Junk DNA Bad, Junk Gene Good

A few weeks ago Carl Zimmer wrote a nice post at The Loom taking science writers to task for leaping at every chance to grab ahold of the “Wow! Junk DNA is not junk after all!” news hook. He correctly pointed out that we’ve known for years that non-coding DNA has lots of function, and so we should not celebrate every new example of functional non-coding DNAs as overturning the conventional wisdom.

I, of course, could not agree more, and his piece said it very well. And I really like Zimmer’s writing – he’s one of the few popular science writers who really conveys a deep understanding of the subtle beauty of evolution.

So it’s with great disappointment that I read Zimmer’s “Now: The Rest of the Genome” in today’s NYT. The hook for this story? “Wow! One gene doesn’t just code for one protein after all!”. The central dogma is dead. Oh my.

Here’s the nut graf:

It turns out, for example, that several different proteins may be produced from a single stretch of DNA. Most of the molecules produced from DNA may not even be proteins, but another chemical known as RNA. The familiar double helix of DNA no longer has a monopoly on heredity. Other molecules clinging to DNA can produce striking differences between two organisms with the same genes. And those molecules can be inherited along with DNA.

Several different proteins can be produced from a single stretch of DNA? No way! Not all transcription is involved in making protein-coding RNAs? Shocking! Identical chromosomes can behave differently because of inherited epigenetic marks? Whoa!

The whole point of Zimmer’s earlier piece was that science journalists need to pay attention to history when they’re pimping a story line:

So, are enhancers an amazing new kind of junk that’s not junk?
Nope. The first reports of enhancers came out in 1981, 27 years ago.

Well, he needs to apply the same standard to himself. Alternative splicing was discovered in the late 1970′s. Non-coding RNAs in the 1980′s. And epigenetic effects were described over 50 years ago, with molecular mechanisms first worked out over 25 years ago.

Yes, new genomic data is providing a more complete description of these phenomena. But for Zimmer to pretend that these new data are reinventing what a gene is is as bad a misrepresentation of science history in the name of a story as anything I’ve seen written about junk DNA.

Science writers play a very important role as honest interpreters of science for the public. But if they don’t present science history accurately, they can’t be taken seriously as authorities on science present.

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6 Comments

  1. Paul Gardner
    Posted November 11, 2008 at 12:37 am | Permalink

    “Non-coding RNAs in the 1980’s.” Is this some sort of tongue-in-cheek joke Michael? The sequence and function of tRNA had pretty much been worked out in the 60s. In fact a Nobel Prize was awarded to Robert Holley in 1968 for working much of this out. That’s all according to that ever reliable source of information Wikipedia (http://en.wikipedia.org/wiki/TRNA#History).

  2. Posted November 11, 2008 at 2:46 am | Permalink

    Weird how this seems in almost direct contrast to the blog posting of Zimmer’s. Is there something about blogging versus print media that leads to this like editor’s cutting out some material? One thing I like about blogging is not having to have my ideas edited down (this gets me in trouble from time to time too) in any way. Maybe this happened here?

  3. Posted November 11, 2008 at 8:45 am | Permalink

    I suppose it won’t come as a big surprise that I disagree. I just defended myself here: http://blogs.discovermagazine.com/loom/2008/11/11/hypocrite-moi/

  4. Michael Eisen
    Posted November 11, 2008 at 9:33 am | Permalink

    (I posted this on Carl’s blog but I thought I’d reproduce it here):

    Just to be clear – I wasn’t criticizing the article as a whole. It is a great exploration of the things that are emerging from our newfound power to systematically characterize transcription, epigenetics and other properties of the genome. And I did read the entire article. But it was the hook that bothered me, so it’s what I wrote about.

    What frustrates me – and you too I think, judging from your post on junk DNA – is that the need/desire to frame complex and inherently inherently science stories as revolutionary. Your nut graf clearly bases its pitch for people to keep reading on the idea that new research is overturning long-held beliefs about the structure of genes.

    But, with all due respect to Mark Gerstein and other scientists who make similar points, I don’t think science viewed alternative splicing, non-coding transcription or epigenetics as oddities until these new studies came along (trans-splicing is another story). Rather, they were accepted as general phenomena whose scale and role in biology were poorly understood. What the new genomic studies have done is give us a detailed picture of precisely which alternative splice forms are made, which regions of non-coding DNA are transcribed, and what types of epigenetic marks are found in different regions of the genome. For all of our acceptance that these existed, we had little idea about what role they play in biology, or how they are generated and regulated.

    Or, said more simply. We already knew that the genome was a dizzyingly complex place. The new data gives us the means to actually understand this complexity, and I don’t see why your story couldn’t have been framed around that idea.

    This is more than just a minor pet peeve. The portrayal of science in the popular press is always around the idea that new experiments are showing that everything we’ve believed for decades was wrong, rather than showing it as a continuous process of discovery and elucidation. Yes, our initial models of genes were overly simplistic. But they weren’t really wrong either. They were useful abstractions of reality that allowed us to uncover the true complexity that exists in biology.
    And let me just end by placing blame where blame is due. The stories on junk DNA that both you and I have criticized originate primarily with the authors of the studies in question and their press offices – who write press releases that pitch every new observation as novel and every new ideas as revolutionary. They do it because they think it’s the only way to get reporters to bite at their stories. We – scientists and science journalists – should work together to make sure this is unnecessary.

  5. Nick (Matzke)
    Posted November 11, 2008 at 11:07 am | Permalink

    It is good to point out some of the problems with the “Wow! Junk DNA is not junk after all!” news hook, but I am still surprised at this combination of facts:

    1. The overwhelming, crashingly obvious biological fact is that genome sizes vary wildly in eukaryotes, over orders of magnitude, with no particular relationship to complexity as far as anyone can tell.

    2. The differences in genome size do not apparently correlate with amount of genes or non-protein-coding-but-coding-for-something-e.g.-regulation DNA, but instead are primarily due to gain or lack of repetitive elements.

    3. Genome size instead seems to correlate with cell volume/nuclear volume. E.g. amphibians with big cells have big genomes, amphibians with small cells have small genomes, even with the same closely-related groups.

    4. This is pretty dang strong evidence that most of that DNA in large genomes isn’t doing anything very sexy by itself — you can perfectly well build a vertebrate with 1/10th the genome size of humans, we know this because we have examples. The “junk DNA” still might have something that might be called a “function” or effect, perhaps in bulk, but this is unresolved, and it might not. Resolving it is the only thing that will settle for once and all whether or not “junk DNA” is an appropriate description of the bulk of the genome.

    5. Virtually all discussions of junk DNA, both in science journalism and from scientists commenting on the science journalism (with the notable exception of T. Ryan Gregory), almost criminally leave out facts #1-4, and thus pretty much aren’t even discussing the major relevant data on the junk DNA question.

    For some reason these facts don’t seem to get any kind of grip with most people who discuss the junk DNA issue. Can’t figure out why.

  6. Chris Tan
    Posted November 11, 2008 at 2:35 pm | Permalink

    I did not get the impression that alternative splicing is a new discovery or a whole new thing in Carl Zimmer’s article, maybe because I am aware of the generality of the phenomenon. However, I do think the article can be better framed such as how new data had further unveiled the intricate of the phenomenon (as Michael had commented).

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  • By Hypocrite? Moi? | The Loom | Discover Magazine on November 11, 2008 at 8:43 am

    [...] now I sit down to find that my next order of business is to respond to a pretty harsh judgment of the article that appeared overnight, from a scientist I [...]