Computational methods and perspectives can transform the history of science by enabling the pursuit of novel types of questions, dramatically expanding the scale of analysis , and offering novel forms of publication that greatly enhance access and transparency. This essay presents a brief summary of a computational research system for the history of science, discussing its implications for research, education, and publication practices and its connections to the open-access movement and similar transformations in the natural and social sciences that emphasize (...) big data. It also argues that computational approaches help to reconnect the history of science to individual scientific disciplines. (shrink)

As the international genomic research community moves from the tool-making efforts of the Human Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work - and for understanding who we are as biological organisms. In this essay we focus on the Human Microbiome Project as one such translational initiative. The HMP is a new 'metagenomic' research effort to sequence the genomes of human microbiological flora, in order to pursue the (...) interesting hypothesis that our 'microbiome' plays a vital and interactive role with our human genome in normal human physiology. Rather than describing the human genome as the 'blueprint' for human nature, the promoters of the HMP stress the ways in which our primate lineage DNA is interdependent with the genomes of our microbiological flora. They argue that the human body should be understood as an ecosystem with multiple ecological niches and habitats in which a variety of cellular species collaborate and compete, and that human beings should be understood as 'superorganisms' that incorporate multiple symbiotic cell species into a single individual with very blurry boundaries. These metaphors carry interesting philosophical messages, but their inspiration is not entirely ideological. Instead, part of their cachet within genome science stems from the ways in which they are rooted in genomic research techniques, in what philosophers of science have called a 'tools-to-theory' heuristic. Their emergence within genome science illustrates the complexity of conceptual change in translational research, by showing how it reflects both aspirational and methodological influences. (shrink)

As the international genomic research community moves from the tool-making efforts of the Human Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work – and for understanding who we are as biological organisms. In this essay we focus on the Human Microbiome Project as one such translational initiative. The HMP is a new ‘metagenomic’ research effort to sequence the genomes of human microbiological flora, in order to pursue the (...) interesting hypothesis that our ‘microbiome’ plays a vital and interactive role with our human genome in normal human physiology. Rather than describing the human genome as the ‘blueprint’ for human nature, the promoters of the HMP stress the ways in which our primate lineage DNA is interdependent with the genomes of our microbiological flora. They argue that the human body should be understood as an ecosystem with multiple ecological niches and habitats in which a variety of cellular species collaborate and compete, and that human beings should be understood as ‘superorganisms’ that incorporate multiple symbiotic cell species into a single individual with very blurry boundaries. These metaphors carry interesting philosophical messages, but their inspiration is not entirely ideological. Instead, part of their cachet within genome science stems from the ways in which they are rooted in genomic research techniques, in what philosophers of science have called a ‘tools-to-theory’ heuristic. Their emergence within genome science illustrates the complexity of conceptual change in translational research, by showing how it reflects both aspirational and methodological influences. (shrink)

Research on the human microbiome has generated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and enterotype—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statistical methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the dimensionality of variation (...) in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of personalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)

Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the (...) dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)