How to Assemble a Human Genome
In July 2013, Dan Graur gave a presentation at the Society for Molecular Biology and Evolution, arguing against the ENCODE 2012 results. From slide 5:
If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If on the other hand organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong.
He goes on to define what he calls the ENCODE incongruity on slides 113 and 114:
The difference between the fraction of the genome claimed by ENCODE to be functional (>80%) and the fraction of the genome under selection (<8%)... The ENCODE Incongruity implies that a biological function can be maintained without selection, which in turn implies that no deleterious mutations can occur in those genomic sequences described by ENCODE as functional. This is akin to claiming that a television set left on and unattended will still be in working condition after a million years."
In other words, since less than 8% is shared with other animals, evolution could not have produced the rest in the available time--or even preserved it from deterioration.
On slide 46, Graur cited Genome size is negativey correlated with effective population size in ray-finned fish, from Trends in Genetics, 2005. The idea is that smaller populations have weaker selective forces against the slightly deleterious accumulation of extra junk, and will therefore have larger genomes. But this argument was rebutted in a 2008 paperby T. Ryan Gregory.