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Well, basically, it's a database optimization thing.
I don't know if the metachat code is proprietary or not, or who owns it, so I don't want to go into greater deatil for fear of talking out of school. (If seanyboy allows me, I'll go on at my normal pedantic and sonorous length.)
Given what seanyboy did to get teh site moving again.
I'm not convinced it's completely the fault of the database yet ortho. There are slow sql queries, but they tend to be cached so they don't tend to make too much of an impact. The reason the site's zippier than it was yesterday may simply be due to the fact that metafilter is up. Compared to the same time yesterday, we're actually only processing about 20% of the page views.
Rimu seem to think the problem is with the PHP. Given the amount of code in there for forcing XHTML compliance, that wouldn't suprise me. There's a lot of string handling, and I've seen situations before where a constant & recursive conversion of text from and to an xml compatible format for validation causes problems.
As discussed, I'll see what I can do about getting some example scripts over to you. And once again, thanks for the help.