Tuesday, January 15, 2008

Greg Laden Gets Suckered by John Mattick

 
Oh dear. Greg Laden reviews a paper from John Mattick's group and he falls for the hype, hook line and sinker. Here's what Greg says [Genes are only part of the story: ncRNA does stuff].
The "Junk DNA" story is largely a myth, as you probably already know. DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that. But we actually don't know a lot more than that, or more exactly, there is not a widely accepted dogma for the role of "non-coding DNA." It does really seem that scientists assumed for too long that there was no function in the DNA.
I hate to break it to you Greg, but junk DNA is not a myth. It really is true that a huge amount of our genome is junk. It's mostly defective transposons like SINES and LINES [Junk in your Genome: LINEs]. It's a lie that we don't know what most non-coding DNA is doing. We do know. It's not doing anything because it's mostly screwed up transposons and pseudogenes like Alu's.

Mattick may have found a few bits of DNA that encode regulatory RNAs but that's only a small part of the total genome. He, and you, have fallen for excuse #5 of The Deflated Ego Problem.

Ryan Gregory has already tried to teach Greg some real science about junk DNA so I won't pile on any more than I have [Signs of function in non-coding RNAs in mouse brain.].

UPDATE: RPM chimes in to expose the flawed thinking of Greg Laden [How Easy is it to Write About Junk DNA?]


9 comments :

  1. I’m following this junk DNA debate with interest. One ID commentator I stumbled across suggested that a prediction of ID is that junk DNA doesn’t exist. Is this one of the things at the back of your mind?

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  2. The original connotation of "junk DNA" was more like the junk drawer in your kitchen - some of the stuff would be useful, most wouldn't be useful, and we would figure it out as we studied more of it.

    The ID "prediction" was made after the fact - we already knew some of the non-coding DNA had regulatory function. So they're claiming they predicted an event that had already occurred when they made the prediction.

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  3. One ID commentator I stumbled across suggested that a prediction of ID is that junk DNA doesn’t exist.

    How can ID make any predictions when its adherents claim not to know the nature or motives of the unspecified designer?

    Also, as gp said, it doesn't really count as a 'prediction' if you predict after the event - even Nostradamus can do that.

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  4. timothy v reeves asks,

    I’m following this junk DNA debate with interest. One ID commentator I stumbled across suggested that a prediction of ID is that junk DNA doesn’t exist. Is this one of the things at the back of your mind?

    No, not really. I was interested in junk DNA and genomes long before I took up the cause against non-scientific stupidity.

    To my mind, the junk DNA debate has more to do with the decline of rationality within science than with the attack on science by religion.

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  5. Why would anyone who could be expected to recognize the limits of _conventional wisdom_ presume to know that there is "junk" in our DNA when they don't understand how the organism's development or physiology is actually controlled?

    Just because genetic stamp collectors notice that the presence or absence of a given gene affects ("regulates") some characteristic or other gene's effects doesn't mean that the global method of organism control simplistically scales up from that apparent relationship.

    It is depressing to encounter researchers that exude such a high degree of certainty despite their ignorance, particularly of topics outside their immediate field. From my perspective, you appear to have much to learn.

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  6. anonymous asks,

    Why would anyone who could be expected to recognize the limits of _conventional wisdom_ presume to know that there is "junk" in our DNA when they don't understand how the organism's development or physiology is actually controlled?

    There are two reasons. First, we don't have to know anything about development in order to recognize pseudogenes and defective transposons, which make up 50% of our genome.

    Second, we know a great deal about development and there's no reason to presume that you need enormous about of regulatory DNA to control expression of our genes.

    It is depressing to encounter researchers that exude such a high degree of certainty despite their ignorance, particularly of topics outside their immediate field. From my perspective, you appear to have much to learn.

    From my perspective, you have much to learn.

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  7. "anonymous asks,

    Why would anyone who could be expected to recognize the limits of _conventional wisdom_ presume to know that there is "junk" in our DNA when they don't understand how the organism's development or physiology is actually controlled?"

    I couldn't agree more. It is ignorant to assume that our current knowledge allows us to identify all important information within apparently 'junk' DNA. It was not long ago that most of the functional non-coding RNAs we now consider vital to complex regulatory networks were also considered junk. How can we be sure that supposedly inactive transposons and pseudogenes serve no purpose? And these do not account for the entirety of the 'junk' genome. Too many times scientists have assumed their knowledge to be more complete than it was, and thereby excluded other more accurate and often more exciting possibilities - let's not forget that proteins were widely accepted as the genetic material before definite experiments to the contrary.
    An open mind and some humility go a long way in taking science forward.

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  8. The problem here are not the data (there is a surprisingly large number of ncRNAs which are developmentrally regulated) ...it's the hype (BEHOLD: it's all functional).
    This hype is not helpful and it will not make all the pseudogenes etc. suddenly become functional... (we are talking here about major proportions of the genome).
    There is (almost)no evidence (yet?) and a lot of counterevidence that most of the non coding nucleic acids are not functional.

    Larry is right. There is not closely enough evidence (yet?) to make a convincing case.
    This has nothing to do with dogmatism. This is how science works.
    Larry will be the first to admit that he was wrong when EVIDENCE shows him to be wrong.

    John Mattick is a very nice guy, the problem is that he has the tendency to give sermons -not talks-. In addition he is very productive in writing (redundant) reviews and comment pieces where he proclaims his visions...
    (there must be dozends of them in the last 2-3 years)
    For my taste, he is behaving a bit too much like a prophet . A bit sad, because in his group they do interesting research...

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