One of the things that’s hammered into your head as a baby scientist is the importance of running controls. Typically, you run a positive control–a ‘gamed’ experiment where you know what the outcome should be and which tells you that the experiment is working–and a negative control which should not give any results at all (e.g., a PCR reaction without any DNA) to make sure there’s no contamination or other spurious results. It’s always puzzled me why people don’t like to run controls because if you don’t do the controls, you’ll have to redo the experiment, which is a lot more work than if you had done it the right way the first time. Sadly, some scientists, even once they’ve done grew up, still don’t do controls and somehow manage to get published.
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.
This actually isn’t surprising, although it is astonishing that a paper could be published without adequate negative controls. When you run a PCR reaction, the enzyme that makes the whole replication procedure happen is known as Taq polymerase. Taq is short for Thermus aquaticus, which is the bacterium this enzyme was first isolated from. Many researchers often use ‘recombinant’ Taq–the gene is cloned into E. coli and then the Taq is produced by the E. coli*. Most people who work on E. coli (or genes found in E. coli) use ‘native’ Taq which is purified from T. aquaticus to avoid any possible contamination from E. coli DNA.
Here’s the really stoopid part: the cloning vector (the engineered mini-chromosome that has the Taq polymerase gene) also has a TEM-1 beta-lactamase gene because ampicillin resistance is used to kill off the bacteria that don’t have the cloning vector (and consequently can’t produce Taq polymerase). So if the manufacturer didn’t do a good job of eliminating DNA from the Taq polymerase, the negative control would indicate that there is a beta-lactamase gene even though there is no bacterial sample that is being tested.
Having said all of this, the rebuttal article begins on a very foul note (bold mine):
In 2004, an Asiatic group published an article entitled ‘Study on the molecular epidemiology of [beta]-lactamase TEM gene in isolated Streptococcus pneumoniae‘.
Asiatic? Sweet Baby Intelligent Designer, why not call them Mongoloid why they’re at it? You never hear someone rebut a paper by referring to a Jewish group**. Stupidity all the way around.
*People use recombinant Taq because it is either cheaper or included in ready-made mixes. T. aquaticus grows at very high temperatures and is far more expensive to culture than E. coli.
**On the other had, we Jews are fucking smart, so we likes our positive and negative controls.