Did Finishing the Drosophila Genome Legitimize Open Access Publishing?

I’m currently reading Glyn Moody‘s (2003) “Digital Code of Life: How Bioinformatics is Revolutionizing Science, Medicine, and Business” and greatly enjoying the writing as well as the whirlwind summary of the history of Bioinformatics and the (Human) Genome Project(s). Most of what Moody says that I am familiar with is quite accurate, and his scholarship is thorough, so I find his telling of the story compelling. One claim I find new and curious in this book is in his discussion of the sequencing of the Drosphila melanogaster genome, more precisely the “finishing” of this genome, and its impact on the legitimacy of Open Access publishing.

The sequencing of D. melanogaster was done as a collaboration with between the Berkeley Drosophila Genome Project and Celera, as a test case to prove that whole-genome shotgun sequencing could be applied to large animal genomes.  I won’t go into the details here, but it is a widely regarded fact that the Adams et al. (2000) and Myers et al. (2000) papers in Science demonstrated the feasibility of whole-genome shotgun sequencing, but it was a lesser-known paper by Celniker et al. (2002) in Genome Biology which reported the “finished” D. melanogaster genome that proved the accuracy of whole-genome shotgun sequencing assembly. No controversy here.

More debatable is what Moody goes on to write about the Celniker et al. (2002) paper:

This was an important paper, then, and one that had a significance that went beyond its undoubted scientific value. For it appeared neither in Science, as the previous Drosophila papers had done, nor in Nature, the obvious alternative. Instead, it was published in Genome Biology. This describes itself as “a journal, delivered over the web.” That is, the Web is the primary medium, with the printed version offering a kind of summary of the online content in a convenient portable form. The originality of Genome Biology does not end there: all of its main research articles are available free online.

A description then follows of the history and virtues of PubMed Central and the earliest Open Access biomedical publishers BioMed Central and PLoS. Moody (emphasis mine) then returns to the issue of:

…whether a journal operating on [Open Access] principles could attract top-ranked scientists. This question was answered definitively in the affirmative with the announcement and analysis of the finished Drosophila sequence in January 2003. This key opening paper’s list of authors included not only [Craig] Venter, [Gene] Myers, and [Mark] Adams, but equally stellar representatives of the academic world of Science, such as Gerald Rubin, the boss of the fruit fly genome project, and Richard Gibbs, head of sequencing at Baylor College. Alongside this paper there were no less than nine other weighty contributions, including one on Apollo, a new tool for viewing and editing sequence annotation. For its own Drosophila extravaganza of March 2000, Science had marshalled seven paper in total. Clearly, Genome Biology had arrived, and with it a new commercial publishing model based on the latest way of showing the data.

This passage resonated with me since I was working at the BDGP at the time this special issue on the finishing of the Drosophila genome in Genome Biology was published, and was personally introduced to Open Access publishing through this event.  I recall Rubin walking the hallways of building 64 on his periodic visits promoting this idea, motivating us all to work hard to get our papers together by the end of 2002 for this unique opportunity. I also remember lugging around stacks of the printed issue at the Fly meeting in Chicago in 2003, plying unsuspecting punters with a copy of a journal that most people had never heard of, and having some of my first conversations with people on Open Access as a consequence.

What Moody doesn’t capture in this telling is the fact the Rubin’s decision to publish in Genome Biology almost surely owes itself to the influence that Mike Eisen had on Rubin and others in the genomics community in Berkeley at the time. Eisen and Rubin had recently collaborated on a paper, Eisen had made inroads in Berkeley on the Open Access issue by actively recruiting signatories for the PLoS open letter the year before, and Eisen himself published his first Open Access paper in Oct 2002 in Genome Biology. So clearly the idea of publishing in Open Access journals, and in particular Genome Biology, was in the air at the time. So it may not have been as bold of a step for Rubin to take as Moody implies.

Nevertheless, it is a point that may have some truth, and I think it is interesting to consider if indeed the long-standing open data philosophy of the Drosophila genetics community that led to the Genome Biology special issue was a key turning point in the widespread success of Open Access publishing over the next decade. Surely the movement would have taken off anyways at some point. But in late 2002, when the BioMed Central journals were the only place to publish gold Open Access articles, few people had tested the waters since the launch of BMC journals in 2000. While we cannot replay the tape, Moody’s claim is plausible in my view and it is interesting to ask whether widespread buy-in to Open Access publishing in biology might have been delyaed if Rubin had not insisted that the efforts of the Berkeley Drosophila Genome Project be published under and Open Access model?

UPDATE 25 March 2012

After tweeting this post, here is what Eisen and Moody have to say:

UPDATE 19 May 2012

It appears that the publication of another part of the Drosophila (meta)genome, its Wolbachia endosymbiont, played and important role in the conversion of Jonathan Eisen to supporting Open Access. Read more here.

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1 Response to “Did Finishing the Drosophila Genome Legitimize Open Access Publishing?”



  1. 1 Fifteenth Linkfest Trackback on July 6, 2012 at 3:16 am

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