Software of the Oppressed: Reprogramming the Invisible Discipline

This dissertation offers a critical analysis of software practices within the university and the ways they contribute to a broader status quo of software use, development, and imagination. Through analyzing the history of software practices used in the production and circulation of student and scholarly writing, I argue that this overarching software status quo has oppressive qualities in that it supports the production of passive users, or users who are unable to collectively understand and transform software code for their own interests. I also argue that the university inadvertently normalizes and strengthens the software status quo through what I call its “invisible discipline,” or the conditioning of its community—particularly students, but also faculty, librarians, staff, and other university members—to have little expectation of being able to participate in the governance or development of the software used in their academic settings. This invisible discipline not only fails to prepare students for the political struggles and practical needs of our digital age (while increasing the social divide between those who program digital technology and those who must passively accept it), but reinforces a lack of awareness of how digital technology powerfully mediates the production, circulation, and reception of knowledge at individual and collective levels. Through this analysis, I hope to show what a liberatory approach to academic technology practices might look like, as well as demonstrate—through a variety of alternative software practices in and beyond the university—the intellectual, political, and social contributions these practices might contribute to higher education and scholarly knowledge production at large. I conclude the dissertation with suggestions for “reprogramming” iv our academic technology practices, an approach that I also explored in practice in the production of this dissertation. As I describe in the Afterword, the genesis of this dissertation, as well as the production, revision, and dissemination of its drafts, were generated as part of two digital projects, Social Paper and #SocialDiss, each of which attempted in their own small way to resist the invisible discipline and the ways that conventional academic technology practices structure intellectual work. The goal of this dissertation and its related digital projects is thus to help shine light on the exciting intellectual and political potential of democratizing software development and governance in and through educational institutions

ARL Digital Scholarship Institute

This poster reflects on the Association of Research Libraries’ (ARL) upcoming inaugural week-long Digital Scholarship Institute for library professionals. Held in June 2017 at Boston College, the Institute introduced librarians and staff who are not currently involved in digital scholarship to the methodologies and considerations of such work. This multi-institutional initiative will provide an opportunity for broader transformation in the academic library ecosystem at the level necessary to create a strong community of practice around digital scholarship wor

Public Scholarship in Practice and Philosophy

This piece offers several threads that bind an ideal together: there are practical actions to increase the public-ness of scholarship, increasingly compelling reasons to adopt an outward-orientation, as well as many challenges to performing public scholarship in higher education. We propose that a more public scholarly practice can be sought through the dissemination of research products, the processes by which research and scholarship are conducted, opening pedagogy beyond the classroom, developing soft skills as a public intellectual, and increasing visibility with/in communities

Kirkwood District

This Historic District Information form and all of its supplementary documents were compiled by the Case Studies class in the spring of 2007. It includes information on the district known as Kirkwood, as well as prints of Sanborn maps, early plattings of the properties, as well as historic photographs and newspaper clippings.https://scholarworks.gsu.edu/history_heritagepreservation/1050/thumbnail.jp

Household air pollution in low- and middle-income countries: health risks and research priorities

Household air pollution (HAP), which results from incomplete combustion of the solid fuels traditionally used for cooking and heating, affects the homes of nearly 3 billion people. It is the leading environmental cause of death and disability worldwide, with highest risks for women and children due to their domestic roles. The high levels of pollutants found in HAP cause a range of diseases, in addition to burns and scalds and injuries or violence experienced during fuel collection. Additionally, household solid fuel use can pose substantive environmental risks, including degradation from fuel gathering as well as climate change from release of both CO2 and short-lived climate forcers, such as black carbon, during combustion. Despite the broad support to find solutions, only a few solid fuel interventions have shown that they might improve health over the long term, especially when implemented at the scale required (Box 1)

PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution

Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS using 2 independent deep-coverage methods that utilize molecular inversion probes and amplicon sequencing in a cohort of 241 samples from 181 individuals with brain and/or body overgrowth. We identified PIK3CA mutations in 60 individuals. Several other individuals (n = 12) were identified separately to have mutations in PIK3CA by clinical targetedpanel testing (n = 6), whole-exome sequencing (n = 5), or Sanger sequencing (n = 1). Based on the clinical and molecular features, this cohort segregated into three distinct groups: (a) severe focal overgrowth due to low-level but highly activating (hotspot) mutations, (b) predominantly brain overgrowth and less severe somatic overgrowth due to less-activating mutations, and (c) intermediate phenotypes (capillary malformations with overgrowth) with intermediately activating mutations. Sixteen of 29 PIK3CA mutations were novel. We also identified constitutional PIK3CA mutations in 10 patients. Our molecular data, combined with review of the literature, show that PIK3CA-related overgrowth disorders comprise a discontinuous spectrum of disorders that correlate with the severity and distribution of mutations

CG dinucleotide clustering is a species-specific property of the genome

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer