Summary of problems:
Science is about the pursuit of reliable knowledge that offers cogent explanations and testable predictions. Explore Evolution cannot show how real science works, because to do so would expose itself as a slick exercise in manufactured controversy.
Full discussion:
From Explore Evolution:
Practicing science should be about making a vigorous effort to make true statements about the natural world, using all the evidence we have gathered, whatever its source, wherever it leads.Explore Evolution, p. 143
Scientists rely on evidence which is disprovable and testable. Sometimes that requires setting aside evidence like intuitions, gut feelings, or religious texts.
How does Paul Nelson, an author of Explore Evolution, foresee "using all the evidence" to make "true statements about the natural world"? Through the inclusion of religious scripture, and through intuition and gut feelings:
Within the past decade, the ID community has matured around the insights of UC Berkeley professor Phillip Johnson, whose central insight is that science must be free to seek the truth, wherever it lies. The possibility of design, therefore, cannot be excluded from science. Under the canopy of design as an empirical possibility, however, any number of particular theories may also be possible, including traditional creationism. Both scientific and scriptural evidence will have to decide the competition between these theories.P. Nelson (2002) "Life in the Big Tent: Traditional Creationism and the Intelligent Design Community," Christian Research Journal 24,4
Elsewhere, he acknowledged that intelligent design creationism relies on non-scientific standards of evidence:
We don't have a theory right now, and that's a problem. Without a theory, it's very hard to know where to direct your research focus. Right now, we've got a bag of powerful intuitions, and a handful of notions but, as yet, no general theory of biological design.Paul Nelson, quoted in "The Measure of Design," interview with Jed Macosko, Phillip Johnson, William Dembski, Paul A. Nelson, et al., Touchstone July/August, 2004, p. 64-65
This is the spirit animating Explore Evolution, a desire to elevate intuition and faith above science within the science classroom.