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)

Interaction between Peter Singer and Christian ethics, to the extent that it has happened at all, has been unproductive and often antagonistic. Singer sees himself as leading a 'Copernican Revolution' against a sanctity of life ethic, while many Christians associate his work with a 'culture of death'. Charles Camosy shows that this polarized understanding of the two positions is a mistake. While their conclusions about abortion and euthanasia may differ, there is surprising overlap in Christian and Singerite arguments, and (...) disagreements are interesting and fruitful. Furthermore, it turns out that Christians and Singerites can even make common cause, for instance in matters such as global poverty and the dignity of non-human animals. Peter Singer and Christian ethics are far closer than almost anyone has imagined, and this book is valuable to those who are interested in fresh thinking about the relationship between religious and secular ethics. (shrink)

In the Summer 2017 NCBQ, Joshua Evans strongly criticized arguments made by Charles Camosy about the possibility of a prenatal child being a material mortal threat to her mother. Here Camosy demonstrates that the formal/material debate remains open for non-dissenting Catholic moral theologians. He also shows that his reference to just-war theory is used to discuss innocence; it is not evidence of a particular methodology. Despite Evans’s claim to the contrary, Camosy notes multiple examples where he affirms the uniqueness (...) of pregnancy and the special duty of parents to children. He argues for full deference to the magisterium in matters where doctrine has been defined and urges solid theological grounding for teachings on abortion when the mother’s life is at risk, especially given the profound personal and political issues at stake. (shrink)

The paper examines the loss of African identity within the modern/ contemporary era. African identity has been a recurrent theme in all domains of African studies, serving as a major intellectual concern of many African scholars. Debates on the reality of African Philosophy are anchored on the questions surrounding African identity giving rise to thoughts and contents of that philosophy. Despite the volumes already generated on the theme, the controversial circumstances that engendered the subject of African identity makes its intellectual (...) concern sustainable and almost inexhaustible. The question of African identity is basically an ontological question of the reality of Africa cum the being of an African. The series of infiltration and appraisals of Africa by foreign elements tend to plunge the continent into crises of identity. In addition to the various approaches to the subject, the nature-culture perspective presents the argument that if culture is ideally the product of a people’s nature, African culture represents the objective manifestation of the Africanity of the continent and its organic/holistic content. Such frame of thought embellished with philosophic tools provides further locus for a more feasible and stable definition of African identity as the holistic nature and character of being African. (shrink)

Philosophy confronts two existential crises: the threats to its existence from scientists like Stephen Hawking who claim that philosophy is dead; and the threat to life itself from catastrophic climate change. The essay’s first theoretical part critiques Nietzsche’s claim that philosophy’s primary function is to guarantee the future of life. The essay’s second practical part claims that philosophy must meet the challenge of life’s extinction through a revised model for ethics in education. Taking its start from recent conceptualizations of philosophy (...) as a ‘field discipline,’ this part considers African American models for delivering ethics in education to under-resourced communities. The third part shows how these theoretical models may be actualized in the practice of an African field philosopher. (shrink)

In the twenty-first century, Stephen Hawking proclaimed the death of philosophy. Only science can address philosophy’s perennial questions about human values. The essay first examines Nietzsche’s nineteenth century view to the contrary that philosophy alone can create values. A critique of Nietzsche’s contention that philosophy rather than science is competent to judge values follows. The essay then analyzes Edward O. Wilson’s claim that his scientific research provides empirically-based answers to philosophy’s questions about human values. Wilson’s bold new hypothesis about the (...) ‘social conquest of the earth’ challenges Nietzsche’s vision of philosophy’s mission. Confronting both Nietzsche and Wilson, the essay then considers three theoretical proposals for a consilience of philosophy, science, engineering and technology. The conclusion presents a working African model of consilience that addresses the existential problem of poverty in the Global South. (shrink)

