March 12, 2009 | David F. Coppedge

More Functional Non-Coding DNA Found

Another finding undermines the concept of “junk DNA.”  A team of scientists in Massachusetts found over a thousand functional RNA transcripts from intergenic sequences.  These RNA transcripts, coming not from genes but from regions earlier thought to be non-functional, take part in diverse functions from stem cell pluripotency to HOX gene developmental processes to cell proliferation.
    The work by Guttman, Rinn et al was reported in Nature.1  The March 12 issue also included a technology feature highlighting the research of co-author John Rinn of the Broad Institute in Cambridge, Massachusetts.2  The research team developed new methods for identifying the activity of large intervening non-coding RNAs (lincRNAs).  They also found that these RNAs are strictly regulated.
    Recognizing that non-coding regions of DNA could be functional has “turbo-charged the field,” he said, “as not only can we identify these things now but we can get a good idea of what they might be doing to test functional relationships.”

1.  Guttman et al, “Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals,” Nature 458, 223-227 (12 March 2009) | doi:10.1038/nature07672.
2.  N.B., “Technology Feature: Transcriptomics: Rethinking junk DNA,” Nature 458, 240-241 (12 March 2009) | doi:10.1038/458240a.

The few mentions of evolution in the main paper are instructive.  One of the methods the scientists used to identify functional RNA transcripts was “evolutionary conservation,” which means the lack of evolution.  Presumably a “conserved” (unevolved) region of DNA or RNA was protected from mutation and selection because it was too functional for Tinker Bell to tinker with.  There is a subset of natural selection called “purifying selection,” which essentially means “defending DNA from the ravages of mutation.”
    The researchers found that these previously-unknown functional transcripts were, indeed, highly conserved in mammals: “In sharp contrast to previous collections,” they said, “these large intervening non-coding RNAs (lincRNAs) show strong purifying selection in their genomic loci, exonic sequences and promoter regions, with greater than 95% showing clear evolutionary conservation.”  The team believes there could be many thousands of these lincRNAs in mammalian genomes.
    If some of the other non-coding DNA is found to be functional, the implications would be hard on evolutionary theory: “the markedly low rate of conservation seen in the current catalogues of large non-coding transcripts ([less than] 5% of cases) is unprecedented and would require that each mammalian clade evolves its own distinct repertoire of non-coding transcripts.”  That would be too much new genetic information for a Darwinian mechanism to create.  For that reason, they are postulating that most of the RNAs represent “transcriptional noise, with a minority of bona fide functional lincRNAs hidden amid this background.”
      The authors did acknowledge one point of logic: “Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function.”  One of their criteria for measuring functionality of lincRNAs was the degree of conservation.  They hedged this criterion by saying, “We do not exclude the possibility that lincRNAs identified by shotgun sequencing that fail to show conservation are nonetheless functional, but other evidence will be required to establish this point.”
    To avoid circular reasoning, they cannot use evolutionary conservation as support for evolutionary “purifying selection.”  If absence of evolutionary conservation cannot prove the absence of function, then neither can it prove evolution; the lack of conservation might be due to other causes, like design.  And if a host of functional unconserved transcripts are found, it will seriously call into question the ability of neo-Darwinism to generate a large amount of unique functional information in each mammal genome.
    For the time being, Guttman et al are banking on the unconserved stuff being transcriptional noise.  The trend against the “junk DNA” paradigm is against them, however (11/07/2008, 02/06/2008, 09/12/2007, 07/16/2007, and especially 06/15/2007).  One additional thing from the paper is apparent: evolutionary theory was only incidental to the story.  What they were searching for was functional information, conservation, regulation, and the lack of evolution.  In a word, that’s design.  Chalk up another turbo-charged research project to the inherent motivation of ID science: seeking to understand the design in nature.

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