John Timmer has a must read post on the coverage of science in the New York Times editorial pages. The science section of the NYTimes is probably the best in the country. Carl Zimmer leads the way, and there are many other solid science writers published by the NYTimes. Even Nicholas Wade, who has a known diction problem, manages to produce some pretty good articles.
This excellence in science reporting does not extend to the opinion pages. From Behe's article on Intelligent Design to Sam Brownback writing about evolution to a questionable piece on fMRI and politics the track record on the opinion pages is far from stellar. These are opinion pages, but they're often presenting opinions that are not based on facts and reality. If the times is fine presenting unsubstantiated opinions, they lose quite a bit of credibility. That may be the direction they're heading in.
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You might be asking too much of the opinion page editors. I doubt that they are qualified to assess the factual basis of every opinion piece they publish (including their own). I also doubt that they have (or think they have) the time to get informed analysis of opinion pieces. This is true not only of science but of every other subject about which they might publish.