The title of Chapter 8 is "Some Recent Defenders of Junk DNA." It is Wells' attempt to deal with a very small percentage of the criticisms of his claim.
He begins with a reference to a 2003 paper that reported on transcription of a pseudogene and proposed a function for that transcript. He then references a 2006 paper that refutes the earlier study showing that the pseudogene transcript has no function. Good for Wells. That means he is aware of the fact that some of the work he references has not been reproduced. It's bizarre that Wells devotes three paragraphs to the discredited reference in Junk & Jonathan: Part 7—Chapter 4 and only mentions in passing that the result has been challenged.
He returns to this result in Chapter 8 and all but admits that the original result—so prominently presented in Chapter 3—is no longer valid. However, Wells can't leave it at that. The 2006 paper by Gray et al. went on to point out that some creationist literature had written up the earlier incorrect result and claimed that this was support for functional "junk DNA" and support for intelligent design creationism. The authors conclude their paper with ...
Furthermore, because Mkrn1-p1 is a nonfunctional pseudogene and does not trans-regulate its source Mkrn1 gene as claimed (6–9), our work reestablishes the evolutionary paradigm supported by overwhelming evidence that mammalian pseudogenes are indeed inactive gene relics.
This is too much for Jonathan Wells. He says, with apparently a straight face ....
Yet even if the results published by Gray and his colleagues were valid, their conclusion would not logically follow. Invalidating a report of one function in one pseudogene cannot exclude other possible functions in that pseudogene, much less possible functions in other pseudgoenes.Recall that this book quoted a dozen or so cases where a psuedogene might have a function in some species or another. This leads to the conclusion that all junk DNA is a myth. I wonder if Wells is irony deficient?
The sweeping pro-Darwin, anti-ID conclusion by Gray and his colleagues was obviously motivated by something other than evidence or logic—that is, by something other than science.Gray and his colleagues appear to motivated by some bizarre bias that Wells doesn't get. It's called truth.
The next example is the debate over pervasive transcription. I've already covered this in another posting [Pervasive Transcription].
Wells would like to believe that most of our genome is transcribed and this is evidence of function. Many scientists dispute the data, claiming that the appearance of pervasive transcription is an artifact. Others dispute the conclusion, claiming that the transcripts are merely junk RNA.
Wells tries to discredit some of the critics—especially the Toronto group—by bringing up technical details but he's in way over his head. The issue just can't be resolved as easily as Wells would like to believe. However, Wells reserves his harshest criticism for PZ Myers who had the audacity to blog about this last year [Junk DNA is still junk].
[PZ Myers] ... did not look at the methodology used by Hugh and his colleagues—a methodology guaranteeing that their results would appear to support the myth of junk DNA.In other words, Jonathan Wells has seen that the methodology of the Toronto group is so flawed that PZ Myers didn't recognize they were wrong. I'd put my money on PZ if I were you.
The Onion Test
The Onion Test]. Here's how Ryan describes it.
The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA1. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?It's important keep in mind that this is a test that you should apply to any general explanation for junk DNA. For example, if you think that pervasive transcription means that almost all of the genome has a function then what kind of function requires five times as much in Allium cepa? And what kind of function requires five times as much DNA in A. ursinum compared to A. altyncolicum?
The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. This comparison is chosen more or less arbitrarily (there are far bigger genomes than onion, and far smaller ones than human), but it makes the problem of universal function for non-coding DNA clear2.
Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?
So how does Wells handle this?
Biologist have long known that the DNA content (the "C-value") of eukaryotic cells varies by a factor of several thousand with no apparent correlation to organismal complexity or to the number of protein-encoding genes. There is a strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus—which affects the rate of cell growth and division.Wells is implying that there's a cause-and-effect relationship between genome size and cell size. Presumably, the expansion of the genome was selected in order to increase cell size and slow down cell division. If that were true then why do different species of onion vary over a fivefold range in their genomic DNA content? And why does the common onion have five times more DNA that humans? Is it because onion plants grow much more slowly than humans?
Wells does not tell us why this correlation is important to his case and how it passes the onion test. Wells goes on to describe a correlation between metabolic rate and genome size in mammals and birds but he doesn't tell us how that relates to the idea that junk DNA is a myth. He also doesn't tell us what that correlation has to do with the Onion Test.
& Junk DNA
... Gregory directs his challenge to "anyone who thinks they have come up with a universal function for non-coding DNA." Yet there probably is no such person. As we have seen, scientists know of many functions for non-protein-coding DNA. Nobody claims that there is "a universal function" that applies both to mammals and to onions.Nonsense! Several universal functions have been proposed: (1) that the huge amount of extra DNA is required for regulation; (2) that the extra DNA serves to protect the genes from harmful radiation; (3) the extra DNA is required for packaging chromatin; (4) the extra DNA is necessary to enhance recombination; (5) that large amounts of transposon DNA increases evolability; (6) large genomes make calls bigger; etc. etc.
When IDiots find it difficult to argue against good science they often shift the focus to something else. Wells likes this tactic and he uses it often.
Gregory misrepresents not only ID but also the logic of the argument. In 2007 he wrote. "It is commonly suggested by anti-evolutionists that recent discoveries of function in non-coding DNA support intelligent design and refute 'Darwinism.'" But Dawkins, Futuyma, Shermer, Collins, Kitcher, Miller, Coyne, and Avise argue exactly the opposite. They all claim that non-protein-coding DNA supports Darwinism and refutes intelligent design. It is their claim that is the issue here—and "recent discoveries of function in non-coding DNA" refute it. Gregory stands the argument on its head.There are two points here. Let's take them in reverse order.
So the onion test is a red herring. Why onion cells have five times as much DNA as human cells is an interesting question, but it poses no challenge to the growing evidence against the myth of junk DNA.
The Onion Test is meant to be a reality check for those who propose functions for junk DNA. In that sense, it poses a real challenge to those who advocate a function for junk DNA. Wells just doesn't get it.
The other point relates to the claim that evolutionary biologists point to the presence of junk DNA as proof of evolution. As a general rule, they do no such thing—although I won't be put in the position of defending every statement made by scientists. What evolutionary biologists often do is point to things like the comparison of pseudogene sequences in different lineages and explain how this is perfectly consistent with evolution by random genetic drift (but not Darwinism). They also point out that IDiots have never offered an explanation for the observed results of such comparisons. Why should known examples of junk DNA be found in the same locations in the genomes of related species?
Wells misunderstands arguments made by evolutionary biologists. He does this quite often. I think it's deliberate.
Gray, T.A., Wilson, A., Fortin, P.J., and Nicholls, R.D. (2006) The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans. Proc. Natl. Acad. Sci. (USA) 103:12039-12044. [doi: 10.1073/pnas.0602216103]