Digital Biology Friday: You make the call!

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Sandra Porter
One time I was watching a football game on TV and they had a short quiz, called "You make the call" or something like that, and you had to watch a play and pretend to be a referee. A short video clip showed football players falling over each other. Then you were three possible calls that a refereee might make and asked to chose which was correct. After the commercial, the announcer would tell you which choice was right and explain why it was correct. I suppose this was a trick to make us watch the commercials, but I thought the game was kind of fun. My SciBling "Mike the Mad" had a great post the other day about a scientific publication that I thought we could use in a similar way. So, like the football fans, we're going to play: "You make the call!" or maybe "You do the review!" or even "What's wrong with this conclusion?" (If you have a catchy name for this, I'm open to suggestions.) Naturally, I liked what Mike wrote about controls, since I like controls, too. But after reading the abstract and looking at the data myself , I concluded that the paper should have been rejected by the reviewers at the outset because the data themselves suggest that there's a problem. Before we begin, here's some background from Mike:
In 2004, a group published a PCR survey that indicated that the TEM-1 beta-lactamase resistance gene was found in 91.3% of examined Streptococcus pneumoniae. This is a surprising result because beta-lactamases aren't found in S. pneumoniae. In a recent paper in the Journal of Antimicrobial Chemotherapy, another research group found that when they ran only negative controls (i.e., just the reagents and no DNA), DNA contaminants yielded false positive results.
Your challenge is to:
  • 1. Get the abstract
  • 2. Have a look at what you can find at the NCBI and
  • 3. tell me in the comments what sorts of things you can find that suggest that there's a problem with the conclusion drawn in the Chinese paper.
And I want to see data and/or citations from peer-reviewed papers - not anecdotes and hearsay. (Yes, yes, we all know that Taq polymerase can be contaminated with DNA, but that's not good enough.) Also - I should point out there's more than one right answer to this problem. And I will even let you use hindsight. The paper was published in 2004, but you if you find evidence from a later year - except for the paper that Mike cited - go ahead and submit it in the comments.

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