I am not sure how official this is, but here is a term I would like to coin right here on my blog: “The onion test”.
The onion test is a simple reality check for anyone who thinks they have come up with a universal function for junk 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?
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 clear1.
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?
Left, A. altyncolicum (7 pg); centre, A. cepa (17 pg); right, A. ursinum (31.5 pg).
There you have it. The onion test. To be applied to any ambitious claims that a universal function has been found for non-coding DNA.
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1 Some non-coding DNA certainly has a function at the organismal level, but this does not justify a huge leap from “this bit of non-coding DNA [usually less than 5% of the genome] is functional” to “ergo, all non-coding DNA is functional”.
The “range in genome size” link pulls up a “The requested document is not available” page.
Chris Harrison(Quote)
Thanks, now fixed.
TR Gregory(Quote)
Well… Danny Vendramini http://www.thesecondevolution.com/
has spent years writing about how instincts, emotions, and intuition is encoded in non-coding DNA by some sort of Lamarkian process.
So the reason we cry when we cut up onions, is just further proof that he is right. All those emotions stored in the onion genome, right???
drpsduke(Quote)
Love the concept used and will try refer to this post whenever I see fit :)
@drpsduke: yes, emotional onions is the answer.
Rick(Quote)
Having read Vendramini’s lunatic ravings in Medical Hypotheses (NB: never read this journal if you wish to stay sane), and been damaged and scarred by his words, I was going to mention his ridiculous “teem theory”. But drpsduke beat me to it.
The emotional-onions idea is awesome. My next stir-fry is sure to be a tragic farce of epic proportions.
TheBrummell(Quote)
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?
Is there any data on correlations between cell size and genome size across onion species?
Anonymous(Quote)
easy. All that extra DNA causes the onion to be bottom heavy, thus, you get an onion. One of god’s better ideas.
Greg Laden(Quote)
Creationists and sundry IDists cannot seem to decide how they want to argue about ‘junk’ DNA. On the one hand, some have touted the experiments in which ~3% of a mouse’s non-coding DNA was removed and the mouse suffered no discernible ill effects as evidence of redundancy (or design, or something) in the genome.
Then along ocmes this article, and they are all about how all junk DNA has a function, just like they ‘predicted.’
But anyone that has ever done any sort of DNA sequence analysis can probably attest to the fact that even within species there can be differing amounts of ‘junk.’ If ‘junk’ DNA were so universally important, how is that possible?
Doppelganger(Quote)
What was removed was about 1.5 million bp if I remember correctly, which is about 0.05% of the genome, not 3%. 3% would be about 90 million bp.
P Garrison(Quote)
Just found this site via Panda’s Thumb. My own take on “junk” DNA is at http://vwxynot.blogspot.com/2007/06/endogenous-retroviruses-and-evidence.html – would appreciate any feedback!
Love the blog BTW!
VWXYNot?(Quote)
So we can say unequivocally that scientist do no know for certain the functioning of DNA. Therefore, evolutionary theory based on DNA is incomplete. Obviously then, common descent which is based on DNA is not proven. It could be that evolution is merely an illusion in the same sense that Dawking’s thinks design is an illusion. Both Dawking’s illusion and an ‘evolutionary illusion’ are equally supported by the facts.
Peter(Quote)
Interesting idea, but my bet, if I did bet, would still be on the UV catastrophe. We didn’t understand it before Max came along and offered some prospect of our doing so.
All those who claim that some of DNA is either junk or non-coding – or whatever term you may wish to use to indicate that we cannot presently find a function for it, may I call it ill-understood DNA? – may wish to consider that the next Planck in our understanding is just around the corner.
The black body survived the UV catastrophe, because that is the way it is in the world in which we live, and I have no doubt that the ill-understood DNA will continue to do what it is supposed to do, for that is the way that it is in the world in which we live, and it will do that whether we understand it or not.
Of course, I hope that it goes without saying that I would like to know what it does and how it does it.
Stuart ARCS(Quote)
All those who claim that some of DNA is either junk or non-coding – or whatever term you may wish to use to indicate that we cannot presently find a function for it, may I call it ill-understood DNA?
