Isn’t it obvious? He has a prior theological commitment to the proposition that de novo evolution of functional genes can’t happen. So when he finds evidence of a taxonomically restricted gene, instead of that constituting evidence against his theological commitment, he takes it as disproof of evolution.
Showing that a highly similar but unexpressed genetic locus exists in closely related species, and that a phylogenetic analysis of such sequences in a more diverse group of such closely related species also fits perfectly with the hypothesis that this locus has been incrementally evolving into the expressed locus in the species with an Orfan gene, is dismissed because of that very same prior theological commitment.
Hunches by individuals from past generations of scientists that this can’t happen are invoked as strong arguments in support of the prior theological commitment. Rather than letting the evidence speak for itself, the evidence is all interpreted through the lens of a previously formed belief about what can or can’t happen.
When one is operating by conclusion first, evidence becomes incapable of changing one’s mind. People who think like this have basically become conspiracy theorists. A phylogeny indicating incremental evolution of a de novo protein coding gene from an unexpressed noncoding locus must have been planted by the intelligent designer.
Yeah, sure, it looks like it evolved over time and became a protein coding gene in this species, but that’s just a fatamorgana. Who knows what the designer was thinking? But because I know, I just really really know that this can’t happen, the designer must have just made it look like it by accident, or because he’s got a bit of a sense of humor. Those other species with a similar but unexpressed locus? That’s just there because, well… the designer is a funny guy, and a bit of an artist.
How is this any different from saying that pictures of a round Earth are doctored by NASA?