First, I can't say I understand Behe's point so it is hard to criticize directly. However, I can say that if one were to look at animal breeds developed by artificial selection, I am fairly sure we can find lots of cases where the breeds differ by multiple mutations. However, it is always difficult to determine what mutations produce particular traits - so it is difficult to say something like "the new breed showed 4 mutations and 3 of those are beneficial".
Suppose you were a pigeon breeder trying to get a breed a fancy pigeon and after 200 generations you get this from a regular pigeon
Ok, now suppose you find that the new pigeon has 3 mutations in their genome. Were these beneficial? Did you need all three of the mutations to get this bird? You could try to do an experiment and change some of the genes back but that would take some clever gene splicing (but possible).
It is possible to also get these different mutations sequentially, which some might consider to be unsurprising micro-evolutionary steps.
I think Behe might be trying to argue that all three are unlikely to occur at the same time. But even there I would need to know the particular assumptions made. Suppose, for example, every new generation has 3 mutations on average at random places. Out of all the offspring with 3 mutations, I take the one I think looks pretty and allow those to breed. Ok, since at least one of those worked out, the answer is about 100% probability that the new breed will have 3 mutations.
None of this seems surprising to me. So I don't know what Behe finds surprising. I don't think he is arguing that plasmodia can't evolve resistance because we know it does. Is he suggesting that plasomodia is helped by God?
Behe appears to know the way most biologists believe information gets added to the genome. To quote Behe:
"Gene duplication is thought to be a major source of evolutionary innovation because it allows one copy of a gene to mutate and explore genetic space while the other copy continues to fulfill the original function."
So he seems to know how it works, but he doesn't think it is probable enough. Unfortunately, I don't get his math.
p.s. The Nova show used transcripts to show what Behe and other said in the trial so I am not sure if you suggesting the show was unfair or that the judge in the trial was unfair.
I need to reread Behe' s book to make sure I am representing his thesis correctly. We may be talking apple's and oranges.
Is he suggesting that plasomodia is helped by God?
No, I don't think Behe is making a statement about God either way. He is making a case against macro-evolution: small changes x millions years = big change
From this web site I found and article that talks about mutation build up. The basic premise is that negative mutations greatly exceed positive ones that the mutation build up is negative. It is actually a case that we are regressing not evolving.
This is important since evolution requires "beneficial" mutations to build up and outpace harmful mutations such that new features and organs can arise (I say "beneficial" loosely, since there are no known examples where a mutation added information to the genome, though there are some that under certain circumstances can provide a temporary or superficial advantage to a species). If over time harmful mutations outpace "beneficial" ones to fixation, evolution from molecules-to-man surely cannot occur. This would be like expecting to get rich despite consistently spending more money than you make.
This may address that A B and C mutation statement you talked about earlier. This is what I think you where saying in my own words.
Mutation B hangs around not providing much benefit until mutation C happens. The combination of mutations B and C are far superior than mutation A.
The article states that negative mutations builds up much faster than positive ones. Hence, the effect of mutation build up is very negative.