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From your first link:

"The heart of the Kansas controversy over what should be taught in schools is a conflict between a naturalistic definition of science and an evidence-based one."

Is this suggesting that the 'evidence' is not addressable through naturalistic methods? If that is the case then how do we test the alternative - the supernatural?

The implicating of this is that naturalistic methodology is incapable of following the evidence. If that is so, how did science develop the technology we see all around us? Before you go claiming that only evolution is not following the evidence because it has a naturalistic bias, you had better take a serious look at all of the other sciences. They all rely on methodological naturalism.

Rather transparent attempt to poison the well, btw.

From the same link:

"Naturalism is a type of philosophy that argues that nature is all there is, has been, or ever will be. It is opposed not only to theism but to any assumption that nature incorporates design or purpose. (A Buddhist or agnostic, for example, may not believe in gods/God, but may accept that there is design or purpose in nature.) However, many prominent scientists are naturalists, and they have a tendency to think that science is the handmaid of naturalism."

This is pure unadulterated bologna. Methodological Naturalism, which is a set of 'methods' not a philosophy, was born from the efforts of a large group of Christians who, several hundred years ago decided that God created a consistent, measurable and testable natural world. This allowed them to draw conclusions from nature without the fear of supernatural interference. Simply put, without the assurance of consistency none of their work would be falsifiable. It in fact says absolutely nothing about the existance of the supernatural.

Naturalism is not used to deny a designer. Even a designer's work would have to be examined using some form of naturalist methodology. So far the best methodology, the one that produces the most new and useful ideas, is the current methodological naturalism.

Right out of he starting gate the author shows he has no clue.