Thank you for providing a link to a paper which demonstrates that even the "genetic engineering" processes in the genome were themselves the result of evolution. Sample quote, chosen from dozens which affirm the evolutionary origins of these processes:
An especially illuminating example of natural genetic engineering is the mammalian immune system. This system evolved from DNA transposons and cellular repair functions (Agrawal et al., 1998; Bassing et al., 2002; Gellert, 2002).It's always nice when you undercut your own side of the argument by providing further evidence for the other side.