Thursday, March 31, 2011

Retraction vindicated? [?]

A headline at The Scientist is Retraction vindicated? A definition of "vindicate" is To provide justification or support for. One might thus read the headline as prefacing a story wherein further evidence is found to support the retraction.

No. The new evidence undermines the retraction. Also, one has to go deep into the article in The Scientist to learn that the new evidence is presented by the author of the retracted paper. This author, by the way, did not consent to the retraction, which was by the journal Cell. [In passing, Hwang Woo Suk did not consent to the retraction, by Science, of his two papers, but they were retracted anyway.]

Within the piece in The Scientist, as to the new papers (published in PLoS ONE paper and in PLoS NTD):

But not everyone is convinced. Much of the evidence presented in all three papers is based on PCR, which revealed bits of hybrid DNA containing genetic sequences from both the trypanosome and its host. But PCR is highly prone to artifacts, said Dunning Hotopp. "Any time you do a PCR and you have a sequence that's common between two pieces of DNA, you have the potential to create a chimera," which is then amplified during the subsequent rounds of PCR, she explained. "The results of the method could be chimeras that look like lateral gene transfer. I don't think that's what happening," she added, "but I think that's still a black mark against the paper."

According to some researchers, Teixeira and his team could easily quell the controversy surrounding the three papers. To validate the PCR results, Feschotte noted, it's important to use specific primers located in the regions flanking the suspected insertion and verify the sequence. "That would really be the nail in the coffin," he said, but "they don't do that."

Another potential validation is to visualize the suspected integration sites using a technique known as a southern blot, something Teixeira and his team did. Unfortunately, some researchers did not find the results of these tests conclusive.

There was one comment:

I'm confused. Why the controversy? This is not technically challenging to complete(subclone genome DNA, pull out insertions, sequence to identify insertion site, check prior to infection, possibly for chimerism in the infected subject and for genome-wide insertion in progeny). If the authors provided that, then it's pretty much a done deal. If the authors did not provide that, then it shouldn't be published. Have we collectively somehow lost the essence of experimental design, execution and conclusions? It's embarassing that we'd be even having this discussion in an online forum.


Post a Comment

<< Home