Strain Mixups and Retractions

Back when I was a younger Mad Biologist, I received dozens of bacterial strains from a Very Prestigious Lab that were supposed to belong to species A and B. Very Prestigious Lab had published several papers on these strains, and had tied them to some experimental evolution work on species A. I was interested in the population genetics of A and B, and was fortunate to have a summer student working with me, so I thought determining the MLSTs–multilocus sequencing types–of these strains would be an excellent project. I get some data I wanted to incorporate into a grant, she would a surefire project that would lead to some interesting sequence analysis and population genetics.

However, we couldn’t even get the PCR to work, never mind the sequencing. We tried everything, and finally we decided to use some universal primers (gyrB for anyone who cares) and finally…successful PCR and sequencing!

Unfortunately, the sequencing revealed that we had a very nice collection of species C and D, which were kind of similar to A and B–if by similar one means that, at a minimum they diverged before the K-T mass extinction event.

Quelle bummer, as the kids used to say.

While I dutifully reported this back to Very Prestigious Lab*, I don’t think anything ever happened. So we read this retraction notice with great interest (boldface mine):

Two samples of bacteria that were mislabeled several years ago have led to the retraction of two papers, including a highly-cited one published in Science.

In 2009, a team of scientists from the University of California, Davis, led by plant geneticist Pamela Ronald, identified a bacterial molecule that is recognized by the immune system of rice plants. It was the culmination of the lab’s longstanding quest to understand how this vital crop thwarts infections, and the paper has since been cited 131 times.

But when new lab members could not repeat the earlier results, the team discovered that one of the previous experiments had been done with mislabeled bacterial strains, while another had used an unreliable test. Ronald announced the problems to others in the field at conferences, and has now retracted the paper.

“There was never any question, even from the people who did the original work, that we do anything different than retract the paper if it was wrong,” said Ronald. “We didn’t want to mislead anyone else.”

Here’s where it gets interesting:

To complicate matters, at least three Chinese labs have successfully replicated Ronald’s Ax21 experiments. “I’ve talked to all the other laboratories, and they’re all confident in their results,” Ronald said. Wenxian Sun from China Agricultural University, who led one of the studies published online in Phytopathology, said that he has delayed formal publication until he can repeat the key results. The other teams did not respond to requests for comments.

“The fact that several labs have reported what might now be viewed as questionable data makes one pause,” said Sophien Kamoun, a plant biologist at the Sainsbury Laboratory. Along with the Chinese studies, he points to three other papers that are either “compromised or questionable” because they also involve Ax21: one from Ronald’s group, which found that XA21 gets cut and relocated after exposure to Ax21; one that lists Ronald as a collaborator, which found that Ax21 interacts with another immune receptor called FLS2; and a third from an independent lab, which found that some bacteria use Ax21 to communicate with each other—a similar result to Ronald’s now-retracted PLOS ONE paper.

I’m not sure what’s going on here, as I know little about phytopathology, but something very weird is going on here. I don’t see how one can build on erroneous work. There very well could be an innocuous explanation for this, but figuring this out is far more important than some bullshit pseudo-sting of crap OA journals. If we can’t trust the existing literature, then we’re in trouble.

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1 Response to Strain Mixups and Retractions

  1. Robert L Bell says:

    We are well and truly fucked.

    In my particular subfield, people rarely “waste” valuable time and scarce resources in replicating the precise work report in the literature. Rather we press on with closely related work that builds upon and extends the literature work. In this way an intricate web of interlocking results encompasses the entire field; individual strands may break, but the web as a whole is sound.

    Until too much strain is placed on too many weak links and frayed strands. Then we face wholesale failure and the destruction of good knowledge along with the bad.

    Good luck on getting this sorted out.

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