You misunderstand. The first paper that I linked was not written for the Bad Science web site, that’s simply where you can most readily find it. Your criticism is ridiculous.
In fact, that paper represents a distillation of over 1,500 that Dr. Bustin (an acknowledged expert on the polymerase chain reaction that was the essential technique Wakefield used in the paper that you cited) devoted to analyzing the equipment, techniques, equipment, and original laboratory notebooks used in Wakefield’s work. The paper succinctly details the problems associated with Wakefield’s work, and shows that Wakefield could conjure a positive result from a reaction where that result should be quite impossible. For a fuller account of Bustin’s smackdown of Wakefield’s work, you can read his testimony at the Cedillo hearing at the Omnibus Autism Proceedings.
“I would think a gastroenterologist who had worked at the Royal Free for 14 years or so before the 1998 paper would be intelligent enough to know the difference between measles virus and human DNA.”
You misunderstand. Bustin’s analysis of Wakefield’s work clearly shows that Wakefield’s reactions produced “positive” results due to the presence of DNA contamination in reactions which included no sample at all, and the other papers clearly show that the PCR primers used in Wakefield’s work produced false-positive results by reacting with human DNA sequences. That’s not surprising: virtually any PCR reaction can produce false positive results with human DNA. The real challenge of PCR work is to make the reaction as specific as possible to reduce that possibility and then to check whether results that initially seem to be positive are truly positive or false positives.
“Again, how do they really know that Wakefield detected human DNA with the Crohns study?”
The authors used the same primers that Wakefield used. They demonstrated that the reactions almost invariably produced false-positive results that could only be shown to be false by performing additional careful analysis that Wakefield did not do. The authors sequenced reaction products and demonstrated that they corresponded to human DNA and not to measles sequences. The authors were not able to perform the tests on the sample that had been used in Wakefield’s work; I understand that those important samples cannot be located. However, Wakefield’s student Dr. Nick Chadwick testified that when he tested gut biopsy samples from autistic children for measles virus RNA in Wakefield’s own lab at the Royal Free Hospital, “I used a method to see whether [the initial results] were real positive results or false positive, and in every case they turned out to be false positive results.”