I looked up what Francis Collins had to say re junk DNA in The Language of God, in his own right, and here it is:
Darwin’s theory predicts that mutations that do not affect function, (namely, those located in “junk DNA” ) will accumulate steadily over time. Mutations in the coding region of genes, however, are expected to be observed less frequently, and only a rare such event will provide a selective advantage and be retained during the evolutionary process.” That is exactly what is observed.” (pp. 129-30)
Is that exactly what is observed?
This latter phenomenon even applies to the fine details of the coding regions of genes. From the previous chapter, you may recall that the genetic code is degenerate: For example, GAA and GAG both code for glutamic acid. That means that it is possible for some mutations the coding region to be “silent,” where the encoded amino acid is not altered by the change, and so no penalty is paid. When comparing DNA sequences of related species, silent differences are much more common in the coding regions than those that alter an amino acid. That is exactly what Darwin’s theory would predict. If, as some might argue, these genomes were created by individual acts of special creation, why would this particular feature appear? (p. 130)
Re AREs (ancient repetitive elements):
Mammalian genomes are littered with such AREs, with roughly 45 percent of the human genome made up of such flotsam and jetsam. When one aligns sections of the human and mouse genomes, anchored by the appearance of the gene counterparts that occur in the same order, one can usually also identify AREs in approximately the same location in these two genomes (Figure 5.2).Some of the may have been lost in one species or the other, but many of them remain in a position that is most consistent with their having arrived in a genome of a common mammalian ancestor, and having been carried along ever since. Of course, some might argue that these are actually functional elements placed there by the Creator for a good reason, and our discounting of them as “junk DNA” just betrays our current level of ignorance. And indeed, some small fraction of them may play important regulatory roles. But certain examples severely strain the credulity of that explanation. The process of transposition often damages the jumping gene. There are AREs throughout the human and mouse genomes that were truncated when they landed, removing any possibility of their functioning. In many instances, one can identify a decapitated and utterly defunct ARE in parallel positions in the human and the mouse genome (Figure 5.2 )” (p. 136)
Okay, so …
Confronted with such facts as the similar ordering of genes cross chromosomes between different mammalian species, or the existence of repetitive “junk DNA” in shared locations along the DNA of humans and mice, YEC advocates simply dismiss this as part of God’s plan.” (P. 173)
And they are wrong, why … ?
Also, question: How many of us would agree to have all our “junk” DNA deleted, to save space?