Thursday, October 08, 2009

Junk DNA: A Case Study in Scientific Controversy

 
I strongly support the concept of junk DNA and I reject the idea that a significant percentage more than 10% of the DNA in our genome has a function. This is my informed opinion.

This is a genuine scientific controversy, one that I bring to the attention of my students. We are discussing controversies, misunderstandings, and frauds. This one counts as a scientific controversy.

Of course, it's also part of the rationalism vs superstition debate since creationists have a hard time explaining junk DNA. The Intelligent Design Creationists, in particular, are almost duty-bound to oppose the concept. For an excellent example of how the IDiots exploit a genuine scientific controversy see: How The Junk DNA Hypothesis Has Changed Since 1980 by Richard Sternberg .

THEME

Genomes & Junk DNA
It all sounds very much like science. The trick is to put as much science into the discussion as possible, while keeping the distortions and misrepresentations to a mimimum. It's best to omit all references to other points of view 'cause that gives the impression that the scientific community is opposed to junk DNA.


15 comments :

  1. That is actually a very disturbing piece. Repost it at a non DI page, and it could have most of my work colleagues convinced by the structure of that argument...

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  2. "I strongly support the concept of junk DNA and I reject the idea that a significant percentage of the DNA in our genome has a function. This is my informed opinion."

    Yes, because you are an evolutionary ideologue who refuses to give up on your mythology and orthodoxy.

    Thankfully, your "opinion" does not inform the progress of real science.

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  3. Charlie, there's scientific fact here no mythology. Put up or shut up. Better still if Sternberg has the fortitude he shouldn't be posting his assertions on some obscure website, he should at the very least be posting his thoughts here. We know he won't because he can't bamboozle scientists. Simple.

    Truti

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  4. My opinion is informed by the peer-reviewed scientific literature, not by bloggers or zealots.

    Read the literature...it's all there.

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  5. Actually, wagner has inadvertantly stumbled onto a valid point: Larry can't mean that the percentage of functional DNA is insignificant; because even if the percentage is low it must still be significant, since without it we wouldn't be here!

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  6. I emailed the printer.

    Hello:

    I would love to acquire a print of "One Nation Under God" (#353). However, you seem to preach that the lawyer counting his money is wrong. Therefore, I would like you to send me a copy free of charge, the only occurrence of exchange being my increase in faith of the kindness of humanity. You may send the print to:

    [address]

    Thank you very much for your generosity. I know that it will not go unrewarded in Heaven, when we all meet our true fate.

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  7. Ah, wrong entry. Disregard the previous comment :P

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  8. Eh, can you clarify "significant percentage"? Clearly, no matter what percentage of the genome is functional, it's still significant - one measure of the significance being that you're alive because of it!

    Are you using it as shorthand for "less than 5%", or what? I thought we were up to 5% already once you take into account coding sequences, promoters and other regulatory stuff.

    How large does the percentage have to get before it counts as "significant"?

    Now if you'd said "majority", I'd have been with you, by quite some margin.

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  9. Charlie,

    There is also this little tidbit in the peer-reviewed literature.
    "Megabase deletions of gene deserts result in viable mice" Nature 431, 988-993 (21 October 2004). 2.3 million "interesting" bases knocked-out in the 2.7 billion base genome.

    The only "everything useful" explanations I have heard are rather unsatisfying;

    1) Dumb luck that they knocked out that nonfunctional bit, but the rest is required.
    2) Well...err... it must be an important sequence... we just can't measure the phenotype (aka Russell's teapot).

    Press release...
    http://genome.wellcome.ac.uk/doc_WTD020724.html

    Paper...
    http://www.nature.com/nature/journal/v431/n7011/abs/nature03022.html

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  10. Re "no junk DNA" - Guys have nipples. End of discussion.

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  11. "There is also this little tidbit in the peer-reviewed literature.
    "Megabase deletions of gene deserts result in viable mice" Nature 431, 988-993 (21 October 2004). 2.3 million "interesting" bases knocked-out in the 2.7 billion base genome."

    These folks (Sternberg et al., including Pellionisz) also like ot engage in some rather easily falsified historical revisionism re: junk DNA. When you show them that they are wrong (by showing them that 'evolution scientists' were proposing and discovering functionin some juk DNA as early as the 1970s) they claim that what you've shown them was doen IN SPITE OF the prevailing wisdom.

    They have an answer for everything. A wrong answer, to be sur,e but an answer that folks like Charlie latch onto.

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  12. 2 points:
    1) I don't see where the 90% as junk number comes from. My reading of the literature says that we can be pretty confident in about 45% of the genome being verifiable junk--I don't see how you can go much higher than that.
    2) The standard of what can be deleted without causing a phenotype is a bad one for determining functionality. First, deletions of some retroelements can alter regulation of true coding regions, not due to anything in the retroelement region but due to structural changes in the chromosome. At the same time, regions that are only nonessential because they are redundant will be categorized incorrectly. We should move away from the "remove it and nothing happens" standard.

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  13. Anonymous says,

    I don't see where the 90% as junk number comes from


    If you follow the link in the theme box )above) you'll see the numbers I got to before I lost interest.

    There are still some essential sequences that weren't identified in previous postings (e.g. origins of replication) but they won't account for much more.

    What we're left with is about 5% of the genome that's known to be functional and more than 50% that's identifiable as junk. Of the remainder, almost all of it appears not to under negative selection. It's intergenic sequence that hasn't any known function nor any that's been reasonably proposed.

    We assume it's junk until shown otherwise. Thus, as a round, convenient, number we say that about 90% of our genome is junk.

    Charlie and other evolution skeptics will tell you that much of this DNA is transcribed. What he won't tell you is that there's less that one transcript per cell per generation and nobody has found a function for these RNAs. (With minor exceptions.)

    Furthermore, this kind of low level transcription of random segments of the genome is perfectly consistent with what we know about the inefficiency of transcription. It's accidental transcription due to non-specific binding of transcriptional activators and/or RNA polymerase.

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  14. Anonymous says,

    The standard of what can be deleted without causing a phenotype is a bad one for determining functionality.

    No, that's not correct. The experiment is actually a very good way of testing functionality. In fact, I can't think of a better way, can you? If the result had demonstrated functionality you'd be singing a different tune.

    What you mean to say is that for those who have a non-rational belief in functionality there are ways of dancing around the result so that you don't have to accept the obvious conclusion.

    This is true. You can make up all kinds of explanations that allow you to preserve your favorite hypothesis in the light of nasty little facts. At some point that kind of excuse becomes tedious.

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  15. Larry, you forget to mention one very important feature of the low-level transcription that Sternberg et al. get so excited about - namely that the products of these transcriptional events become more abundant when components of the quality-control machinery that removes non-functional RNA are mutated. This property argues very strongly against the assertions of the DI that this vast underground of transcription actually has function.

    My own halting attempt at introducing the subject is here.

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