The onion test.

Posted on by

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 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?

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?

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.

____________

1 I do not endorse the use of the term “junk DNA”, which I think has deviated far too much from its original meaning and is now little more than a loaded buzzword; the descriptive term “non-coding DNA” is what I use to refer to the majority of eukaryotic sequences (of various types) that do not encode protein products.

2 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”.



17 thoughts on “The onion test.”

  1. The “range in genome size” link pulls up a “The requested document is not available” page.

  3. 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???

  4. Love the concept used and will try refer to this post whenever I see fit 🙂

    @drpsduke: yes, emotional onions is the answer.

  5. 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.

  6. 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?

  7. easy. All that extra DNA causes the onion to be bottom heavy, thus, you get an onion. One of god’s better ideas.

  8. 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?

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Couldn't "junk DNA" be an awkward way of scaling cell/organism size? I.e. doesn't multiplied DNA length inflate the cell somewhat?

  15. 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? 🙂

  16. 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?

  17. 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.

Comments are closed.