Correct me if I'm wrong, but I get the impression that he thinks our current approach to science is wrong due to our tendency to attribute cause and effect to things where we have no conclusive proof of cause and effect?
Well, if he has a better suggestion on how to approach research, I'm all ears!
First off, I don't think ANYONE who was involved with the development of torcetrapib thought it was a "slam dunk". The success rate of drugs that have reached phase III is only slightly north of 50%.
Second, there is no way you could possibly figure out all the effects a particular drug has on the human body. You'd be doing research for the next 100 years and you still wouldn't come close. So what we do is we come up with a hypothesis (high HDL is good), we gather evidence in the most efficient manner we can (other drugs that raise HDL help prolong life in humans and animals), then we move forward with our BEST GUESS. That's how science works, you create a hypothesis, then test it.
Are our hypotheses wrong sometimes? Of course. Do we learn something from the failures? Yes. Trying a being successful 10% of the time is far better than not trying at all and being successful 0% of the time.
Merck's CETP inhibitor is in phase III right now and there is a chance that it will fail too. And I don't think any scientists feels that high HDL is the cause of reduced cardiac risks. A more accurate description would be to say "High HDL is associated with reduced cardiac risks, this drug increases HDL levels, so it stands a chance of reducing cardiac risks".
I think the author does a bad job of describing how scientists approach their work. If anything a scientist would be the first to call out a claim that something _causes_ something else. That's how their trained!