"I gather this means that it's not respected?"

Firstly, skepticism is basically just a new name for a discredited philosophical movement called 'logical positivism', in the same way that intelligent design is basically just a new name for creationism.

The section on positivism here has a brief summary:

http://plover.net/~bonds/nolongeraskeptic.html

I'm not sure where the best place to go for information on this would be though to be honest. Wikipedia has a brief article also but it's not especially helpful: http://en.wikipedia.org/wiki/Logical_positivism

"Are there any examples of this from the blog?"

- "It turns out that physicians view pharma funding sources negatively"

When there is disclosure that the studies were pharma funded. Often times this isn't disclosed even though it's supposed to be. Additionally, it's been proven beyond a doubt that pharma reps, dinners, gifts, etc. influence doctor's prescribing habits, but this is never mentioned, even though the point of the blog post is supposedly to show that it's rare for doctors to be under the influence of pharma.

- "On the other hand, this study also made me wonder if perhaps we place too much confidence in research funded by the NIH. [...] NIH funding is not a guarantee of quality science by any means."

Again the research unambiguously shows that pharma-funded research is vastly for more likely to find positive results for the drug in question than NIH research.

- "For example, a recent study found a correlation with government funding of a trial and positive results, and another study found no higher likelihood of positive outcomes in industry-sponsored trials but a higher likelihood of reporting double-blinding"

Even when he mentions that pharma sponsored studies are 'associated with' increased likelihood of favorable results, he cites one or two minor studies instead of the most important meta-studies on this topic.

- "Moreover, several studies have suggested that from a methodological standpoint industry-funded studies published in peer-reviewed journals are of equivalent or higher quality than clinical trials funded by other mechanisms."

Citation needed.

- "This is not surprising, given that many clinical trials funded by pharmaceutical companies are done for the purpose of winning FDA approval for a drug, either initially or for expanded indications, and the FDA has stringent requirements for these clinical trials."

So what he's really saying is that he's comparing apples and oranges.

- "Indeed, as I mentioned, this NEJM study doesn’t tell me anything that I didn’t already know"

The classic tactic of claiming that everything negative isn't important because it's 'something we already knew'

- "I’ve come to the conclusion that most doctors, at least in this sample, probably have it about right or may even be a little more skeptical of pharma than necessary."

You've got to be freaking kidding me. Again, look at the list of the most prescribed drugs, both psychiatric and non-psychiatric. And then look at what percentage of those are actually better than placebos or generics.

> "If you mean something else, then do elaborate.

In this case I was kind of referring to how preachers will get up on stage and do the gish gallup as an attempt to discredit evolution, as well as using emotional arguments and emotional tricks rather than facts or logic.

I generally do think that a lot of science falls into the category of scientism, but that isn't what I was getting at here. I also generally think there are good reasons for considering science to be a religion, but that's also not what I was getting at.