Stephen C. Meyer was asked about the role of molecular evidence in supporting the case for evolution:
The other problem with this method of investigation is that it begs the question. It says the degree of difference between two proteins or genes in different animals is an indication of how long ago they diverged from a common ancestor. But that they diverge from a common ancestor is presupposed from the outset of the investigation, and it’s presupposed in all the algorithms that analyse and compare the gene sequences. So you can’t use a method of investigation that presupposes a common ancestor to establish the existence of a common ancestor—that’s a question begging strategy.
Meyer, S.C. (2013). Darwin’s Doubt, Intelligent Design and Evolution on C-SPAN Booknotes. Available https://www.youtube.com/watch?v=UZTzMNRO_7I&app=desktop. Last accessed 11th Jul 2015.