Genome reduction in bladderworts vs. leg loss in snakes.

In one sense, I am happy that there is enough interest in the concept of “junk DNA” (and by extension, my area of research in genome size evolution) that the subject gets regular media attention. A few months ago, it was all about the ENCODE project and its “finding” of “function” for 80% of the human genome. This week, it’s a story that has the exact opposite message: that large amounts of so-called “junk DNA” can be deleted without apparent consequence. This most recent story was prompted by the publication of the genome sequence of the carnivorous plant known as the floating bladderwort. This plant is of interest because it has a very small genome that is nearly devoid of transposable elements and other non-coding DNA, while also containing more protein-coding genes than the human genome and exhibiting signs of past genome duplication events. We’ve known that the genome was small for several years, but having the genome sequence provides some important insights into what a genome this size contains, and (most interestingly) what it doesn’t.

In typical style, Ed Yong has written up a very nice summary of the paper and the potential implications for the junk DNA debate. Following the lead of the original paper and the associated press release, many media reports similarly took the “this plant can get rid of junk DNA, so maybe it isn’t functional after all” line (a few examples: here, here, and here).

I was quoted in Ed Yong’s article as follows:

“The study further challenges simplistic accounts of genome biology that assume functions for most or all DNA sequences, without addressing the enormous variability in genome size among plants and animals,” says T. Ryan Gregory, who studies the evolution of genome sizes at the University of Guelph.

In 2007, Gregory coined the “Onion Test” to challenge anyone who thinks that non-coding DNA isn’t junk. If that DNA is important, why is it that the onion needs so much more of it than a human, or even other closely related plants? “The Onion Test could just as easily have been called the Bladderwort Test,” he says. “If non-coding DNA is vital for gene regulation or some similar function, then how can a plant such as the bladderwort get by with so little of it?”

For me, the logic of the authors of the paper is straightforward. Here we have a complex plant with a lot of genes but very little non-coding DNA, and this calls into question the idea that you need a lot of non-coding DNA to regulate genes in a complex organism. Jonathan Eisen, on the other hand, has objected in his usual snarky way, awarding MSNBC and the authors of the bladderwort genome paper one of his “Twisted Tree of Life Awards”. As he summarizes the claim,

So – basically – if ONE FUCKING ORGANISM DELETES SOME OF IT’S [sic] NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.

In the comments thread on his blog post, he expanded on what he sees as the problem with this argument:

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.

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?

No, that isn’t the logic, and the legless snakes or eyeless cave fishes analogy is flawed. Why?

1. We know that legs and eyes are functional, and we know what they are functional for (walking and seeing, respectively). By contrast, we do not have strong evidence that non-coding DNA is functional or what it may be functional for. Worse, the very existence of so much non-coding DNA itself is taken as “evidence” that it must be doing something. Therefore, the observation of a plant that lacks a substantial amount of non-coding DNA but gets by just fine suggests that this kind of DNA isn’t strictly necessary in order to make a complex plant.

2. If most of the non-coding DNA in a larger genome does serve an important regulatory function, then it means this plant with a tiny genome must have evolved a totally different system for regulating its genes. This strikes me as a rather large assumption — and in any case, it’s one for which we have no evidence. As such, I would argue that it is at least as parsimonious to take this small genome as evidence that non-coding DNA in general does not serve a key regulatory function for the most part.

3. When snakes lost their legs or cave fishes lost their eyes, they also lost the specific ability that legs or eyes provided. Legless snakes can’t walk, because the function of legs is walking. Eyeless fishes can’t see, because the function of eyes is seeing. The proposed function for non-coding DNA is gene regulation. Unlike the snake or fish example, the bladderwort has lost most of its non-coding DNA but it can still regulate all of its genes just fine.

I think Jonathan raises a valid point about the dangers of overzealous extrapolation, but I think his criticism of the authors (much less its tone) in this case is unwarranted.


29 comments to Genome reduction in bladderworts vs. leg loss in snakes.

  • gillt

    The proposed function for non-coding DNA is gene regulation.Unlike the snake or fish example, the bladderwort has lost most of its non-coding DNA but it can still regulate all of its genes just fine.

    The comparison should be to a blind cave fish that lost its ability to make eyes but can still see. But blind cave fish haven’t lost their “eyes” or their ability to makes eyes. All the genes for eye-making are still there and the embryos make eye buds. It’s all about gene expression/regulation. 

    FYI: The genome of another aquatic plant, the Sacred Lotus, was just published. From the abstract: “The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape.” 
     

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  • Jess Tauber

    In linguistics we have many layers of coding of meaningful elements. The degree of indirectness of information management is a relevant factor. Languages with relatively few roots (such as Inuktitut with maybe 900 or so) has to make up this dearth by heavy utilization of grammatical morphological mechanisms (derivation, inflection). When there is little such management then the root lexicon tends to be very large. But syntax, which also includes pragmatic ordering shifts, also varies by its importance and apparently in complementary distribution with the other mechanisms.  In the genome we have very similar organizational principles. One can have many unique genes each activated independently, or they can be generated by editing mechanisms from larger storage sequences (but then you have to have a means to know when and where to edit them), and so on. Indirectness of the level of management has several degrees also here. If you reduce the relevance of one level you may be able to rely more on another, because the entire system is massively functionally redundant potentially (though it takes time to shift responsibilities).

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  • E Dallas

    Eisen’s tone may be a bit strident, but his point is a very good one.  Generalizations from small amounts of data often lead us in very wrong directions, and when unjustified generalizations are widely accepted as facts, those false facts impose false constraints on further study. 
    Note the previously accepted “facts” that healthy lungs are sterile (no, it’s just that culturing the bacteria found in lungs is difficult) and bacteria can’t live in the stomach so ulcers must be caused by stress (no, h. pilori are quite happy in an acid environment and eat through the stomach lining) and condoms don’t protect against HIV because latex is porous (no, it takes a long time for HIV to get through a condom, so condoms are effective for at least an hour) and a few hundred other mistaken conclusions promoted by scientists who jumped to unjustified conclusions, to the detriment of us all,  
    “Trust the data, but not the conclusions” is still excellent advice to follow when reading published studies.  I haven’t yet seen actual evidence that human junk DNA has no function. 
     
     
     

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  • SLPage

    “I haven’t yet seen actual evidence that human junk DNA has no function. ”
     
    I haven’t yet seen any that 80% of it does have a function.

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