You state: "To subject God to this tool is to ask man to define Him by virtue of what is not included in nature. Therefore, if this is the measure of God, then whenever something is at last understood it is another piece of God that is taken from Him. I don't like that idea."
I have not said the scientific method is the measure of God. Science is a tool that investigates nature in a determined fashion with tests using measurement and quantification.
The debate is about empirical observations of an order/design. Philosophers have argued that this order means that there is an Orderer responsible for the observed order. Christian revelation provides that this Orderer is the God of Abraham, Isaac and Jacob, the God of the Scriptures and Christianity.
St.Paul argues for this in Romans 1:Since the creaton of the world...God's eternal power and divinity have become visibile, RECOGNIZED THROUGH THE THINGS HE HAS MADE. (emphasis added) Romans 1:20
God is not subject to the tool. The tool reveals an order and design, which ultimately comes from the Creator.
Hmmm. These guys were wrong about the sun rotating around the earth and you want us to believe they have discovered the "Orderer"? Obviously, their "Orderer" was terribly flawed ...