Twisted tree of life award #15: NBC News on "Junk DNA mystery"

Oh for fu$*# sake.  Really MSNBC?  I mean, I know perhaps I should not expect much from some in the press but this is just awful: 'Junk' DNA mystery solved: It's not needed.

Brought to us by NBC News and LiveScience (which actually can have some pretty good science coverage).  This article has some complete and utter crap:

Some parts that I have issues with:
  • The headline: "'Junk' DNA mystery solved: It's not needed."  The headline is silly but alas it is consistent with what is in the article.
  • "So-called junk DNA, the vast majority of the genome that doesn't code for proteins".  So - they have redefined junk DNA as all non coding DNA?
  • "For decades, scientists have known that the vast majority of the genome is made up of DNA that doesn't seem to contain genes or turn genes on or off."  Apparently there is an entity out there known as "The Genome".  
And then we get into the quoting of author and researcher Victor Albert with no comments or responses from anyone is painful too.
  • "At least for a plant, junk DNA really is just junk — it's not required."  Except that they did not show this - they just showed that one plant can have a small genome and not have a lot of "junk" as they call it, which of course does not really say anything about what "junk" does or does not do in other organisms.
  • "Nobody's really known what junk DNA does or doesn't do" apparently calling into question the some 10,000 plus papers on the topic.
Apparently, from reading the rest the whole point of this article is that it turns out that people sequenced the genome of a bladderwort and it has a small genome but a lot of genes.  Oh and the organism is complex.  Therefore, apparently, it follows that

"The findings suggest junk DNA really isn't needed for healthy plants — and that may also hold for other organisms, such as humans."

And this leads us to 'Junk' DNA mystery solved: It's not needed.

So - basically - if ONE FUCKING ORGANISM DELETES SOME OF IT'S NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.

Aaaaaaaaaaaaaaaaaaargh.

And for this evolutionary logic, I am awarding NBC News, Tia Ghose (the author of the piece) and Victor Albert, the 15th coveted Twisted Tree of Life Award.

Past winners:

UPDATE 5/17/13

Some other discussions of this paper and related to my critique (though not always agreeing with me)

24 comments:

  1. This comment has been removed by the author.

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  2. Obviously it's a simplification to say that all noncoding DNA is not needed, but given how the media has been obsessed with the horrid ENCODE hype claiming that most of it is "functional", using their own misleading meaning of the term, if the public needs a simplification, I'd much rather have it be that it isn't functional because that's closer to the truth. But yeah, this article seems to be based on a press release overhyping the bladderwort genome, so it is annoying in that sense.

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    1. Yes, as a counter to the ENCODE crap this is a refreshing twist. But a twist nevertheless.

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  3. Thanks for the award Jonathan! Best regards, Vic Albert

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  4. Wait wait wait! It doesn't seem that bad, at all!

    EVERY press release on science issues is over-simplified, of course, but, well, it's a PERFECTLY GOOD argument to note that there is a complex angiosperm that has basically ALL the genes of a typical plant/typical multicellular eukaryote -- with maybe even a few extra due to multiply polyploid events -- but has almost NONE of the noncoding DNA / DNA formerly known as junk / DNA which should still be known as junk.

    It's a damn good argument, actually. At the very least, most of the DNA that most large-genomed eukaryotes have isn't strictly needed to build a complex organism. This has always been obvious for those of us who paid attention to the literature on genome size variation -- and the fact that genome sizes change a huge amount, while the number of genes and the (subjective) "complexity" of the organisms stays about the same. But, for whatever reason, a fair percentage of the science community and the press apparently needs it in the form of a genome paper to "get it".

    One can argue that "dispensible" != completely nonfunctional, yadda yadda, but these are comparative details. The dominant pattern is that the genes are most important, and it doesn't actually require that much DNA to regulate them in complex enough ways to build a nice complex critter. This is mainstream science, but defies many peoples' naive intuitions, and thus is worth a fair bit of press. IMHO.

