Today you're in for a treat, dear readers, 'cause I'm going to respond to a daffy creationist who happens to be Jonathan M. It's a twofer!
The subject is junk DNA, a subject that's almost guaranteed to bring out the worst in IDiot rationalization [Thoughts on the “C-Value Enigma”, the “Onion Test” and “Junk DNA”].
Jonathan M wants to discuss the "Onion Test" that was originally proposed by Ryan Gregory as a way of assessing the validity of arguments against junk DNA. Here's the original link: The Onion Test. And 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 DNA. 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?Note that the Onion Test is for people who think they have a functional explanation for the vast amount of putative junk in our genome. What Ryan is suggesting is that such proposals should be able to account for the huge genome of onions as well as the huge genome of humans.
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 clear.
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?
Let me give you some examples. Some people suggest that we need a big genome in order to protect our genes from mutation. If that's true then why do onions need five times more DNA? Some people suggest that we have big genomes because we're so complex and we need huge amounts of regulatory sequence. If so, why do onions need more?
Keep in mind that the Onion Test is "... a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA."
Let's see how Jonathan M handles the discussion.
Briefly stated, the “onion test” (which originates with T. Ryan Gregory) observes that onion cells have many times more DNA than we do. And since the onion is considered to be relatively simple as compared to the human, this discrepancy can only be accounted for within the context of the view that much of its DNA is, in fact, junk. This phenomenon is also known as the “C-value enigma”, and describes the lack of correlation (among eukaryotes) with respect to genome size and organismal complexity.No, Jonathan, that's not quite right. The Onion Test is a test for those people—like Jonathan Wells—who think that most of our genome has a function. He's supposed to "test" his speculation to see if can explain onion genomes. The Onion test is not about proving the existence of junk DNA and its not about explaining the C-Value Paradox [Genome Size, Complexity, and the C-Value Paradox].
& Junk DNA
This whole argument for junk DNA seems to rest on the critical assumption that having seemingly excessive amounts of repetitive DNA has no positive bearing on an organism’s physiology. But this assumption has been invalidated by the scientific evidence.I hate to break it to you Joanathan M, you being such a great scientist and all, but the Onion Test is not an argument for junk DNA. It's a test of possible functional explanations. (Didn't I mention that already?) Jonathan M has completely misunderstood the Onion Test. Would it surprise you, dear readers, to learn that Jonathan Wells also flunks the test [Junk & Jonathan: Part 11—Chapter 8]. This isn't rocket science.
One correlation which has been established is that highly-expressed genes tend to have short introns (Castillo-Davis et al., 2002), a likely reflection of the selective-pressure on transcriptional economy with respect to very highly expressed genes.This is correct. And very highly expressed genes don't have any introns. But introns only make up 25-30% of the genome. The largest category of junk is defective transposons.
Let's assume that the presence of junk DNA as intron sequences is selected in order to slow down transcription. Why do onion cells need so much more junk DNA. And why do related species of onion differ so greatly in their genome sizes? What's that got to do with introns?
Perhaps some of the C-value enigma can be accounted for in terms of alternative splicing and alternative polyadenylation. Alternative splicing allows a single form of a pre-mRNA transcript to be spliced into a number of different forms by skipping exons or by recognizing alternative splice sites, as shown in the diagram above. It is known that the level of alternative splicing exhibited in humans (about 60%, with an average of 2 or 3 transcripts per gene) is much higher than that for C. elegans (about 22%, with less than 2 transcripts per gene).I don't agree with the facts. I don't think it's true that most human genes produce multiple functional copies of mRNA by alternative splicing.
But let's assume that it's true. Let's assume that a large fraction of putative junk DNA is there because it promotes alternative splicing. Why do onion cells need so much more alternative splicing and why do related species of onion differ so much in their need for alternative splicing? That's what the Onion Test asks.
Approximately 10% of human genes code for transcription factors (a special class of protein which binds to specific sequences of DNA, namely, enhancers or promoters which are adjacent to genes which they regulate the expression of). In contrast, only about 5% of yeast genes code for transcription factors. When coupled with a much larger network of transcriptional enhancers and promoters, such a difference could result in a much larger set of gene expression patterns. This could lead to a non-linear increase in organismal complexity (see Levine and Tjian, 2003).I don't even understand the point. Is Jonathan M saying that a huge percentage of our genome is devoted to regulatory sequence? If so, why do onions need so much more regulatory sequence? (The actual amount of regulatory sequence amounts to no more than 1% of the genome. That still leaves 90% junk.)
The graph shows a clear quantitative correlation between cell volume and DNA content. The trap into which the “junk DNA” advocate has fallen — as he so often does — lies with the (erroneous) assumption that all functions associated with DNA are sequence-dependent. But this need not universally be the case (in fact, it has long been shown not to be). This correlation holds not only true of vertebrate animals, but also for plants and unicellular eukaryotes (protozoa). It has been suggested by many that DNA possesses a structural role in controlling nuclear volume, cell size and cell-cycle length. With increased cell size comes selective pressure for a corresponding increase in nuclear volume.
In summary, to point to the C-value paradox — or the so-called “onion test” — as evidence for the preponderance of junk or nonsensical DNA within animal genomes is based on several critical assumptions which are contradicted by recent data. The common naive supposition that having a larger genome size is neither here nor there in terms of organismal physiology has been shown to be untenable. With the ever-increasing expansion of our knowledge of the nature and functional inter-relatedness of the genome, those who choose to continue using the “junk DNA” argument as a club with which to beat intelligent design should find these facts disconcerting.Hey, Jonathan M! Did you hear that "whooshing sound" when you were writing this posting? That was the sound of a point going over your head.1
UPDATE: Denyse O'Leary has found this posting [Biochemist Larry Moran responds to Jonathan M’s junk DNA post]. So far, the comments on Uncommon Descent just confirm my conclusion that Intelligent Design Creationists are IDiots. I'm waiting for a "real scientist" like Jonathan M to weigh in and explain why he misrepresented the Onion Test. (It's interesting that Denyse didn't make any editorial comment. Usually she defends her fellow IDiots. Maybe she realizes that Jonathan M blew this one?)