June 3, 2004 | David F. Coppedge

Gene Regulation: When Nonsense Makes Perfect Sense

Nature June 31 reports on another use for “junk DNA.”  A portion of previously-considered “nonsense” genetic code, which does not produce a protein as does a gene, nevertheless has an important role: it regulates the expression of the neighboring gene.  This opens a whole new realm of function for portions of our genetic material that were thought to be useless leftovers of evolution: it’s a new kind of gene that regulates other genes (see the Reuters summary on MSNBC News).
    Molecular biologists have been intrigued by the fact that the DNA translation machinery seems busier than required to produce proteins: “Why is there such a heavy traffic of RNA polymerases, the enzymes that copy DNA into RNA, and the production of large quantities of apparently non-coding and non-functional RNAs?” the reporters say.  The new work by Martens et al. reported in the same issue shows that “RNA polymerases are evidently doing more than we thought.”  The resulting “nonsense” RNAs produced by reading non-coding segments act as regulators, controlling the amount of protein that is expressed by the true genes by a process of “transcriptional interference.”  What was considered nonsense, therefore, actually makes perfect sense on a higher level:

Taken together, these studies highlight the importance of intergenic transcription in regulating gene activity, even in the relatively densely packed genome of yeast.  It seems that RNA polymerases are not only required for the production of particular RNA species, but by travelling along DNA they can also control the occupancy of regulatory sites by transcription factors.  Widespread transcription of intergenic sequences has also been described in the human genome.  Surprisingly, many of these non-coding transcripts seem to be regulated in a manner that is intimately connected to the transcription of protein-coding genes.  So the high proportion of non-coding regions in the genomes of higher organisms is probably not due to the accumulation of nonsense DNA, but rather represents the evolution of ever more complicated gene-regulatory systems.

EurekAlert puts this finding into perspective:

If so, the findings would carry an important message for the post-human genome era-namely, that researchers’ attempts to turn the masses of data churned out by the Human Genome Project into an understanding of what actually happens in the human body may be even more complex than they anticipated.  One of the main challenges for that effort is to figure out how and when genes are turned on and off during normal development and disease.  Rather than look only at how genes are regulated by proteins, they would have to turn their attention to a new, and possibly more-difficult-to-detect form of control.  And given that junk DNA makes up 95 percent of chromosomes, the mechanism could be fairly common.

The article gives the bottom line to one of the researchers, Fred Winston of Harvard Medical School: “Every time we thought we understood everything going on here, we have been wrong.  There are additional layers of complexity.”


1Sabine Schmitt and Renato Paro, “Gene regulation: A reason for reading nonsense,” Nature 429, 510 – 511 (03 June 2004); doi:10.1038/429510a.

You are witnessing the collapse of an evolutionary myth, the myth of “junk DNA” and “nonsense” genetic code.  We have been chronicling the demise of this mischaracterization for years (see 05/10/2004 headline and work your way back).  No less than Nobel laureate David Baltimore and co-discoverer of DNA structure James Watson propounded this myth (see 08/24/2004 headline).  Though scientists have not yet found a function for all the non-gene segments, every time they look deeper into the genetic code, they see less nonsense and more design.  Evolutionists used to call the vast expanses of non-gene-coding DNA the “gene desert” and supposed it to be the accumulated junk from our evolutionary past.  (As we have pointed out before, this assumption effectively shut down scientific research on these “uninteresting” regions for a long time; an intelligent design approach would have, instead, inquired about their functions – see 10/16/2003 headline).  The “Central Dogma” was that only genes were important, they coded for proteins, and that was that.  Now, the non-gene segments appear to have a coded function of their own, producing RNA molecules that have a key role to play in an even more complex choreography of functional parts working together in a sophisticated ballet.  How then, can they say this “represents the evolution of ever more complicated gene-regulatory systems”?  I didn’t see any evolution here; did you?
    Their ending sentence thus qualifies them as winners of Stupid Evolution Quote of the Week, i.e., a claim in support of evolution, based on findings that point to the opposite conclusion.

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Categories: Intelligent Design

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