It would be nice if science were a nice neat package -- but it's not (that's an acceptance of reality, not a criticism)
And that's true for the uninformed criticism of the creation brigade as well as the cheerleading of the New Atheists. Whatever knowledge that we have of the universe derives from the data produced by scientific inquiry; but it's not some sort of unmediated contact with reality. We organize and interpret this data according to cultural and personal constructs that condition how we define facts and evidence.
It's handy to keep in mind that science is a human endeavor, and that whatever truth we derive from the exercise has to be assessed in a human context and not as "objective" truth.
Edited by MrHambre, : Clarification and stuff.