One reason that I have doubts about thimerosal as a cause of autism goes back to mechanism of action. Are there any specific compounds that are know to cause specific neurological problems? (There are plenty that cause more diffuse symptoms, often motor-related, such as tardive dyskinesia.)

Well, there's one prominent example: MPTP, known to the trade as 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine. It's a reasonably simple organic molecule, and to a medicinal chemist it certainly looks like a central nervous system agent (if I had a dollar for every CNS-active piperidine or piperazine that's been reported in the patent literature, I could retire.) But no one could have predicted what it actually does.

The compound gets oxidized by monoamine oxidase B, which is a common fate for molecules of its type. That produces a pyridinium compound which is the real problem. As fate would have it, it's a fine substrate for the dopamine transporter protein, which imports dopamine into cells that require it. And in a further stroke of bad luck, the same compound is also an inhibitor of a key enzyme in mitochondria - and you don't want to do anything to your mitochondria. Cell death follows in short order if you shut them down too hard.

So everything's set up for a disastrous cascade: MPTP's turned into something dangerous, which is taken up selectively into cells that import a lot of dopamine, which process then kills them. Unfortunately, the cells that import the most dopamine are those in the substantia nigra, up in the forebrain. Which is why in the late 1970s and early 1980s, a number of young drug users started showing up in emergency rooms on the west coast with what appeared to be some sort of catatonia. They didn't move; they weren't responsive - everyone waited for whatever it was to wear off so they could start to recover.

It didn't, and they didn't. At first, no one recognized what was going on, mainly because no one had ever seen a twenty-year-old with advanced Parkinson's disease before. These patients had taken batches of some sort of home-brewed meperidine (better known as Demerol) or a derivative, and the synthetic route had produced some MPTP as a contaminant. Quality control isn't a big feature of the basement drug industry.

The affected users improved slightly when given L-Dopa, as you'd expect from a Parkinson's patient. But not much, and not for long. The damage is permanent - they skipped years of the normally slow progression of the disease and went straight to its worst phase in one night. Is this what's happening with thimerosal and autism?

I strongly doubt it. Here's why: Parkinson's is caused by a lesion in a specific area of the brain, in a specific (and unusual) cell type. MPTP is toxic to some specific and unusual cell types, and it's just a terrible stroke of misfortune that they happen to overlap. But despite a tremendous search, no one has been able to tie autism to primary lesions in a specific region of the brain, much less down to certain cells. I'm not saying that it's impossible - just that it's been looked for strenuously, and thus far in vain. Studies of brain activity in autistic patients show a variety of differences, but nothing that can be pinned down as a cause.

The other half of the story is the reactivity of thimerosal itself. There's nothing known about the compound that would suggest that it has a particular affinity (or particular toxicity) to any one type of cell over another. Organomercury compounds are (in high doses) pretty bad news in general, causing all sorts of neurological problems. They just don't seem to be specifically toxic.
So there's no evidence, mechanistically, on either side of the hypothesis. That doesn't disprove it, of course - it's not impossible that there would be some sort of subtle effect that we've missed so far. It's just that I believe that the odds are very much against it. We'd have to string together too many (big) assumptions in a row, and the evidence isn't nearly compelling enough to make us do that.
If thimerosal is cleared as a possible agent for autism, that'll be good news and bad news. The good news is, of course, that we haven't been damaging children without realizing what we're doing. The bad news will be that we still won't know why some children become autistic and others don't, a lack of knowledge that's hard to bear.

The only other good news I can think of - and a hard, sour piece of good news it is - would be that parents of autistic children who have feared that they were the cause of their children's condition - just by having them vaccinated - could at least put that part of their burden down. It's not enough, but it's something. Believe me, I have two small kids myself, and the thought of either of them showing signs of neurological trouble makes me start to double over. I can't even imagine what it must be like. But to those in that situation, all I can say is that I really don't think that some doctor did it to your child. Or that some drug company did it to your child. Or that you did, either. For what it's worth.