Monday, April 20, 2009

International team cracks mammalian gene control code

International team cracks mammalian gene control code

Stop the presses! Revise the textbooks! John Mattick and his collaborators have discovered how genes are controlled in mammals.

Anyone who knows Mattick's past history will know what's coming—Mattick overthrew the Central Dogma of Molecular Biology over six years ago (Mattick, 2003; Mattick, 2004).1,2
An international consortium of scientists, including researchers from The University of Queensland (UQ), have probed further into the human genome than ever before.

They have discovered how genes are controlled in mammals, as well as the tiniest genetic element ever found.

Their discoveries will be published in three milestone papers in leading journal Nature Genetics.


1. See Basic Concepts: The Central Dogma of Molecular Biology for the truth about the Central Dogma.

2. See Greg Laden Gets Suckered by John Mattick for an example of how easy it is to get fooled by John Mattick.

Mattick, J.S. (2003) Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25:930-939.

Mattick, J.S. (2004) The hidden genetic program of complex organisms. Sci. Am. 291:60-67.

6 comments :

  1. "...the tiniest genetic element ever found...."

    Tinier than a methyl group?

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  2. If I'm correct, the ones mentioned in those articles are 18nt nc-transcripts

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  3. Particularly, in light of your previous comments on the junk status of LINEs/SINEs (http://sandwalk.blogspot.com/2007/10/junk-in-your-genome-lines.html), it is rather disingenuous to not at least link to the associated Nature Genetics paper that now provides compelling data to the contrary (http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.368.html). Surely it is of greater value to your readers to focus on the science rather than the personalities.

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  4. This is the one I was talking about..

    http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.312.html

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  5. Anonymous says,

    Particularly, in light of your previous comments on the junk status of LINEs/SINEs (http://sandwalk.blogspot.com/2007/10/junk-in-your-genome-lines.html), it is rather disingenuous to not at least link to the associated Nature Genetics paper that now provides compelling data to the contrary (http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.368.html).In my experience, it is often very difficult to evaluate these papers. In many cases the authors exhibit extreme bias in favor of one kind of explanation and they do not perform the kinds of experiments necessary to falsify their favorite hypotheses.

    This paper shows all the characteristics of such bias. It begins with exaggerated claims about the role of retrotransposon sequences and goes downhill from there.

    I have two criteria that I use to judge the quality of genomic RNA expression studies.

    1. Does the paper discuss the role of transcription noise as a possible explanation of the data? [e.g. Hurst, 2009]

    2. Does the paper describe the estimated number of transcripts per cell when it attributes function?

    This paper fails to mention the alternative possibility of transcription noise and it fails to evaluate their findings in light of this possibility.

    This paper mentions RNA abundance briefly in the discussion but doesn't give any firm estimates. What is their explanation for the low abundance of specific transcripts?

    ... it could still be pointed out that transcript abundance is not necessarily important for function, as noted for ncRNA epigenetic regulators.Another possibility is that the low abundance is because these are accidental transcripts produced as a result of the known error rate for transcription initiation.

    Anonymous, why do think the authors fail to mention this possibility? Is that an example of good science?

    Surely it is of greater value to your readers to focus on the science rather than the personalities.Mattick has a history of hype and self-promotion. I think it's relevant.

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  6. "The dogma in the field is that retrotransposons are only active in cancer cells and cells that turn into eggs and sperm," Dr Faulkner said. "Our results showed that retrotransposons that can no longer move around the genome may still be expressed in a broad range of cells, and thereby regulate the expression of nearby genes."OHMYGOD! NO! NOOOO!!!

    WHY DIDNT ANYONE TELL ME?!?!?!

    LIFE NO LONGER HAS ANY MEANING NOW THAT TEH DOGMEH HAS BEEN OVERTHROWN!

    *hurls self out 10th story window*

    ReplyDelete