You seem to be confusing arguments. The Darwin comment was only to show that competing evolution theories are "contradictory". There is evidence that natural selection is not necessary to explain functional changes in organisms. I have often cited Dr. James Shapiro as support.
The other topic is the fact that unchanged areas cannot be explained by random mutation/natural selection when those areas have no apparent selective advantage.
Interesting site:
http://isis.bit.uq.edu.au/front.html