If you think about it, any classification system is "artificial" in that it depends solely on the criteria specified to define the classification system. Sure we try our best to classify things in a "natural" way, but we have to define what that "natural" system is.
This is one of my pet peeves, along with "that's just an assumption."
The fact that classification systems (and assumptions) are "artificial" (I would use the term "models" instead of "artificial") does not automatically make them wrong, or even suspect.
They may very well be wrong, and in need of correction or refinement, but it is an annoying habit of creationists and others who oppose the
results of scientific investigation to use "assumption" and "classification systems" so as to imply they are wild-ass guesses. This is usually done because scientific investigations lead to conclusions which contract scripture, dogma, religious belief, etc.
If one disagrees with either a classification system or an assumption, one should be able to show precisely where it is incorrect, and propose some idea of an alternative. For example, DNA research is showing that some branches of our classification system are wrong, and it is showing where these branches should instead be placed. That is the correct way to do things.
But to claim or even imply that because these models are "artificial," or based on assumptions, that they are automatically incorrect is just plain sloppy reasoning--yet that is frequently the case in the creationist and ID literature.
Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.