Monday, July 16, 2007
Rated my first paper in PLoS One
Well, PLoS One has announced its rating system is open. See Chris Surridge's Blog for more detail here. This is basically the first good system for trying out ratings for scientific publications in much the way it is done at YouTube and other Web 2.0 type systems.
I personally am not sure if I think PLoS One is the perfect system for scientific publishing. But we desperately need to try out new systems and as an Open Access Web 2.0 scientific publishing system, the concept is worth trying. So - I decided to try it.
I rated my first paper. I picked a paper by Xiang Xia Min and Donal Hickey on DNA barcoding. Why did I pick this paper. Well a few reasons. First, when I searched PLoS One for "metagenomics" and "metagenomic" it was one of the papers that came up. As soon as I saw the Barcoding title line I knew I had to look at this paper. Why? Well a few years ago, I posted a "dissent" on Faculty of 1000 about a paper on Barcoding. I stand by my dissent in that article. Basically I said that Barcoding sounded a heck of a lot like what Pace and others have been doing with rRNA surveying of uncultured microbes for a long long time. And it seems to me that the barcoding researchers are rediscovering some of the same findings and challenges that Pace and others found. Of course, not all can see my Faculty of 1000 review. Why? Well it is not Open Access. Bummer. Especially since the response by Hebert was unconvincing too ... he basically said that rRNA was not used to delineate species. Apparently he had never heard of phylotypes or any of the extensive work using rRNA to do EXACTLY what they are suggesting mitochondrial genes could be used for in plants and animals.
Anyway - enough about Faculty of 1000. In the new paper, the authors discuss some aspects of barcoding and in particular they address whether one gene can represent all the genes in a mitochondrial genome. Basically, they say yes. But that is beside the point here. You want to know more. Read there paper here. And my comment here. That is yet another benefit of Open Access.
I call on everyone out there to find a paper in which you are interested and rate it and comment on it at PLoS One.
Min, X., & Hickey, D. (2007). DNA Barcodes Provide a Quick Preview of Mitochondrial Genome Composition PLoS ONE, 2 (3) DOI: 10.1371/journal.pone.0000325