Timothy Murphy has done those of us in the field of bioethics a great service by being forthright about how irreligious centers of power work against theology and theologians. This has opened the door to direct and honest conversation about some facts that were previously known but rarely discussed publicly. Now, eight years after Murphy’s important article appeared in the American Journal of Bioethics, there is room to engage the facts and arguments surrounding the role for theology in the field. (...) It is important, first of all, to agree that if theology is to be excluded while other normative traditions included this must be defended on the basis of a coherent set of defensible claims, not merely raw assertions and power plays. Once the field comes to terms with the fact that no coherent set of defensible claims exist which can justify excluding theology from the field, this will create the conditions for the possibility of the kind of intellectual solidarity which can transform bioethics into a field that is at once much more diverse and inclusive while also of its very nature interested in robust debate which includes references first principles and metaphysical foundations. (shrink)

Applied Christian Ethics addresses selected themes in Christian social ethics. Part one shows the roots of contributors in the realist school; part two focuses on different levels of the significance of economics for social justice; and part three deals with both existential experience and government policy in war and peace issues.

Previous studies have found Forsyth’s Ethical Position Questionnaire (EPQ) to vary between countries, but none has made a systematic evaluation of its psychometric properties across consumers from many countries. Using confirmatory factor analysis and multi-group LISREL analysis, this paper explores the factor structure of the EPQ and the measurement equivalence in five societies: Austria, Britain, Brunei, Hong Kong and USA. The results suggest that the modified scale, measuring idealism and relativism, was applicable in all five societies. Equivalence was found across (...) Britain, Brunei and USA, but the original scale cannot be used validly. (shrink)

There is perhaps no more important value than fundamental human equality. And yet, despite large percentages of people affirming the value, the resources available to explain and defend the basis for such equality are few and far between. In his newest book, Charles Camosy provides a thoughtful defense of human dignity. Telling personal stories like those of Jahi McMath, Terri Schiavo, and Alfie Evans, Camosy, a noted bioethicist and theologian, uses an engaging style to show how the influence of (...) secularized medicine is undermining fundamental human equality in the broader culture. And in a disturbing final chapter, Camosy sounds the alarm about the next population to fall if we stay on our current trajectory: dozens of millions of human beings with dementia. Heeding this alarm, Camosy argues, means doing two things. First, making urgent and genuine attempts to dialogue with a secularized culture which cannot see how it is undermining one of its most foundational values. Second, religious communities which hold the Imago Dei sacred must mobilize their existing institutions (and create new ones) to care for a new set of human beings our throwaway culture may deem nonpersons. (shrink)

This essay explains the appearance of tragic narrative patterns and motifs in the Croesus logos not as a passive manifestation of "tragic influence," but as a self-conscious textual strategy whereby Herodotus makes his narratives familiar and engaging while also demonstrating the distinctive traits of his own innovative discourse, historie. Herodotus' purposive appropriation and modification of tragic technique manifests the critical engagement with other authors and literary genres that is one of the defining features of the Histories. Herodotus embellishes the story (...) of Atys and Adrastus with numerous formal and thematic features of Attic tragedy. Uniquely in the Histories, the story traces the full arc of a tragic drama, from the king's ominous dream of Atys' death to catastrophe, lament, and burial. The celebrated climactic description of Adrastus' suicide, however, transcends Herodotus' dramatic model. In describing Adrastus as the most unfortunate man "of all that he himself knew," Herodotus introduces an idiom used elsewhere in the Histories to portray the activity of the histor, and thus places the unmistakable stamp of his own genre upon tragic narrative. In a fully mimetic episode that lacks the author's characteristically intrusive "voiceprint," Herodotus seems to suggest that he could beat the dramatists at their own game if he chose to play it. Two other episodes make similar use of tragic motifs on a smaller scale. In the story of Gyges and Candaules Herodotus adapts the Aeschylean motif of the decision made under duress to focus attention on human causation and socio-political issues of fundamental interest to him. Finally, the tragic stylization of Croesus' pyre scene allows Herodotus to manipulate audience expectations while subtly demonstrating, through the use of indirect discourse, the interest in source criticism that sets Herodotean historie apart from the poetic tradition. (shrink)