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    1. Not buying your argument Nick. Small plant genomes are very interesting and what a plant lineage such as this one did as it's genome was reduced is also quite interesting. But many are overblowing the implications of this study. The fact that a plant can function without much non coding DNA really says nothing about the function or role of such non coding DNA in other species. All it says it that such non coding DNA is not absolutely essential for a plant to function. But this plant lineage could have evolved new means of regulation or other functions that were found in the non coding DNA of its ancestors. Or, in other words, a plant with a small genome says as much about non coding DNA in other plants and in humans as a fish with no eyes says about the role of eyes in vertebrates that see. Or should I try another? This says as much about the role of non coding DNA in other plants as the existence of snakes say about the role of legs. And so on.

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    2. Hey Jonathan - you said it yourself! "All it says it that such non coding DNA is not absolutely essential for a plant to function." We thought that was important in light of ENCODE; we made no absolutist arguments. OK, so 1+1 does not equal 3.... Don't know why you seem so picky though.... I think the general point and importance to the C-value discussion was clear enough, and without the "what-if's" you mention (like evolving new regulators); progress comes in stages. I think the burden of proof of function lies on those that ascribe function; same goes for natural selection. And 10,000 papers on what "junk" DNA actually does? Come on! Last, I for one /do/ think that eyeless fish and limbless snakes illuminate the science of eyes and limbs....

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    3. Yes, sure if we base everything we do on the idiocy of ENCODE and the press coverage of ENCODE then sure there are lots of things we might want to do differently. But I saw a lot I did not like in the NBC News story. Do you agree or disagree that the headline was misleading?

      "'Junk' DNA mystery solved: It's not needed"

      And they imply that all non coding DNA is junk DNA and then quote you as saying "Nobody's really known what junk DNA does or doesn't do". Well, are you saying nobody knows what non coding DNA does? Certainly there are 1000s upon 1000s of papers that have shown some function for some part of it (e.g., transcriptional regulation).

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    4. And - there is no doubt that eyeless fish and limbless reptiles tell us an enormous amount. They tell us, for example, that eyes are non absolutely necessary for fish to function. And their adaptations to being eyeless tell us all sorts of great things about senses. But the existence of eyeless fish does not tell us that eyes are useless in fish.

      Here is how I see the logic:

      Most plants have junk DNA
      One lineage doesn't and the plants seem pretty OK.
      Therefore junk DNA is useless

      Most reptiles have legs
      One lineage doesn't have legs and these seem pretty OK.
      Therefore legs are useless.

      Isn't that the logic here?

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    5. There are several lineages of legless reptile, actually. (I think all are squamates.)

      A minor point, but it would be pretty interesting to know if there is parallelism with the massive loss of noncoding DNA, too. Are there other examples? Are the examples more common in certain clades? Etc.

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    6. While on the topic of reptiles (or sauropsids, anyway), as I recall avian genomes are smaller than those of other sauropsids. There was a hypothesis that this was due to the evolution of flight (less DNA = less mass), but then it was discovered that early theropods (e.g., Coelophysis) likely had smaller genomes, too (based on bone cell size, which correlates well with genome size).

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    7. Sorry to but in, but I have to disagree with you, Jonathan. This is not the logic (at least from the paper).

      This genome specifically lacks retrotransposable elements, which have long been identified as a key selfish genetic element leading to the genome bloating and the sort of sequences actually defined as junk DNA (in contrast to this "all stuff we didn't know the function of was called junk" falsehood being thrown around in the media). This organism seems to have been a very good test of this hypothesis. And instead of having ~50% the genome occupied by TE, this genome only has 379 of them - 2.5% of it's genome, with an additional 0.5% being other "repetitive DNA elements". This seems to match the hypothesized selfish element - genome size correlation prediction quite well.

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  5. The headline was overly decisive to be sure; but that's headlines! I did indeed say that we don't really know much about what junk does or doesn't do, i.e., I was not referring to well-known noncoding items like promoters, enhancers, introns, etc. (note that the quote says "junk") -- I was referring to JUNK in the classic sense, as I understand it. As I already admitted, 1+1 does not equal 3, but the point seems clear enough -- be careful when ascribing "function" to junk DNA ... anywhere.

