Monday, September 21, 2009

More Junk DNA Fallacies

 
BiOpinionated is a blog written by a molecular biologist named Nils Reinton. He tries to see every side of an argument but there are times when this attempt goes astray.

The "debate" over junk DNA is an example. Here's how Nils responed to claims by Ryan Gregory and me that most of our genome is junk [How to have your cake, eat it, and then complain].
First: State that most of our genome is junk.

Second: When more and more promoters, enhancers, repressors and other regulatory elements are discovered, claim that this of course was not included in the definition of “most of the genome”. The perfect excuse because it means you’ll never be wrong.

Last: Complain when the press does not understand that “most of our DNA” actually meant “much of our DNA , but with a lot of exceptions” and that science reporters don’t intuitively know which exceptions these are.

Post written using the zpen in dire agony over extremely poor science communication from the same persons who most eagerly criticize science communication from others.
[see the original article for links - LAM]
Oh dear. There's so much wrong with the logic of this posting that I hardly know where to begin.

Nils is mostly upset about a recent posting on Genomicron: The Junk DNA myth strikes again (next up: media hype). This isn't very complicated so let me give you the short version.

Most of our genome is junk. That does not mean that all of our genome is junk and it certainly never meant (among intelligent scientists) that all of our non-coding DNA is junk. Here's a short list of non-coding DNA that is absolutely essential in our genome: all genes that produce functional RNAs instead of proteins; all regulatory sequences including enhancers; sequences that control splicing and other RNA processing events such as capping and polyadenylation; some 5′-leaders and 3′-tails of mRNA; chromatin domain markers (regulatory); scaffold attachment sites (SARs); some recombination hotspots; origins of replication; centromeres; telomeres.

Ryan was complaining about a paper that's about to be published in Molecular Biology and Evolution. The authors say this in their abstract.
Protein-coding sequences make up only about 1% of the mammalian genome. Much of the remaining 99% has been long assumed to be junk DNA, with little or no functional significance.
I agree with Ryan Gregory that this is extremely misleading. It implies that there are legitimate scientists who think that all non-coding DNA is junk. It would be far better to say something like this ...
Genes that encode proteins, and other genes, make up only a few percent of our genome. If you add in all of the other DNA sequences that are known to be essential you still can only account for no more than 5% of our genome. Most of the rest is thought to be junk DNA with no biological function. There are no respectable scientists who think that none of it will ever be shown to have a function but the general consensus among the defenders of junk DNA is that the vast majority of these DNA sequences, consisting mostly of defective transposons and pseudogenes, will turn out to have no function.
The authors of the paper go on to present evidence that about 5.4% of non-coding DNA has a function.

Big deal. That's not much more than what the textbooks have been saying for several decades.

Nils, there's an interesting debate going on about the amount of junk DNA in our genome. You're welcome to participate but please make sure you understand the issue and, please, don't spread false information. When we say that most of our genome is junk that does not mean that some of what we now consider to be junk DNA won't turn out to have a function. We're not that stupid—please don't imply that we are.

What we're saying is that the vast majority of DNA sequence in our genome is junk. I think the amount of junk is going to be >90%. That still leaves room for discovering a function for about twice as much DNA as we already know to be functional.

Get back to me when someone publishes solid evidence that more than 10% of our genome is essential.


20 comments :

  1. I have linked to your response in the post so that both sides are represented, bringing me back on the narrow path. Just to clarify, I'm not upset about the presentation of the paper. What upsets me is the way you and Gregory keep blaming these "not junk after all" headlines on reporters. The message you send is that our genome mostly junk, of course you'll get these headlines then - expecting anything else would be naive. If you wanted nuances, then you should have included them in the first place.

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  2. Unless we discover that 50% of our genome is not Junk than the statement "most of our genome is junk" is factually correct. The poitn of the posts here by Larry, and by T. Ryan Gregory is that any study or headline that essentially says "this isn't true!" while showing that some percentage less than this isn't junk is false and misleading.

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  3. When more and more promoters, enhancers, repressors and other regulatory elements are discovered, claim that this of course was not included in the definition of “most of the genome”.

    "It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use ... would be for control purposes at one level or another."
    - Orgel and Crick 1980

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  4. The logical fallacy in your "More Junk DNA Fallacies" argument is the false dichotomy that DNA must be either essential or alternatively must be junk with no middle ground possible.

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  5. DG. By your logic: Unless we find that half the population is not evil, then the statement "half of the population is evil" is true. Not a valid argument as you can see. Therefore the headlines are not false and if anything only slightly misleading. That's nevertheless besides the point I am making: bombastic (and misleading ?) statements from scientists will necessarily bring about tabloid headlines.
    Gregory. Nice quote. By using that are you implying that what Orgel and Crick are saying is what you yourself have been saying all along ? If so you have communicated that in a strange manner. If you had communicated this correctly, then maybe the science reporters would have gotten the point by now.

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  6. I'm just pointing out what the literature actually says, as I have been for quite some time.

    Here's another one you may find interesting. It's by Comings (1972), in the first explicit discussion of "junk DNA" (Ohno only used the term in the title).

    These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn't mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.

