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I've wondered about this, too. Luckily, we've got the answer from the ultimate source, New Yorker Head of Library Jon Michaud. Here's the reader's question:
I was trying to find that really, really long profile of Matthew Barney that ran a year or two ago, but I can't find it—I only come up with some Talk of the Town references and a review or two. And some of the Google hits lead to dead links anyway.
Any idea?
It's a complicated answer, so here goes:
The New Yorker web site only publishes selections from each week's print issue. Those selections go up each Monday, except for the second Monday of a double issue.
At the end of a given week, the links to the stories on the web site are broken, but those stories remain on the web site (except, in some cases, when there are electronic rights restrictions) and are searchable through the search engine on the NewYorker.com site. That search engine will only find articles from February of '05 to the present. (This is not an arbitrary cutoff: The Complete New Yorker goes up to Feb. of '05.) Stories published on the web site prior to Feb. '05 are still up and can be found using Google.
As for the Matthew Barney, it did not run on our web site. It appeared in the magazine on January 27, 2003, by Calvin Tomkins. If your correspondent wants to read it, he has four options: get it from Lexis-Nexis or ProQuest, make a copy from a library, buy a back issue from 1-800-825-2510, or buy The Complete New Yorker.

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Comments
Amazon is filled with people complaining about the glitchy interface the DVDs have--have you had any problems? I was set to buy last Christmas, but didn't when I read all the whining.
I'd buy it. I've found that the usefuless far outweighs the glitches--there are definitely kinks to be worked out, but it's still an exhilarating experience and incredibly handy for research.