Part II of the thimerosal-autism controversy will be ready soon, but first I’d like to bring up a somewhat related topic: the notion that the medical or scientific community will reject out-of-hand any theory they don’t “like”, because it’s cumbersome, inconvenient or threatening to the “establishment”. This is called the Galileo gambit, to commemorate how Galileo was persecuted by the church for having unorthodox ideas. Similarly, those referring to this logical fallacy hope to convince others that their ideas are being rejected merely because they’re unpopular. It’s a favorite of the proponents of the autism/mercury hypothesis as well.
In fact, nothing could be further than the truth today*. While scientists may initially scoff at what sounds like an outlandish idea, if it has a semi-plausible mechanism, the people proposing the idea can demonstrate that it works scientifically, and other research teams can replicate their results, the idea will indeed gain traction. Though the scientist’s name is often invoked as a modern Galileo (even by himself), Dr. Barry Marshall’s 1982 discovery that ulcer disease is caused by a bacterium, Helicobacter pylori, the methods he used to prove his theory and its eventual acceptance and reward by the medical community (Dr. Marshall and his colleague, Dr. Robin Warren, won the Nobel Prize for medicine in 2005), show exactly how such ideas can gain legitimate traction within the medical community.
You might want to compare this chain of events to the proponents of the mercury/autism hypothesis: despite nearly a decade of scientific research by many groups all over the world and millions of dollars spent, no reliable studies have shown any evidence of autism being a form of mercury poisoning, nor has removal of thimerosal from vaccines caused any difference in autism rates.
A case of medical persecution of sorts did happen with Dr. Semmelweiss, father of asepsis.