I'll try to do this at some point, so tag me if I haven't done this in the next day or two...just need to carve out some time, as you might guess this is a complex topic requiring some explanation. Before delving into any specifics of saturated fat and cholesterol. I do have a few thoughts on "research/process" in general and the way scientific thinking in a field gets shaped and preserved:
Dogma dies hard. Just my anecdotal experience in collaborating with physicians on research papers for a couple of years - I believe that most physicians are driven by a desire to do good, but I also believe that once they've attached themselves to a certain school of thought, some physicians have a really hard time letting go - even in the face of very strong evidence against. It doesn't happen much, but I have seen doctors abandon papers that we started working on because the findings didn't show what they expected, and they simply said "Well, we can't explain this, it makes no sense" and decided not to write a paper on the results; this is the so-called "file drawer" effect, where unattractive research findings are left sitting in the file drawer instead of being published.
Even when the lead author wants to proceed and we write a paper, sometimes you'll get resistance from the journal editors and/or peer reviewers if your message goes against conventional wisdom in that area. A year or two ago, I co-authored a paper comparing outcomes with a "new" antiplatelet drug (more expensive) compared against an "old" antiplatelet drug (which is available as a generic and costs a few pennies per day) in patients receiving a stent. When we looked at ongoing "real world" data of patients treated with the newer drug vs. the older drug followed over several years, it seemed that the benefit was at best trivial (and maybe none at all). We encountered stiff resistance from journals in trying to publish these findings - even though the data were analyzed properly and there was really no arguing with the results - simply because the editors and/or peer reviewers would say things like "How can you explain that the results with X are not any better than Y?" (our answer, of course, was "maybe the new drug isn't actually so superior to the old drug").
Point is, once something becomes mainstream thinking, it can be very hard to change people's minds, even in the face of strong evidence. Here's a well-written article on that particular subject, which I think everyone should read:
That is full of great nuggets, but here's one specific to this topic:
"Brown, the Washington University cardiologist, says that once doctors get out of training, “it’s a job, and they’re trying to earn money, and they don’t necessarily keep up. So really major changes have to be generational.”
This quote probably isn't fair to "doctors" as a whole - plenty of terrific doctors do make real efforts to stay on top of the latest science - but I think that last part is key, that really major changes have to be generational. If we have an entire generation of physicians that have been trained with a particular way of thinking, that will never just reverse itself overnight. It will only happen once that generation ages out and gets replaced by a new crop whose training included a different way of thinking.
Those are just a few thoughts on the scientific publishing process and how it can be difficult to go against or change mainstream thinking. I'll come back later with more specific thoughts on "cholesterol -> CHD" and "saturated fat is bad for you."