Showing posts with label museum collections. Show all posts
Showing posts with label museum collections. Show all posts

Tuesday, April 08, 2014

The Experimenter’s Museum: GenBank, Natural History, and the Moral Economies of Biomedicine

An undergraduate student (Aime Rankin) doing a project with me on citation and impact of museum collections came across a paper I hadn't seen before:
Strasser, B. J. (2011, March). The Experimenter’s Museum: GenBank, Natural History, and the Moral Economies of Biomedicine. Isis. University of Chicago Press. doi:10.1086/658657


Unfortunately the paper is behind a paywall, but here's the abstract (you can also get a PDF here):

Today, the production of knowledge in the experimental life sciences relies crucially on the use of biological data collections, such as DNA sequence databases. These collections, in both their creation and their current use, are embedded in the experimentalist tradition. At the same time, however, they exemplify the natural historical tradition, based on collecting and comparing natural facts. This essay focuses on the issues attending the establishment in 1982 of GenBank, the largest and most frequently accessed collection of experimental knowledge in the world. The debates leading to its creation—about the collection and distribution of data, the attribution of credit and authorship, and the proprietary nature of knowledge—illuminate the different moral economies at work in the life sciences in the late twentieth century. They offer perspective on the recent rise of public access publishing and data sharing in science. More broadly, this essay challenges the big picture according to which the rise of experimentalism led to the decline of natural history in the twentieth century. It argues that both traditions have been articulated into a new way of producing knowledge that has become a key practice in science at the beginning of the twenty-first century.

It's well worth a read. It argues that sequence databases such as Genbank are essentially the equivalent of the great natural history museums of the 19th Century. There are several ironies here. One is that some early advocates of molecular biology cast it as a modern, experimental science as opposed to mere natural history. However, once the amount of molecular data became too great for individuals to easily manage, and once it became clear that many of the questions being asked required a comparative approach, the need for a centralised database of sequences (the "experimenter's museum" of the title of the paper) became increasingly urgent. Another irony is that the clash between molecular and morphological taxonomy overlooks these striking similarities in history (collecting ever increasing amounts of data eventually requiring centralisation).

Bruno Strasser's article also discusses the politics behind setting up GenBank, including the inevitable challenge of securing funding, and the concerns of many individual scientists about the loss of control over their data. A final irony is that, having gone through this process once with the formation of the big museums in the 19th century, we are going through it again with the wrangling over aggregating the digitised versions of the content of those museums.

Update: See also
Strasser, B. J. (2008, October 24). GENETICS: GenBank--Natural History in the 21st Century? Science. American Association for the Advancement of Science (AAAS). doi:10.1126/science.1163399
(via Guanyang Zhang).

Thursday, May 16, 2013

The impact of museum collections: one collection ≈ one Nobel Prize

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Ideas on measuring the "impact" of a natural history collection have been bubbling along, as reflected in recent comments on iPhylo, and some offline discussions I've been having with David Blackburn and Alan Resetar.

My focus has been at the specimen-level, with a view to motivation the adoption of persistent specimen-level identifiers so that we can citations of specimens over time (e.g., in publications and databases such as GenBank). Not only does this provide a measure of the "impact" of a collection, it helps with provenance. If we sequence a specimen that is subsequently assigend to a different taxon and we have a way of tracking that specimen via its identifier, then we can transmit that new identification to other consumers of data based on that specimen. For example, we could automatically notify GenBank that what we thought was an x is actually a y.

So I made a simple "league table" of museum collections based on specimens cited in BioStor. There are all sorts of issues with this approach. Once you rank collections, people may use that to argue some can be axed and more resources funnelled into others. A more positive approach would be to indetify collections that are underused, and try and figure out why. And in the same way that taxonomic papers may have a citation long life, specimens may sit in a museum for a long time before being cited (for example, when eventually recognised as a new species doi:10.1016/j.cub.2012.10.029). So, metrics can be a double-edged sword.

Citing specimens is a useful metric, but not all citations are equal, and not all citations are immediate. A specimen that yields DNA sequences that are published in, say, Nature, arguably has more weight than a specimen listed in a rarely cited paper. Likewise, subsequent citations of a paper that cites a specimen should confer more weight on the value of that specimen. Elsewhere (doi:10.1093/bib/bbn022, preprint here: hdl:10101/npre.2008.1760.1) I've argued for a Google PageRank-style way to measure the impact of a specimen that takes into account papers and other objects derived from a specimen (e.g., images, sequences).

Meanwhile, Morgan Jackson alerted me to a quicker way to get a measure of the impact of the collection.

The "short note" Morgan refers to is by Kevin Winker and Jack J. Withrow:
Winker, K., & Withrow, J. J. (2013). Natural history: Small collections make a big impact. Nature, 493(7433), 480–480. doi:10.1038/493480b

They constructed a Google Scholar profile and collected papers that cite the University of Alaska Museum's bird collection (see here for full details). The h-score of this collection of papers is 42, which Winkler and Withrow note is "equivalent to an average Nobel laureate in physics". Here's the graph of citations over time:

Chart  1
It's a neat trick, if a little time consuming. But one advantage it has is that it puts collections on a similar footing to individual researchers. You could imagine asking the question "how much money would you spend supporting a researcher at this level?" How does this compare to the resources actually being spent?

One thing I hope will emerge from discussions like this is a desire to make specimens first-class citizens of the web, with stable identifiers that enable them to be cited in the same way we cite papers and, increasingly, data sets.