The Discovery Institute says it has been misinterpreted.

The Discovery Institute has claimed that its aims in the Wedge document have been misinterpreted and that fear of a coming theocracy are misplaced. In a paper entitled "The Wedge Document": "So What?", a Discovery staff writer (unidentified) writes:

Darwinian activists and self-identified "secular humanists" claimed that the "Wedge Document" provided evidence of a great conspiracy by fundamentalists to establish theocracy in America and to impose religious orthodoxy upon the practice of science.

Things get a bit murky further down when he (or she?) writes:

It is in the context of our concern about the world-view implications of certain scientific theories that our wedge strategy must be understood. Far from attacking science (as has been claimed), we are instead challenging scientific materialism--the simplistic philosophy or world-view that claims that all of reality can be reduced to, or derived from, matter and energy alone. We believe that this is a defense of sound science.

This is a conflation of terms. The dichotomy the writer is driving at is the difference between methodological naturalism (the idea that the real world can be described in scientific terms and investigated using scientific methods) and philosophical naturalism (that the natural world is all that exists). Here, there is no separation between the two concepts.

Nevertheless, some good points are made:

To say that challenging a particular scientific theory constitutes an attack on science itself is to misunderstand science profoundly. Science advances precisely by such challenges.

In an attempt to identify how research is performed by fellows of the institute, the author notes:

Dembski and Meyer have argued that certain evidences from the natural world provide what they call "epistemic support" for theism even though (we have to repeat) such evidences can't "prove" the existence of God or a specific religion.

Here one would reasonably ask 'What kind of epistemic support?' I have read the work of Dembski and his "support" often amounts to a negative assessment of evolutionary theory. Once again: just because my theory about x is wrong, it does not make your theory right, especially if you cannot tell me how the mechanics of your theory play out.

The author makes an assertion that the arguments of ID are analogous to those of Richard Dawkins' in that Dawkins uses evolutionary theory to argue against the existence of God. The author states that, if Dawkins' science is acceptable, so is that of the Discovery Institute fellows. This is, in some senses, a straw man argument. It presupposes that the conclusions that Dawkins draws leading him to argue against the existence of God are valid, scientifically. They are not. And if they are not, then, conversely, the arguments made by Dembski and Meyer run the risk of not being correct either.