That’s a very interesting paper, aquaticus. I think the neutrality of the author comes into immediate question when you see a choice quote like this:
The situation becomes much more absurd and untenable if we assume that the entire genome is functional, as proclaimed by creationists such as Francis Collins, director of the National Institutes of Health
This is the guy who founded BioLogos that he’s talking about, right? And he’s essentially smearing him with the term ‘creationist’…
I infer that the entire logic of his thesis is skewed when I see the following obviously wrong statement:
Finally, we note that in addition to inferring an upper limit on the functional fraction of the human genome, we can also conclude that the fraction of deleterious mutations out of all mutations in functional regions should be very small. If >20% of all mutations in functional regions are deleterious, then the upper limit on the functional fraction of the human genome would be <2%, which is clearly false.
Which is in direct conflict with all sorts of known data as I quoted here:
“Although a few select studies have claimed that a substantial fraction of spontaneous mutations are beneficial under certain conditions (Shaw et al. 2002; Silander et al. 2007;
Dickinson 2008), evidence from diverse sources strongly suggests that the effect of most spontaneous mutations is to reduce fitness (Kibota and Lynch 1996; Keightley and Caballero 1997; Fry et al. 1999; Vassilieva et al. 2000; Wloch et al. 2001; Zeyl and de Visser 2001; Keightley and Lynch 2003;Trindade et al. 2010; Heilbron et al. 2014).”