Thursday, March 05, 2015

Is most of our DNA garbage?

Carl Zimmer's article on junk DNA has appeared in the online edition of the New York Times magazine at: Is Most of Our DNA Garbage?.

Carl was in Toronto and Guelph last December gathering information for his article. You can see that Ryan Gregory is featured and my colleague Alex Palazzo gets quoted.

Here's a picture of us having dinner. That's Alex on the left, second from left is some old dude who everyone ignores, Ryan is next and Carl Zimmer is on the right.

Carl is still the best science journalist on the planet and I appreciate that he has alerted the public to a serious problem in genome studies. The general public has been snowed by the ENCODE publicity campaign and by naive journalists who have enthusiastically reported that junk DNA is dead.

It is not. The most knowledgeable scientists recognize that the issue is not settled. The very best ones () know that 90% of our genome is junk.


13 comments :

  1. Yeah I thought that he did an excellent job.

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  2. I don't think "best science journalist on the planet" is an exaggeration, either. Only fellow I've read who comes close (usually doing book length, with an occasional article) is David Quammen. Song of the Dodo, about island biogeography, is a particular favorite.

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  3. I agree with you, but I think Sydney Brenner's distinction between garbage (stuff you get rid of) and junk (stuff you keep around because it isn't doing any harm) is useful.

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    1. Why is that distinction useful? "Garbage" would just seem to be another term for deleterious alleles of functional sequences, except in very fast replicating, high population organisms, in which junk is actively selected against. And junk DNA isn't something you keep around; that implies some active mechanism for preservation.

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    2. I keep broken stuff if it has parts that can be applied to current appliances. Perhaps I'm a bit nuts, but fixing things is a hobby. I take no active steps to preserve junk. My reading of the word garbage is stuff that causes harm if left lying around.

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    3. So what in your genome would the term "garbage" apply to? And if there's nothing, then why would we need a term? Or perhaps you're just complaining about the article's title.

      Anyway, I think you're still implying that you actively keep the junk even if you take no steps to maintain it, rather than passively accumulating it because you have no mechanism to get rid of it.

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    4. John,

      Consider that, indeed, the so called jDNA accumulate in some genomes, such as the human genome, because its rate of origin is higher than that of its deletion. So, there is *no* selection for maintaining it. Can this sequence-nonspecific jDNA, which in the human genome represent well over 90%, have biological functions or not?

      Obviously, I’m not asking about potential biological functions for small quantities of this DNA, which would be deceiving, but about putative functions for most of it.

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  4. Carl... I love your blog.. and this article was spot on.

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  5. Now I have to complain about Zimmer's article.

    Zimmer makes it seem like scientists believed all non-coding DNA was junk until "recently." Uh, what's recently? He makes no mention of the discovery of regulatory regions in non-coding DNA back in the 1950's or the CONTINUOUS stream of discoveries of function in ncDNA since then. The article makes it seem like it's a recent paradigm shift. Zimmer probably knows better than that, he just wrote that part poorly.

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  6. You guys and gals wanna cry? Read the comments on Zimmer's article. Lotta non-scientists who are FURIOUSLY angry at the "arrogance" and hubris of the scientists who believed in Junk DNA, for slandering and besmirching the dignity of their regal and sacred charged acidic biopolymers. How dare you arrogant scientists insult my charged acidic biopolymers! How DARE you!

    It's like somebody said their wife was ugly. They're mad as wet possums over this insult to their nucleic acids. They're not necessarily creationists either, just muggles with giant egos. The arrogance of the NON-scientist is hard to swallow sometimes.

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    1. What about your arrogance? You're just a dead Greek philosopher.

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    2. But I live in a barrel, and my only friends are stray dogs.

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  7. What is disturbing is that we again meet the same names and supporters of the junk-DNA myth. Also in the article of Zimmer:

    “You say, ‘I found it — America!’ ” says Alex Palazzo, a biochemist at the University of Toronto.

    Pallazo's papers are, prior to publication, reviewed by Moran. Small world, isn't it?

    Apparently, there is club desparately defending the junk DNA myth (which they require for their own beliefsystem).

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