The scientific method prizes experience (investigation and observation) over ideology. Reason over faith. The starting point of experience is not God's existence ("In the beginning, God"), but the person's ("I think, therefore I am"). How do I know I exist? Not because God tells me ("God said ..."), but because I can experience myself asking the question. The self- awareness of the thinking being is the start of sure knowledge, which is why close attention to such awareness (observation, investigation, experiment) is the absolute value of science.
He seems to think that if a president wants to veto a bill for moral reasons, she must first be like Descartes and reconstruct all of human knowledge from first principles. That, after all, is what scientists do, isn't it?
Some related thoughts from First Things.
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