerned parent? Is it all about her flawed character, or are there situational factors at work? In the article, I first foreground the slipperiness of technology implicated in Albert Borgmann’s notion of the “device paradigm” and Hans Jonas’s analysis (...) of modern technology. Then I analyze the character of the Arkangel system in the light of the two philosophers’ works and show how the technology turns Marie into a failing parent. In the end, I offer tentative answers to the two questions; the answers shall also shed light on the problem of under-parenting driven by digital technology. (shrink)

Mark Coeckelbergh (Int J Soc Robot 1:217–221, 2009) argues that robot ethics should investigate what interaction with robots can do to humans rather than focusing on the robot’s moral status. We should ask what robots do to our sociality and whether human–robot interaction can contribute to the human good and human flourishing. This paper extends Coeckelbergh’s call and investigate what it means to live with disembodied AI-powered agents. We address the following question: Can the human–AI interaction contribute to our moral (...) development? We present an empirically informed philosophical analysis of how the AI personal assistant Siri changes its users’ way of life, based on the responses obtained from 20 semi-directive individual interviews with Siri users. We identify changes in the users’ social interaction associated with the adoption of Siri. These changes include: (1) the indirect effect of reducing opportunities of human interaction, (2) the second-order effect of diminished expectations toward each other in a community, and (3) the acquired preference to obtain hassle-free interaction with Siri over human interaction. We examine them in relation to concerns that are voiced in the current debates over the rise of AI, namely the suspicion that humans could become overly reliant on AI (Danaher 2019) and the worry that social AI could impede on moral development (Fröding and Peterson, Ethics Inf Technol 23:207–214, 2012; Li, Ethics Inf Technol 23:543–550, 2021). We analyze the ethical costs that come from these changes in light of virtue ethics and address potential objections along the way. We end by offering directions for thinking about how to live with AI personal assistant while preserving favorable conditions for moral development. (shrink)

Some practical problems in the teaching of ethics to medical students are described. The definition of the objectives of the course remains the central aspect, and is more important than the specific content. The use of student projects, buzz groups, case histories and discussion points is described. There is a need for student assessment or examination at the end of the course. The teachers require a broad background in philosophy, clinical medicine and teaching skills. The learning of the teachers may (...) be as important as that of the students. (shrink)

Quality of life is a difficult concept to define and to measure. An hypothesis is proposed which suggests that the quality of life measures the difference, or the gap, at a particular period of time between the hopes and expectations of the individual and that individual's present experiences. Quality of life can only be described by the individual, and must take into account many aspects of life. The approach is goal-orientated, and one of task analysis. The hypothesis is developed in (...) a diagramatic way, and several methods of testing the hypothesis suggested. (shrink)

I Propose to re-explore here some aspects of a very shop-worn question: ‘Was Hobbes in any sense an atheist?’ Three centuries ago, Hobbes's personal security in part depended on the way his contemporaries answered this question; today, the validity of several current accounts of his philosophy are similarly bound up with it. These accounts vary extraordinarily, all the way from Polin's confident assertion that ‘ pour qui sait lire entre les lignes, … c'est ľatheísme qui triomphe implicitement ’, to Taylor's (...) equally firm belief that ‘a certain kind of theism is necessary to make [Hobbes's] theory work.’ 1 And now the latest of the Taylorians, Prof. Howard Warrender, has published his book The Political Philosophy of Hobbes , in which Hobbes's statements regarding the place of God are again treated as an essential part of his theory; and the charge explicitly made, that there are no sound grounds for regarding them as ‘the product of confusion or pretence on Hobbes's part’. (shrink)

The hypothesis that values change and evolve is examined by this paper. The discussion is based on a series of examples where, over a period of a few decades, new ethical issues have arisen and values have changed. From this analysis it is suggested that there are a series of core values around which most people would agree. These are unlikely to change over long time periods. There are then a series of secondary or derived values around which there is (...) much more controversy and within which differences of view occur. Such changes need to be documented if we are to understand the process involved in the evolution of differences in ethical views. (shrink)

