Well, what I've read and heard so far about the recent publications on doping in Athletics boils down roughly to two sides. One is the classic "Armstrong defence", no athlete has tested positive (see the IAAF statement). The other side, the doping accusers (or maybe those who are tired of being fooled), are asking why the individuals involved are not prosecuted. I think both sides are, quite possibly deliberately, ignoring the (empirical/statistical) methodology used, focusing erroneously on individual cases. I think the methodology does not allow that, but still tells us a telling tale.
Let me explain:
In 1986, the Chernobyl disaster released a radioactive cloud that spread radioactive material over an estimated 40% of Europe's mainland. Long story short, after the event, there was a noticeably increased incidence of thyroid cancer in children in regions of Belarus, Ukraine and Russia. Due to the lack of other possible explanations and given the fact that exposure to radioactive material is linked to thyroid cancer, it is generally accepted that the Chernobyl disaster was the cause of the cancer spike. However, that does not mean that every individual case of thyroid cancer was caused by the exposure, as thyroid cancer has other caused as well. The reverse is also not true: Despite not being able to prove, for any single case, that the thyroid cancer was caused by the Chernobyl disaster, the sheer unlikelihood of the total number of cases occurring "naturally" gives credibility to the conclusion that at least some of the cases (most likely most of the cases) were caused by the Chernobyl disaster.
The same is true for the report on the number of abnormal blood values in Athletics. The vast number of abnormal values makes it unlikely that they are all naturally occurring, so the conclusion that something is going on (e.g., doping) is likely. However, while "abnormal" or "unlikely", we do know that those values occur naturally as well, in relatively rare cases. So while the total number suggest something is going on, we cannot use that fact to say that any individual case must be caused by something unnatural, just like we can't say that all of the thyroid cancer case were caused by the Chernobyl disaster.
This, in turn, show that the "defence" of the IAAF is besides the point: This report does not try to prove for any single case that doping was the cause of the abnormal values, so saying that it cannot prove what it does not pretend to prove ("no single athlete has tested positive") is no defence at all against the claim that the sheer number of abnormal values point to an unnatural cause (e.g., doping). The total number of athletes with abnormal values shows that something is going on, so their statement only makes it worse for them: They were not able to catch a single one of the dopers.
However, unfortunately for the accuser, the reverse it also true: While we know that something sketchy is going on, it is quite probable that for some individuals those numbers are in fact natural. So, just like with the thyroid cancer cases, while we know that a lot of the cases were probably caused by doping, we have no way of discerning which.
In a perfect world, we would now update the prior probability of doping use for the suspect individuals in their ABP (athlete's biological passport). However, we're currently bound to the "innocent until proven guilty" principle, thus artificially setting the prior probability of doping use to zero. Still, I would have liked to know if changing the parameters of the Bayesian network would highlight some "interesting" individuals.