    So, by my count, we still await evidence for functions in another 15% before we even get to the original expectation from 35+ years ago.

    I don't think I'll continue in a back and forth, but you can see the Quotes of Interest for lots more.

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  7. Nils,

    I find it amusing, and a bit bizarre, that you are criticizing others for their "bombastic (and misleading?) statements."

    This from someone who titles a blog post Hammering nails in the junk-DNA coffin.

    You don't think that title is bombastic? To me, it implies that the "junk-DNA" hypothesis is dead. It's certainly not my idea of a nuanced message.

    Honestly, which do you think is more consistent with available data: that the junk-DNA hypothesis is dead, or that most of our genome is in fact junk?

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  8. Even if 99% of the genome had no “function”, as determined by observations that organisms seem to get by without it, that is still only a very small portion of the mass of that organism.

    The economy of nature predicts that the mass of the organism, the substance, need be accounted for, it should have some function or the survival game favors its removal or degeneration. Experiments show that most macromolecules have functions that rely on the agency of all, most, or many of the atoms that makes up that molecule.

    The “waste” observed in the genome seems to makeup a relatively large portion of the “wasted mass”. Perhaps the energy and resources conserved by the removal of portions of the genome are negligible, and thus, do not offer an advantage to species that have less of the “junk”.

    Or perhaps, the “junk” has a role to play in the evolvability of organisms: a large, stocked, laboratory; a spacious art studio. Thus, the trade-off of mass-spared may be a decreased ability to evolve – which we may not see with “function” experiments aimed at affects on one or few generations. Function may stretch beyond our measurements.

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  9. Oh scientific journalism! Where Asn stands for 'Asinine'.

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  10. Those on the sidelines of science need something to write about. They need to get published in some manner. What better way than to exaggerate.

    Move along - nothing to see here. Next exaggeration around the corner.

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  11. I say the anti-junkists should go play around with some maize or dinoflagellates or something...

    Although transposons are actually functional and non-junk - for themselves! Somebody think of the parasites please!

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  12. @N. Ataie
    Or perhaps, the “junk” has a role to play in the evolvability of organisms: a large, stocked, laboratory; a spacious art studio.
    Maybe, but nonfunctional DNA is not maintained for that reason, as you seem to suggest. The one thing you cannot select for is future reproductive success. If the benefits of a large genome are not immediately apparent within one or a few generations, than it is not adaptive. Until it acquires a function, it still is junk.

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  13. The logical fallacy in your "More Junk DNA Fallacies" argument is the false dichotomy that DNA must be either essential or alternatively must be junk with no middle ground possible.

    If junk DNA is defined as non-essential, then this is not a false dichotomy.

    Or perhaps, the “junk” has a role to play in the evolvability of organisms: a large, stocked, laboratory; a spacious art studio.

    This is what IDers refer to as "front-loading," which is an ad hoc rationale they came up with which does not refute the claim that the DNA in its current form is in fact junk, because this idea implies that the DNA has to change and be different to be non-junk.

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  14. If junk DNA is defined as non-essential, then this is not a false dichotomy.

    Yes, but that's a silly way to define junk DNA. Are genes for eye color junk do you suppose, or is eye pigmentation essential?

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  15. Are genes for eye color junk do you suppose, or is eye pigmentation essential?

    No definition of junk DNA includes a recognizable, functional protein gene.

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  16. What is selected for is that which aids in the survival and reproduction of a given organism in a given environment - but environments change, we know this. The adaptation of new traits requires the shuffling, deleting, adding, copying, and changing of digital information- the genome (we know this too).

    If having less junk means a decrease in the ability to do the above tasks, then an organism with less junk (by chance) may also have less of a chance at survival and proliferation given some pressure. Thus, the “less junk” kind may have a lower probability than the “more junk” kind of having acquired any useful digital information. More junk becomes more common – we observe this and try to figure out why.

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  17. Thus, the “less junk” kind may have a lower probability than the “more junk” kind of having acquired any useful digital information. More junk becomes more common – we observe this and try to figure out why.

    Your argument is interesting, but I am not really convinced.
    Bacteria get by with very sleek genomes, and they can rapidly adapt. Thus, there seems to be no need for huge reserves of non-functional DNA to sustain adaptability. Also, within taxa there is a huge variation in the DNA content. It is really hard to explain this in your scenario, as directional selection for increased genome size would minimize differences.

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  18. I could be wrong, but one significant difference might be that bacteria have relatively rapid generational turn over vs. us bigger creatures. Thus maybe sleek genomes, aren't as much of a problem.

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  19. All these conjectures about what junk DNA is for are begging the question. I've not heard any reasonble evidence to suggest that the majority of junk DNA is 'for' anything.

    Given what's known about copying errors, sequence duplication, mobile genetic elements, etc., the simplest explanation still seems to me that junk DNA is exactly that. Junk that has no particular function, but doesn't cause enough of a fitness burden to be purged faster than it's created.

    The idea that junk DNA serves as some kind of reservoir to support 'evolvability' is intriguing. But, without some supporting evidence, it sounds to me like an ad hoc conjecture based on the unstated and irrational belief that junk DNA must be doing something.

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  20. Thank you, Nils Reinton, for calling these bozos on their sh--.

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