Thursday, November 02, 2006

Paramecium whining

I just got an announcement from Linda Sperling, announcing the publication of a paper on the Paramecium genome
Dear ciliate researcher,

We are pleased to announce that the Paramecium genome article is now available as an advanced online publication at the following address:

We thank all of you for your interest and support.

Jean Cohen and Linda Sperling

Linda Sperling
Centre de Génétique Moléculaire
Avenue de la Terrasse
91198 Gif-sur-Yvette CEDEX
+33 (0)1 69 82 32 09 (telephone)
+33 (0)1 69 82 31 50 (fax)

She sent this to an email list for ciliate researchers. I am writing about this in my blog because a blog is where you are supposed to write things these days when you are pissed off. Why am I pissed off about this? Well, the Paramecium paper makes no mention whatsoever of our paper on the genome of a close relative of Paramecium (Tetrahymena thermohila for those interested) which was published in August. And they do not even explicitly mention the Tetrahymena genome project (even though they say they took our data and used it). I guess I am not too surprised since their paper is published in Nature, which recently seems to be taking many liberties with referencing things in Open Access journals (ours was in PLoS Biology).

What is most annoying about this whole thing is that Linda Sperling is on the Scientific Advisory Board of our project, and has been privy to all of our work from the inside and was I am sure fully aware of our paper being accepted long before theirs was. Common courtesy in science would have been for them to have made a reference to our paper in press or at least our project. But for whatever reason, they carefulyl crafter their words to make no mention of our work. Interestingly, here is the email I sent to the same ciliate list on August 29, 2006

For those interested, our paper on the Tetrahymena MAC genome has been published online at PLoS Biology

Jonathan Eisen
Strikingly, their paper was then accepted August 31, 2006. I hate to believe in conspiracies, but it seems just a little too coincidental that their was accepted just after ours was published. And yet still no mention of our work in their paper. Hmmm ...

Fortunately, since our paper was in PLoS Biology, they cannot say "sorry - we did not have access to it." Whatever they say, I can say clearly that Linda Sperling will not be invited to our next SAB meeting.


  1. When I received Linda's email from the mailing list yesterday, I immediately read the Paramecium genome paper online. And I am, too, very surprised that they didn't even mention a word about Tetrahymena genome project (other than a link in the method section) and the PLoS paper. Tetrahymena and Paramecium are the only two ciliates that the whole genome sequences are available at this moment. In my opinion, any global comparison at the genomic level should be worthy to be addressed at least in a sentence or two in the discussion. But the Paramecium colleagues didn't do that. They did use some data for analysis from Tetrahymena genome project, as they indicated the TIGR website in the Methods, but they just ignored the reference, which has been published before this Nature paper was accepted.

    In this context, I do, too, feel that the Paramecium team "carefully crafter their words to make no mention" of the Tetrahymena work, as Jonathan pointed out. Facing the fact that nowadays the ciliate research community is somehow not proliferating comparing to the researchers working on other more fashionable, mainstream model organisms (i.e., fewer young scientists choose to work on ciliates), I always think the Tetrahymena and Paramecium people (and those studying other ciliates) have to be very cooperative and mutually supportive. I'm upset about the Paramecium peers' lack of courtesy shown in this Nature paper.

  2. Thanks for the comments --- I get more and more pissed off about this every day ...