The philosophy of mainstream science that nature has its own method, without the possibility of supernatural influence on, say, how DNA is sequenced. William S. Harris, a chemist who helped write Kansas' alternative science standards questioning evolution, said that methodological naturalism puts blinders on the search for truth.
I'd say that science doesn't forbid the possibility of the supernatural, it just says that science can't do anything with supernatural explanations. It's possible that your computer froze up yesterday because of an evil spirit, but the only useful questions to ask are naturalistic questions.
That's why I prefer "practical" to "methodological." It's not about dogma; it's about practicality.
She does discuss the Wedge Strategy, and pokes fun at the IDolators' fear of common descent. She also got into the semantics of "Darwinian evolution" vs. "biological evolution" vs. "neo-Darwinian evolution." What a pile of foolishness that is.
Overall, I give it a C. Not exceptional, and it could have benefitted from some more research to work out some minor errors. It tends to give the creationist view and assume the reader sees the other side.
Letters to the editor or to Jodi Wilgoren would probably not be out of order. The Times won't publish more than 150 words, and you should cite "The Terms of Debate in Kansas," May 15, 2005.