Nope, you are the one who has misunderstood.
For the largest part of what’s called junk DNA, we know that it has no function.
Do you know what a retrovirus is? A very large part of our genome consists of retrovirus corpses in various stages of decay. We keep carrying them around simply because we haven’t managed to cut them out.
Then there’s all the repetitive stuff (e.g. GAGAGAGAGAGAGAGAGAGAGAGAGAGA and so on for thousands of repetitions) that looks like an inflated copying mistake. What can that possibly be good for? Why can’t it be a copying mistake?
Oh, and the “non-coding” bit. Whether a stretch of DNA codes for a protein can be found out by simply looking at the sequence. If there are transcription factor-binding regions followed by a start codon, and if the first stop codon in the reading frame occurs after something like 100 codons at the minimum, you are looking at a protein-coding gene. If not, you aren’t.
Whether a stretch of DNA generally codes for an RNA can be figured out the same way: signals for the start and stop of transcription have to be there. These are just more variable and therefore less easy to identify.
David Marjanović(Quote)
I know why an onion needs 5x more non-coding dna than a human. a human has intelligence. The onion lacks the ability to intelligently avoid things like radiation, disease etc. a human doesnt need as much non-coding dna to ward off mutation from excessive ultraviolet light for example because a human is (or should be) smart enough to get out of the sun. In short, non-coding dna is ‘stupidity protection’ on a genetic level. humans arent that stupid so we need less.
Anonymous(Quote)
Couldn't "junk DNA" be an awkward way of scaling cell/organism size? I.e. doesn't multiplied DNA length inflate the cell somewhat?
Esko Heimonen(Quote)
Oi! Mr. blogger. 9/14 was a serious proposal. There never was a condition that the universal function could not be wasteful to the extreme. What was the prize again? :)
Esko Heimonen(Quote)
Unlike humans, onions can't control their environment or move away from it. Onions have no choice but to adapt. It could be that onions were designed with a lot of adaptive capacitance allowing its descendents to morph into onions that could thrive in many different environments. Deletion of some "junk" DNA could then easily result in a viable onion, because it would be an onion with less adaptive capacitance than the original but still able to produce offspring that could thrive in the current environment. Multiple lines of deletion of DNA used for adaptive capacitance could also result in speciation and account for the various sizes for onion DNA.
Also, why would anyone think there is a universal function for “junk” DNA. Isn't it more probable that there are many functions performed by "junk DNA" waiting to be discovered and that it will take hundreds of years of tedious research to decipher it all?
Intelligent Designer(Quote)
Sorry, Anonymous and Intelligent Designer. Your propose solution fails the second part of the Onion Test; why do some species of onion need vastly more DNA than others.
In particular, the bit about dealing with more varying environmental stresses: It’s the different environments that lead to the speciation.
Again, evolution fits the facts and design does not.
Also, re Esko Heimonen: A bigger genome wouldneed a bigger nucleus, at least in those cells that have them. But the nucleus is a small size compared to the whole cell.
eddie(Quote)
I don’t think that either “no-function” or “protective” hypotheses need to explain vastly differing genome sizes. Neither propose that genome size evolved to fit specific needs, rather, the protective hypothesis would propose that the repair mechanisms evolved to the necessary fidelity required to cope with whatever circumstances existed (including the amount of non-coding DNA). Both no-function and protective accept that the non-coding DNA happened by chance and was allowed to build up because there is not strong reason to get rid of it, since it is not such an energy consuming resource to replicate it etc (except maybe for high metabolic rates where some needs to be discarded?). regarding genome size and life-span the only proviso for a protective property is that there would need to be sufficient non-coding DNA to support a life-span long enough to reproduce. This does not predict though that genome size is tightly linked to lifespan – for protection, a genome with a majority of non-coding DNA would be necessary but not sufficient for an adequate life-span, but this is not at all incompatible with widely varying genome sizes, including enormous genomes in short lived organisms.