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  6. Two new quotes just ascribed to me (pretty accurately), as reported by the LA Times:

    "Junk DNA is probably well named as junk. There doesn’t seem to be any glorious reason or function behind it"

    and

    "The bladderwort certainly shows that at least one plant makes a perfectly good plant without it," Albert said. "By extension, I would say it's suggestive that maybe junk DNA in general isn't of much importance."

    See http://www.latimes.com/news/science/sciencenow/la-sci-sn-junk-dna-carnivorous-plant-bladderwort-gene-20130513,0,3143571.story

    I stand by these comments, which really don't seem too contentious to me. I said "probably", "seem", "at least one plant", "suggestive", and "maybe"!

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    1. thanks - those quotes are much better ...

      just to be clear - I generally agree that the claims of function of "junk" DNA are woefully overblown --- I am generally an anti-adaptationist --- I was not really taking issue with your conclusions --- I was taking issue with the evolutionary logic which implied that we can infer something about the function (or lack thereof) of a feature by an example of organisms that have lost that feature ...

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    2. Maybe it would help if you would clarify what you define feature. It makes quite some difference if you talk about a phenotypic feature that can be selected for or against or about pieces of DNA that most likely don't have any phenotypic effect. Emphasis added to indicate that this is not adaptionist at all although. Just having an organism without those DNA sequences wouldn't say much about the lack of function of junk DNA. It only does if you add additional knowledge from other studies. The problem with ENCODE is that they keep ignoring this knowledge although they could have known better for more than a decade.

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    3. I personally find it disconcerting to make this about ENCODE. The claims of the ENCODE group and the press coverage were inane and were appropriately eviscerated by the community. But I was not in any way claiming the ENCODE claims were right. I was just questioning the logic of the claims made here. So let's forget analogies and again focus on what the claim was I did not like.

      Observation:There is a plant. It has a small genome. It has lots of genes. It has complex features.

      Conclusion 1: This means this plant does not need much non coding DNA to do it's stuff.

      Conclusion 2: This means that all non coding DNA (or, all junk DNA - which was what the article I was critiquing called it) is "not needed."

      It is conclusion 2 that I have a problem with. I suppose we could debate what "It is not needed" means. I took this to imply that in all organisms, junk DNA had no function of any kind. Maybe I overinterpreted this. But it seemed like a way too big of a leap - an unsupported one. I do not see how one can go from "This organism can get rid of its non coding DNA" to "non coding DNA in other organisms has no role". None of the arguments presented here or elsewhere that come to this conclusion seem sound.

      So - yes, the claims by and about ENCODE were ludicrous. But let's not go over the top in the other direction.

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  7. Oikopleura beats this plant. And generalizes the argument.

    At 70mb it is a chordate!

    53% of intergenic regions <1000bp.
    Mode of intron length = 47bp.

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  8. With regards to the leg-metaphor.

    The Victor Albert argument is about the genotype to phenotype transition. Apparently you do not need the "junk DNA" to _make_ a complex multicellular organism such as a flowering plant or a chordate (oikopleura). Hence the metaphor breaks down there already because legs are not genotype. But still you can follow it through. You do not need legs to make a vertebrate.

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  9. I didn't get around to getting back to this -- but the one point I would make about the "legless things still move, so you can't say legs aren't important" analogy (which is a much better analogy than the eyeless one, since eyeless things don't see) would be this:

    In the case of legs, we know, or think we know, their basic function and how it works. Furthermore, we know enough about function to distinguish e.g. general movement (which can work in several ways), from the specific sort of function that legs allow (walking, digging, whatever). In the case of noncoding DNA, we actually don't know the function of most of it, and many have long suspected that a lot of it is junk.

    Even in the numerous cases where function has been claimed for noncoding DNA, a lot of these claims are weak and based more on wishful thinking, uncritically functionalist/adaptationist assumptions, confusion of "detectable effect" with "function", and/or possible confusion of correlation with causation. Just because some noncoding element has increased expression along with a gene, developmental event, or whatever, doesn't necessarily prove anything about function -- this could be a by-product of some other regulation activity going on in that portion of the chromosome or some such.

