Jeanson’s “anticipated response” boils down to: “well sure you have an explanation, but if it doesn’t make the specific set of predictions that I claim it has to, it’s not scientific”.
He simply ignores the many actual fulfilled predictions made by the hypothesis of natural selection. For example, from one of my blog posts responding to “Replacing Darwin”:
Another prediction this hypothesis can make is that synonymous sites should display far less signature of time-dependence than non-synonymous sites, as mutations in these sites would be less likely to cause any fitness effect that could be acted upon by natural selection. For example, mutation rates estimated from 3rd codon positions should be fairly similar regardless of timescale, while the estimates from 1st and 2nd codon positions should differ, following the trend in Figure 5. This is a prediction that has been fulfilled (Endicott and Ho, 2008; Subramanian et al., 2009). Put more simply, deeper (older) branches in the phylogeny should display a lower ratio of non-synonymous to synonymous mutations than more recent branches, which is what we find (Kivisild et al. 2006).