An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Imagining a Maya Archaeology That Is Anthropological and Attuned to Indigenous Cultural Heritage

Taking an aspirational approach, this article imagines what Maya Archaeology would be like if it were truly anthropological and attuned to Indigenous heritage issues. In order to imagine such a future, the past of archaeology and anthropology is critically examined, including the emphasis on processual theory within archaeology and the Indigenous critique of socio-cultural anthropology. Archaeological field work comes under scrutiny, particularly the emphasis on the product of field research over the collaborative process of engaging local and descendant communities. Particular significance is given to the role of settler colonialism in maintaining unequal access to and authority over landscapes filled with remains of the past. Interrogation of the distinction between archaeology and heritage results in the recommendation that the two approaches to the past be recognized as distinct and in tension with each other. Past heritage programs imagined and implemented in the Maya region by the author and colleagues are examined reflexively

INCENTIVES AND PARTICIPATION IN DEVELOPMENT COMMUNICATION. Evidence from 63 recent projects

Economic incentives and the participation of communities can both be powerful drivers of successful innovation and expansion. This article explores a sample of “best cases” applying innovative technologies to solve urgent problems and looks into how the communication of innovative ideas for development could be fostered in order to make solutions available to those who need and might use them

Assessing Retinal Structure In Complete Congenital Stationary Night Blindness and Oguchi Disease

Purpose To examine retinal structure and changes in photoreceptor intensity after dark adaptation in patients with complete congenital stationary night blindness and Oguchi disease. Design Prospective, observational case series. Methods We recruited 3 patients with complete congenital stationary night blindness caused by mutations in GRM6, 2 brothers with Oguchi disease caused by mutations in GRK1, and 1 normal control. Retinal thickness was measured from optical coherence tomography images. Integrity of the rod and cone mosaic was assessed using adaptive optics scanning light ophthalmoscopy. We imaged 5 of the patients after a period of dark adaptation and examined layer reflectivity on optical coherence tomography in a patient with Oguchi disease under light- and dark-adapted conditions. Results Retinal thickness was reduced in the parafoveal region in patients with GRM6 mutations as a result of decreased thickness of the inner retinal layers. All patients had normal photoreceptor density at all locations analyzed. On removal from dark adaptation, the intensity of the rods (but not cones) in the patients with Oguchi disease gradually and significantly increased. In 1 Oguchi disease patient, the outer segment layer contrast on optical coherence tomography was 4-fold higher under dark-adapted versus light-adapted conditions. Conclusions The selective thinning of the inner retinal layers in patients with GRM6 mutations suggests either reduced bipolar or ganglion cell numbers or altered synaptic structure in the inner retina. Our finding that rods, but not cones, change intensity after dark adaptation suggests that fundus changes in Oguchi disease are the result of changes within the rods as opposed to changes at a different retinal locus

Social Entrepreneurship and Communication for Development and Social Change - Rethinking Innovation

This article argues that social entrepreneurship has not yet been adequately defined even though it is increasingly being used in social change/development practice. Muhammad Yunus, creator of the Grameen Bank and microlending, and Bill Drayton, founder of the global change agency Ashoka, have practiced social change through social entrepreneurship for more than 30 years. Increasingly, the development community has been adopting many of its practices. The basic process of social entrepreneurship involves: defining a social goal for the solution of a serious problem; innovation in solving the problem; ability to expand the organization to serve large numbers of people (scaling up); focusing on the social bottom line with empirical evidence (impact evaluation). Three cases are briefly reviewed to illustrate this process. Finally the article examines how these practices might help Communication for Development (C4D) to better adapt its own practices in achieving real change with people