Excerpted from http://www.ncseweb.org/resources/articles/147_proposed_west_virginia_science_2_14_2003.asp
It is standard intelligent design creationist jargon to deliberatly confuse and misuse the terms ontological (philosophical) naturalism and methodological naturalism. The former is the view that nothing supernatural exists - a point which may engender heated debate among theologians and philosophers but is irrelevant to the pursuit of science.
Methodological naturalism is not a "doctrine" but an essential aspect of the methodology of science, the study of the natural universe. If one believes that natural laws and theories based on them will not suffice to solve the problems attacked by scientists - that supernatural and thus nonscientific principles must be invoked from time to time - then one cannot have the confidence in scientific methodology that is prerequisite to doing science. The spectacular successes over four centuries of science based on methodological naturalism cannot be gainsaid. On the other hand, a scientist who, when stumped, invokes a supernatural cause for a phenomenon he or she is investigating is guaranteed that no scientific understanding of the problem will ensue.
Here is an example. Let us imagine a geocentrist astronomer in the era of Newton. Newton uses his dynamics to account for the perturbation of the elliptical orbit of Mars around the Sun due to the gravitational influence of Jupiter, and cranks out numbers that are quickly verified by astronomical observation. The entire exercise makes no sense to the geocentrist, who (a) on the basis of the central importance of mankind in the eyes of God, does not grant the ellipticity of the orbit of Mars around the Sun but insists that the Earth be the center of the universe; (b) insists that the orbits of the planets (and the Sun) are guided by angels. The intelligent design creationist arguments may be couched more subtly and elusively than this geocentric view, but they are of the same kind.
As for the phraseology,
"not designed," there is here a slipping around the need to
define the term "design." Living things certainly have organs
and systems that are best described in terms of Aristotle's "final
cause" - that is, the function which their form enables them to accomplish.
But design can mean either of two things. It can mean the form itself,
without reference to the way that the form came to be. No one doubts that
the wings of birds are admirably designed to the function of flight, in
this sense of design. What the intelligent design creationists are after,
however, is the other meaning of design - the end-product of the work
of a designer. Intelligent design creationists often hide the essentially
theological nature of this meaning by insisting that the designer might
have been some space aliens and not the God of their scriptures. But they
do not maintain this position when addressing sympathetic church groups
of their own or similar persuasion.