"Returning to the original question of Darwinism and metaphysics, I have argued that even the assertion of the special creation of organisms is not incompatible with the scientific theory of evolution, which explains how organisms evolve now, and that it is incompatible with the scientific fact of phylogeny only under the assumption that actualism is not just normative for scientific reconstructions but true of the real world. There may just be a sense in which scientific facts are not historical facts. Most of the worldview implications of Darwinism come from taking materialism and actualism not just methodologically but metaphysically. I certainly do not want to dissuade anyone from doing this; and indeed narrow Darwinism's lack of worldview implications may even provide a motive to take one's naturalism metaphysically. Materialism is certainly a legitimate metaphysical position, and it is arguably better than any of the available alternatives; but is is not without alternatives and it is not identical with science. And while scientific naturalism and philosophical naturalism fit well together, they are not the same thing."
McLaughlin makes a case that truth can be different from scientific evidence and scientific evidence might not be the truth. Hi gives the example of a geology teacher who makes a trip into the future and discovers that the earth was fabricated by another species for experimental purposes. Now the historical truth is in contrast with the scientific evidence on the earth..... OK, but as long there is no evidence for the trip into the space/future the truth is with science!
The story of the trip in the space has no other reality value than the story about god. There is no possibility to prove that it is wrong, but there is also no evidence that it is right.