    In general, it seems like the amount of DNA physically needed to regulate genes might not be that much -- just enough to have binding sites of different strengths. The Utricularia genome indicates at least that it is possible to encode the development of a complex angiosperm (complete with flowers etc.), and furthermore one with extra-complex organs (the traps) and metabolism (eating things) with a relatively small amount of non-genic DNA.

    Dan Graur said similar things over on his blog a few days back, with his usual style. :)
    http://judgestarling.tumblr.com/post/50369538611/the-logical-fallacy-of-jonathan-eisen-a-k-a

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    1. I think either I was unclear or you missed the point. I am not arguing that non coding DNA does anything. I am about as anti adaptationist as one can be and have spent years railing against the genomics people (and others) who observe something in a genome and conclude not only that it must be functional but also they conclude that the first function they can think of for said thing must be correct. My problem here is with the logic of the conclusions made. It is very interesting that this organism has little non coding DNA. But all that really tells us as far as I am concerned is what you say at the end

      " it is possible to encode the development of a complex angiosperm (complete with flowers etc.), and furthermore one with extra-complex organs (the traps) and metabolism (eating things) with a relatively small amount of non-genic DNA."

      I completely agree. But what I was critiquing was those who took the next step and used this to infer that non coding DNA in other organisms has no function. That does not compute. It is bad logic. And bad evolutionary biology. And I stand by the leg and eye argument. It is not about function or whether we know the function. The point of my using those semi-absurd arguments was to say that the fact that an organism throws something away does not tell us what that thing does in the organisms that kept it. You and Dan Graur and others have not made any convincing arguments to the contrary.

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  10. For those who didn’t have the chance to read Ford Doolittle’s recent paper in PNAS: “Is junk DNA bunk? A critique of ENCODE” (http://www.ncbi.nlm.nih.gov/pubmed/23479647), here is his conclusion: by using a “larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon …much that we now call junk could then become functional.”

    Most people who commented here are probably familiar with the ‘nucleo-skeletal hypothesis’ proposed by Thomas Cavalier-Smith, and the ‘nucleotypic hypothesis’, proposed by Michael Bennett and Ryan Gregory, on the biological role of the so called ‘junk DNA’ (jDNA). These theories have been discussed in dozens of articles and books, so I’ll not elaborate on them here. However, I’ll like to bring forward another old model on genome evolution, C-value paradox, and the function of jDNA, which I described in more detail in a series of mini-essays (Science only allows short comments) at: http://comments.sciencemag.org/content/10.1126/science.337.6099.1159 .

    According to this model, jDNA provides a defense mechanism against insertional mutagenesis, particularly against insertional oncogenic transformation by endogenous and exogenous retroviral elements. Given the enormous number of somatic cells and high turnover rate during reproductive span, the number of insertion events, particularly by exogenous retroviruses, that would potentially lead to neoplastic transformations in the absence of protective mechanisms could be evolutionarily drowning for many species.

    Considering that most of the jDNA has originated from inserting elements, this genomic defensive mechanism is a classic case of ‘fighting fire with fire’, which is similar to the CRISPR system, in which viral sequences have been co-opted as part of an adaptive antiviral defense mechanism.
    Expectedly, as an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the insertional mutagenesis activity and evolutionary constraints on genome size, which might explain the overall evolution of genome size and the c-value enigma.

    In the case of bladderwort, apparently, the scarcity of food/nutrients has been a strong selective force against increasing the genome size; moreover, the number of endogenous mobile elements in this species is minimal.

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  11. I wish the food scarcity via-a-vis selection made sense, but most bladderworts have larger genomes, up to 400 Mb, and members of the bladderworts' carnivorous sister genus vary from 60-1500 Mb... And the sister genus to these two, Pingiicula, is always medium to large, as are the genomes of all other carnivorous plants... And they all live in comparable habitats re: nutrient availability

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    1. If nutrient scarcity/energy costs are unlikely to be a constraint against large genome size, perhaps we are left with a low insertional mutagenesis activity as the primary reason for the the bladderwort’s genome small. The relative small number of mobile genetic elements in the bladderwort’s genome is consistent with this model.

      You reported some time ago that nucleotide substitution rates in Utricularia and Genlisea were much higher that in some sister groups, supporting a ROS mutation hypothesis. Can you expand on that?

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