Welcome to the world of cutting-edge math, physics, and neuroscience, where the search for the ultimate vacuum, the point of nothingness, ground zero of theory, has rendered the universe deep, rich, and juicy. "Modern physics has animated the void," says K. C. Cole in her entrancing journey into the heart of Nothing. Every time scientists and mathematicians think they have reached the ultimate void, new stuff appears: a black hole, an undulating string, an additional dimension of space or time, repulsive (...) anti-gravity, universes that breed like bunnies. Cole's exploration at the edge of everything is as animated and exciting as the void itself. Take Cole's hand on this adventure into the unknown, and you'll come back informed, amused, and excited. (shrink)

Upshot: The commentaries concentrate mostly on ontological issues but overlook the main epistemological argument in my target article. This argument refers to the conditions that make cognition possible, and to the limits of cognition. These are important for two reasons: they have ontological consequences and they limit the theory’s contingency.

Context: In the literature concerning the theory of social systems, interest in epistemological and ontological questions has increased in recent years. The controversies regarding a realist vs. constructivist interpretation of Luhmann’s theory, as well as the concept of many realities that correspond to many ontologies, deserve attention. Problem: The paper discusses interrelated ontological and epistemological problems in Luhmann’s systems theory, such as ontology and de-ontologization, realism vs. constructivism, contingency and its limits and one vs. many realities. Method: The paper proposes (...) an interpretation, according to which systems theory is based on an epistemology - radical operative constructivism. Results: Luhmann is not a realist. The last word belongs to radical operative constructivism, and naïve realism with reference to social systems has only a preliminary, methodological significance. However, taking a position in the dispute between realism and constructivism inevitably involves an ontological “vocabulary,” that is, usage of the reality/construction distinction. Furthermore, operative constructivism formulates the necessary conditions of the possibility of cognition, which limit the contingency of the theory and constitute one reality that is a construction of systems theory. Luhmann rejects ontology, but he does not renounce epistemology, and consequently the project of de-ontologization remains incomplete. Implications: The paper offers a new, coherent interpretation of ontological and epistemological questions in Luhmann’s theory, and also throws light on some problems of radical constructivism in general, such as the ontological implications of epistemology or the constructivist self-reference of theories. Key words: Radical operative constructivism, social systems, Luhmann, ontology, reality, contingency. (shrink)

Resource allocation is a central part of the decision-making process in any health care system. Resources have always been finite, thus the ethical issues raised are not new. The debate is now more open, and there is greater public awareness of the issues. It is increasingly recognised that it is the technology which determines resources. The ethical issues involved are often conflicting and relate to issues of individual rights and community benefits. One central feature of resource allocation is the basing (...) of decisions on the outcomes of health care and on their subsequent economic evaluation. The knowledge base is therefore of great importance as is the audit of results of clinical treatment. Public involvement is seen as an integral part of this process. For all parts of the process, better methodologies are required. (shrink)

The challenges public comprehensive universities face today are expanding—they have been challenged to enroll and graduate more students, adopt new technologies that lower cost without sacrificing quality, and align program and curricular offerings with the skills that employers require. While these universities have a long history of adapting to change, today’s environment will likely test the capabilities of even the most adaptive institutions. This volume assembles a team of experts from a variety of disciplines to examine both the history of (...) the comprehensive university and what lies ahead. Overall, the book grapples with such questions as: How do these institutions adapt to serve the growing population of non-traditional students? How well do they prepare graduates for the labor market? Can partnerships between community colleges and comprehensive universities bolster student success? The University Next Door draws much-needed attention to a set of institutions that has historically received little notice, yet play an important role in meeting our new attainment goals and helping the American economy grow. Book Features: Examines the role of comprehensive universities from start to finish—their history and future. Uses empirical analysis to explore complex questions about which students choose these universities and why. Explores how these institutions might struggle under a federal ratings system such as the one proposed by President Obama. Discusses how these institutions can better monitor the needs of the economy and better educate students to fill those needs. Provides recommendations to inform future decisions about higher education policy. (shrink)