Are the problems with peer review anything to do with Open Access?

I just read a dreadful article by John Bohannon about dubious scientific practice that, itself, contained a pretty basic logical/scientific error.

Bohannon explains that he conducted a "sting" operation where he sent a set of spoof papers, containing deliberate and obvious flaws, to a large number of Open Access journals and 157 of the 304 journals accepted the article (he goes on to use a few selective variants to make the percentages look bigger, but let's agree that over 50% failure to detect the spoof article is already quite a bad record).

All well and good so far. We already know that peer-review is flawed (a google search for problems with peer review raises 39 million hits) due partly to the fact that many journals are run as profit-making entities. This data highlights that nicely. Now, the problem lies in Bohannon's implicit claim that this is caused by open access. He makes this claim carefully with phrases like, "reveals little or no scrutiny at many open-access journals" and says that his data raise, "questions about peer-review practices in much of the open-access world". These phrases are designed carefully to put in your mind that the problem is with open access, but note that he doesn't explicitly state that. He can claim afterwards that he only specified open access because that's the only domain for which he has data. But let's be clear, he intends to imply that open access is the cause.

Probably many of you have already spotted the issue here. Most of the comments following the article point it out. Certainly Bohannon himself understood it, which is why the digs highlighted above are phrased so carefully. But let's just spell it out with a study of analogous logic. If you were to run a study showing that nearly all men have ears, you don't get to claim afterwards that ears seem to be a feature of being male. You don't even get to imply that result from your data. To say anything about whether ears are a male-specific feature you also have to measure their occurrence in non-males. You might be right - ears might turn out to be a male feature - and when you have data to show that their occurrence in women is less common then feel free to discuss that. But not before then.

This is a basic scientific error, and a man claiming to be identifying problems in our scientific culture should be embarrassed to be making such deliberately misleading statements.

See also:
Michael Eissen, pointing out that Science Magazine also has also made some pretty shocking errors in their peer review
Jeroen Bosman's post, including links to many others