These journal publications that refute Dr. Wakefield's findings (Lancet, 1998) are only looking at the relationship between autism and MMR in terms of statistical revelance. The recent one you mentioned (JAMA, March) compared the increase in autism rates with the increase of MMR vaccination rates during 1980 to 1994 in California. They found that even though MMR vaccinations rates increased after its licensure for use and then leveled off, the rates of autism continued to increase. There are serious problems with this type of research that only looks at statistical data to refute a physical discovery. In this case, the first problem lies with the fact that it did not address the fact that Dr. Wakefield found the live vaccinal (not wild) measles virus in his autistic patients' guts. I might add that Dr. Wakefield did not claim the MMR to cause autism, he only suggested that an investigation needed to be undertaken to determine if the MMR was causitive in the children's subsequent development of autism. Secondly, recent independent autism reseach implicates all vaccines containing thimerasol (50% mercury) in the increased rates of autism. MMR may just be one of several environmental exposures our children are damaged by. The March, JAMA research's statistical evidence cannot possibly refute a causative role. The mitigating factors are of significant consequence.
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