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"Stevens, Hallam"
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Globalizing Genomics: The Origins of the International Nucleotide Sequence Database Collaboration
Genomics is increasingly considered a global enterprise – the fact that biological information can flow rapidly around the planet is taken to be important to what genomics is and what it can achieve. However, the large-scale international circulation of nucleotide sequence information did not begin with the Human Genome Project. Efforts to formalize and institutionalize the circulation of sequence information emerged concurrently with the development of centralized facilities for collecting that information. That is, the very first databases build for collecting and sharing DNA sequence information were, from their outset, international collaborative enterprises. This paper describes the origins of the International Nucleotide Sequence Database Collaboration between GenBank in the United States, the European Molecular Biology Laboratory Databank, and the DNA Database of Japan. The technical and social groundwork for the international exchange of nucleotide sequences created the conditions of possibility for imagining nucleotide sequences (and subsequently genomes) as a \"global\" objects. The \"transnationalism\" of nucleotide sequence was critical to their ontology – what DNA sequences came to be during the Human Genome Project was deeply influenced by international exchange.
Journal Article
Crowdfunding Conservation Science
Who gets to practice and participate in science? Research teams in Puerto Rico and New Zealand have each sequenced the genomes of parrot populations native to these locales: the iguaca and kākāpō, respectively. In both cases, crowdfunding and social media were instrumental in garnering public interest and funding. These forms of Internet-mediated participation impacted how conservation science was practiced in these cases and shaped emergent social roles and relations. As citizens “follow,” fund, and “like” the labor of conservation, they create new relational possibilities for and with science. For example, the researchers became newly engaged and engaging by narrating and displaying the parrots via an Internet-inflected aesthetic. The visibility of online modalities shifted accountabilities as researchers considered whom this crowdfunded work answered to and how to communicate their progress and results. The affordances of the Internet allowed researchers from the peripheries of the scientific establishment to produce genomic knowledge for globally dispersed audiences. The convergence of genomic and Internet technology here shaped scientific practice by facilitating new modes of participation—for laypeople in science but also for scientists in society.
Journal Article
Evidence-based medicine from a social science perspective
Background: Since the emergence of evidence-based medicine (EBM) in the 1980s, social scientists - including historians, sociologists, anthropologists, political scientists and philosophers - have attempted to reckon with the movement's origins, implications and consequences.
Objectives: This paper reviews the social science literature related to EBM and attempts to draw some conclusions for the future improvement of EBM.
Discussion: The paper divides the discussion of evidence-based into three critiques: the 'statistics' critique, the 'cookbook' critique and the 'neo-liberal' critique. Incorporating social sciences approaches into clinical education and clinical research will be critical to the future development and success of EBM.
Journal Article
Life Out of Sequence
Thirty years ago, the most likely place to find a biologist was standing at a laboratory bench, peering down a microscope, surrounded by flasks of chemicals and petri dishes full of bacteria. Today, you are just as likely to find him or her in a room that looks more like an office, poring over lines of code on computer screens. The use of computers in biology has radically transformed who biologists are, what they do, and how they understand life. In Life Out of Sequence, Hallam Stevens looks inside this new landscape of digital scientific work.
Stevens chronicles the emergence of bioinformatics—the mode of working across and between biology, computing, mathematics, and statistics—from the 1960s to the present, seeking to understand how knowledge about life is made in and through virtual spaces. He shows how scientific data moves from living organisms into DNA sequencing machines, through software, and into databases, images, and scientific publications. What he reveals is a biology very different from the one of predigital days: a biology that includes not only biologists but also highly interdisciplinary teams of managers and workers; a biology that is more centered on DNA sequencing, but one that understands sequence in terms of dynamic cascades and highly interconnected networks. Life Out of Sequence thus offers the computational biology community welcome context for their own work while also giving the public a frontline perspective of what is going on in this rapidly changing field.
eBook
High-throughput ectopic expression screen for tamoxifen resistance identifies an atypical kinase that blocks autophagy
Resistance to tamoxifen in breast cancer patients is a serious therapeutic problem and major efforts are underway to understand underlying mechanisms. Resistance can be either intrinsic or acquired. We derived a series of subcloned MCF7 cell lines that were either highly sensitive or naturally resistant to tamoxifen and studied the factors that lead to drug resistance. Gene-expression studies revealed a signature of 67 genes that differentially respond to tamoxifen in sensitive vs. resistant subclones, which also predicts disease-free survival in tamoxifen-treated patients. High-throughput cell-based screens, in which >500 human kinases were independently ectopically expressed, identified 31 kinases that conferred drug resistance on sensitive cells. One of these, HSPB8, was also in the expression signature and, by itself, predicted poor clinical outcome in one cohort of patients. Further studies revealed that HSPB8 protected MCF7 cells from tamoxifen and blocked autophagy. Moreover, silencing HSBP8 induced autophagy and caused cell death. Tamoxifen itself induced autophagy in sensitive cells but not in resistant ones, and tamoxifen-resistant cells were sensitive to the induction of autophagy by other drugs. These results may point to an important role for autophagy in the sensitivity to tamoxifen.
Journal Article
A Feeling for the Algorithm
The term “Big Data” may serve as a useful marker for particular kinds of questions, practices, and relationships for collecting and using data. Some of the ways of talking about Big Data suggest that there might be something, if not entirely new, then at least importantly different at work in Big Data practices and problem-solving approaches. By using three examples taken from the biomedical sciences—artificial neural networks, the construction of reference genomes, and the usage of the Ensembl database—this essay shows how Big Data practices cannot be understood as mere scaling up of pen-and-paper methods but constitute qualitatively different kinds of knowledge-making practices. These practices are characterized particularly by types of human-computer interaction that are labeled “a feeling for the algorithm.”
Journal Article
Starting up Biology in China
BGI (hua da ji ying;华大基因; “China Great Gene”) counts among the world’s largest and wealthiest institutions for biomedical research. Located in Shenzhen, the new megacity in southern China, BGI is now a critical site for understanding the relationship between biomedicine and the economic development of China. This essay uses performance studies and the notion of shanzhai (“copycatting”) to understanding how this laboratory poses a challenge to traditional modes of understanding technoscience. This marks an attempt to understand BGI, its work, and its workers on their own terms, or at least on local terms. Just as shanzhai challenges our notions of originality, BGI’s hybridity challenges our notions of where and how scientific knowledge is produced. Performing not merely as a “laboratory,” but also, and at the same time, as a “factory,” and a “company,” BGI is an unfamiliar kind of hybrid scientific-industrial-commercial-governmental-philanthropic space that draws its repertoire from its very particular regional, national, and local-urban circumstances.
Journal Article
Hadooping the genome: The impact of big data tools on biology
This essay examines the consequences of the so-called ‘big data’ technologies in biomedicine. Analyzing algorithms and data structures used by biologists can provide insight into how biologists perceive and understand their objects of study. As such, I examine some of the most widely used algorithms in genomics: those used for sequence comparison or sequence mapping. These algorithms are derived from the powerful tools for text searching and indexing that have been developed since the 1950s and now play an important role in online search. In biology, sequence comparison algorithms have been used to assemble genomes, process next-generation sequence data, and, most recently, for ‘precision medicine.’ I argue that the predominance of a specific set of text-matching and pattern-finding tools has influenced problem choice in genomics. It allowed genomics to continue to think of genomes as textual objects and to increasingly lock genomics into ‘big data’-driven text-searching methods. Many ‘big data’ methods are designed for finding patterns in human-written texts. However, genomes and other’ omic data are not human-written and are unlikely to be meaningful in the same way.
Journal Article