Wells addressed those arguments in: Jonathan Wells on Darwinism, Science, and Junk DNA.
Not Interested in How Much of Our genome Is Junk
Second, "paulmc" wrote that "there are a number of strong lines of evidence that suggest junk DNA comprises a majority of the human genome." The lines of evidence cited by "paulmc" included (1) mutational (genetic) load, (2) lack of sequence conservation, and (3) a report that "putative junk" has been removed from mice "with no observable effects." In addition, (4) "paulmc" wrote that "there is an active other side to the debate" about pervasive transcription. I’ll address these four points in order.As I pointed out in my review, Wells really isn't interested in explaining to his readers how much of our genome is known to be functional. It would be embarrassing. Wells goes on and on about the discovery of little bits of functional DNA in a variety of species but he never says anything about how much functional DNA has been discovered, as a percentage of the total.
Before I start, however, I’d like to say that I’m not particularly interested in debates over what percentage of our genome is currently known to be functional. Whatever the current percentage might be, it is increasing every week as new discoveries are reported—and such discoveries will probably continue into the indefinite future. So people who claim that most of our DNA is junk, and that this is evidence for unguided evolution and evidence against ID, are making a “Darwin of the gaps” argument that faces the inevitable prospect of having to retreat in the face of new discoveries.
I figure that over the past twenty years or so there has been credible evidence that about 1% of putative junk DNA has a function in any given species. With that kind of "trend," we only have to wait 2000 years until all junk DNA has been found to be functional!
There's a very good reason why Wells doesn't want to tell his readers about percentages.
The other point I want to make about Wells' statement is that it's internally inconsistent. He opens with an admission that there really is positive evidence for junk DNA and closes with an accusation that it's all a "Darwin of the gaps" argument from ignorance.
Isn't that strange?
Genetic Load Is Just a Theory
The genetic load argument dates from the late 1960s when several experts in molecular evolution realized that humans could not survive if most of their genome was susceptible to mutation. They calculated that only small percentage could actually be functional and the majority had to be impervious to nucleotide substitutions and insertion/deletions [Genetic Load, Neutral Theory, and Junk DNA], Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].1
& Junk DNAThe argument is based on the rate of mutation, which is largely due to DNA replication errors. The biochemistry is very well understood [Mutation Rates]. All recent data on genome sequencing confirms the mutation rate; the only scientific controversy is whether it could be as much as 2× higher than the biochemstry suggests. That dispute doesn't have any significant affect on the genetic load argument.
Wells correctly points out that the exact mutation rate is controversial. He then uses this as a way to discredit the genetic load argument because it's just "theoretical."
In other words, the first line of evidence cited by "paulmc" is not evidence at all, but a 40-year-old theoretical prediction based on questionable assumptions. The proper way to reason scientifically is not "Ohno predicted theoretically that the vast majority of our DNA is junk, therefore it is," but "If much of our non-protein-coding DNA turns out to be functional, then Ohno’s theoretical prediction was wrong."Imagine that! The positive evidence for junk DNA is just "theory" based on mutation rates that aren't known exactly and on our understanding of genetics. The mutation rates are known facts so I assume Wells is questioning genetics. I guess that's why he didn't feel the need to tell his readers anything about the genetic load argument.2
BTW, does everyone appreciate the irony of Wells dismissing genetic load because it's "just a theory"? Even if it were true that genetic load is entirely a theoretical argument, why should Wells dismiss it? Isn't his whole book about supporting a "theory"?
The correct way to interpret the genetic load argument is ...
Everything we know about mutations tells us that a significant percentage are deleterious, or harmful. The evidence from decades of study on mutation rates tells us that the average human embryo will have over one hundred new mutations. Even if only a five percent of these are deleterious, it means that every new-born human will carry at least 5 new lethal mutations. At at that rate, the human species will go extinct in a very short period of time based on our understanding of population genetics.
However, if only a small percentage of our genome (~10%) is dependent on specific DNA sequences, then the number of lethal mutations falls below one per zygote and this is tolerable.
1. The Genetic Load argument doesn't preclude a function for most junk DNA. It could still have a function that's independent of sequence—like some form of "stuffer." What it rules out is the idea that large portions of our genome have sequence-dependent functions. Those are exactly the kind of functions that Wells emphasizes in his book.
2. The posting by Wells has all the hallmarks of a tentative position that he's not certain about. I strongly suspect that the reason why Wells "forgot" to describe genetic load in his book is because he didn't know about it. (He still doesn't seem to understand it.)