Monday, September 03, 2007

Quality Genomic Reporting Award - Seeking Nominations

Well, Genome Technology magazine got on my case for being a bit too snarky with my "awards" saying
If Jonathan Eisen Offers You an Award, You Probably Want to Decline
Fair enough. I can be both passive aggressive and just plain aggressive about my opinions on how things should be done out there. And yes I have ended up focusing frequently on the negative (which is the case for both the awards I have begun dishing out here - the Adaptationomics Award and the Overselling Genomics Award). Plus, my giving out the latest award has taken away a bit from what should be an enormous positive vibe for the latest Wolbachia paper by Julie Dunning Hotopp and Jack Werren and colleagues, which is a spectacular piece of science.

So I have decided to try and be positive (occasionally) and have created a new award to give out - the Quality Genomic Reporting Award.

This award will be given to news articles (or blogs occasionally) written for the general public (e.g., in newspapers or news magazines) that do a good job of covering a scientific study involving genomic data.

At first, I wanted to give the award to HENRY FOUNTAIN for his article in the NY Times on September 4, 2007 entitled: "When Bacteria Transfer Genes to Invertebrates and Spread From There." This would have been ironic since this story is about the same scientific study that led me to give out the first Adaptationomics Award a few days ago (also see Larry Moran's discussion on his Sandwalk blog and Evolgen's).

I confess, when I saw the NY Times had an article in this Tuesday's Science Times about this Wolbachia story, I expected to find the same stuff that I went after in the Adaptationomics award and I was expecting an easy blog topic. But on first glance, Fountain seemed to do a pretty good job. For example he reports:
The researchers looked for Wolbachia genes in the genomes of more than 24 invertebrates, including wasps and nematodes, and found it in 8.
Thus providing a level of detail normally missing from genomic reporting. In addition, he does a good job of setting up the story:
But lateral gene transfer between bacteria and multicellular organisms has been assumed to be exceedingly rare, for the reason that most cells in a higher organism are somatic; their genetic material does not get passed on.
Alas though the story is good, it does contain some bits I am not keen on. For example, he reports that
This genome-within-a-genome involves Wolbachia pipientis, a bacterial parasite that is one of the most prevalent in the world, infecting close to three-quarters of all invertebrate species, typically in the reproductive cells
This is a bit misleading. The statement that Wolbachia infect 3/4 of all inverts is not really accurate. It would be better to say "some researchers estimate that Wolbachia infects up to 3/4 of all inverts." The research that I know of on Wolbachia prevalence in different species has focused on surveys of insects and arthropods (which are only a subset of invertebrates). And these studies have given conflicting results with some showing 20% of species surveyed being infected and others showing up to 70%.

But this is a minor quibble. And I was still getting ready to give Fountain the award. But then it ends the article with a quote by Jack Werren that fits into the Adaptationomics paradigm for the award I gave a few days ago:
“It’s happening frequently enough,” he added, “that it’s inevitably going to be leading to the evolution of new genes.”
Sure Werren might be right. And, in case people thought I was saying otherwise - he is more than welcome to state his opinion about things and give his insight even when evidence is not there. That is after all part of what makes science fun and interesting. And I should make clear, this is NOT meant to disparage the science in the Wolbachia paper. But when a scientist makes such a statement, it would be good for reporters to at least say specifically the speaker is predicting something that is not yet known. That is, just try to clarify what was supported by evidence and what was more of a jump.

So alas - this article is not going to get my Quality Genomic Reporting Award, even though overall it is pretty good. But pretty good is not good enough. So if anyone out there has good candidates for the award, let me know and I will keep looking too.


  1. So, how do you rate Nickolas Wade's today's NYT article on Venter's genome?

  2. You didn't protest the use of this "...for the reason that most cells in a higher organism are somatic...". I guess it might be a bit misleading since I don't think you'd differ between somatic and germ line cells in some of the highest organisms we got, Giant Sequoia. On another hand, I guess that most invertebrates stand a bit higher over the ground than the bacteria.

  3. "Junking the genome", New Scientist July 14, by Aria Pearson.

    Larry and I both approved.

  4. Yes, I meant to comment on the "higher" organisms and simply forgot.

    As for the Wade article, I have not yet read it completely. Although I did write to Wade from the Times online site since they misspelled Haemophilus.

  5. Thanks for the info about the New Scientist article. Alas I do not have a subscription so can now only read your blogs and the first paragraph of the article.


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