I think that a key is in the definitions of purpose. If it is proposed that the non-coding DNA evolved to fulfil a universal function then I think it fails the onion test. If it is proposed that other mechanisms such as DNA repair apparatus evolved to the necessary complexity then this is not proposing a universal “role” for non-coding DNA, it assigns a useful property to non-coding DNA but does not I think fail the onion test
Keith Grimaldi(Quote)
Ok, but if it doesn’t account for genome size, it is very uninteresting.
T. Ryan Gregory(Quote)
There are actually much better examples that comparing Onions and people. Take the grass Brachypodium (a close relative of wheat). Wheat has a 20 times larger genome than Brachypodium. Both are grasses, both look very similar, both are happily growing. The Junks seems to have no effect.
Thomas Wicker(Quote)
Actually, wheat is a poor choice because it is polyploid. Note that I wrote the following in the post:
T. Ryan Gregory(Quote)
Okay, I’ll bite. Not to try to suggest some function, but to inquire more about the onion family.
Is the extra material (from “small” member of the onion family to “big”) mostly transposable elements? What’s the theory on why one set of DNA would get invaded so incredibly more than an almost identical set? Is it thought to be based on geographical range or environment, ie one growing in a “hotbed” of transposable invasions, versus the other “sheltered”? Or is the larger genomic size attributed to later variations, accumulating over time (but why wouldn’t the modern descendants of the smaller family have also accumulated over the same time)? Is it possible selective pressure might actually have culled some of the transposable elements in one variety?
Have both “small” and “large” members been sequenced? Are there notable differences in the _coding_ regions of DNA, for example, large diversity in mechanisms to fend off infection? If planted together and cultivated for multiple generations, do small and large coexist or does one outcompete the other? Is small known to be more or less disease resistant than large? Are there notable differences in the regulatory regions for the different strains?
If one strain can out-compete the other, are they both “making do” with vastly different amounts, or has one simply found an environment which requires much less function? Sort of a gingerbread house needing a lot less structure than a real house. I suppose “less” can be viewed as negative selective pressure for more, or positive selective pressure for less?
Has anybody started trying to strip out transposable elements, to breed an A. ursinum with genome size near 7pg? Would that still be an A. ursinum? I’m guessing you would have to throw back in some transposable elements for which the organism has found a selective purpose–that amount, in itself, would be an interesting number to find out. What if you cross your “cleaned-up” A. ursinum, but which would still include elements with clearly piece-wise measurable selective function, with the wild-type A. ursinum and the cleaned-up version breeds out–does that imply function in the large amount of TEs, or does it simply mean the measurement for selective function is too weak?
matt(Quote)
Hi,
That was a nice read, thanks.
I’d like to turn the question on its head and pose one to you, if I may: how do you explain the differneces between and human and an onion?
Cheers,
G.S.
G. S.(Quote)
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Cazare Durau(Quote)
I think I can give you at least one universal function for that part of noncoding DNA which doesn’t have regulatory or other functions – it alters the structure of the genome and allows species (or families) to be distinct from each other. This explanation I believe passes your onion test. It doesn’t matter where genes are in the genome, they’ll be found when needed. However if pairs of chromosomes don’t match the organism is usually non-viable or unable to reproduce.
Jimbo(Quote)
Sorry, nope. This would most likely not be a “function” it would be an “effect” of changing genome size. The argument is similar if you are discussing chromosome number, and again it would be difficult to support the claim that chromosome number is adaptive and is universally functional as a species separation mechanism. Yes, there are features that can be selected for because they prevent costly hybridization, but this would be an extremely inefficient way of doing so. Also, lots of closely related species (i.e., the most likely to hybridize) have similar genome sizes. Often, the very divergent genome sizes are between distantly related species — which would not be able to hybridize anyway.
T. Ryan Gregory(Quote)
Isn’t a function something which produces an effect under given circumstances? Anyway, I don’t claim that the effect produced is totally predictable or always as effective (your point about hybridisation and closely-related species). However, along with other factors, it’s likely to contribute in a fairly major way (in the course of time) towards reproductive isolation without necessarily affecting the fitness of the species. That, it seems to me, is pretty important, especially where ecosystems are concerned.
Jimbo(Quote)