December 14, 2009 | David F. Coppedge

“Messy” Genomes: Did They Evolve?

The genomes of most eukaryotes are riddled with introns – intragenic regions – that have to be cut out by sophisticated DNA-transcribing machinery so that the true gene sections (called exons) can be spliced together.  Introns can vary from 20 base pairs to over 500,000 – significantly impacting the energy required to duplicate the genome.  This mysterious phenomenon provides a test case for the explanatory power of design vs evolution.
    Two recent articles can inform the discussion of this mystery.  The first from Science Daily called introns “meaningless junk.”  Titled “DNA Needs a Good Editor: Researchers Unravel the Mysteries of DNA Packaging,” the article mentioned work going on at Tel Aviv University.  “How cells differentiate between what’s useful and what’s garbage in our complicated and messy genetic code is a fundamental biology question – one with extremely important implications,” the article stated.  One finding is that exons (the gene sequences) are packaged differently than introns.  Understanding this may help to target improperly spliced transcripts that cause cancer and genetic disease.  The article did not delve into the question of how introns evolved, but assumed they are meaningless, functionless pieces of genetic garbage.
    Another article in Science Daily (see also PhysOrg) reported that “Introns Nonsense DNA May Be More Important to Evolution of Genomes Than Thought.”  Is there any sense in the apparent nonsense of introns?  A team of scientists from University of New Hampshire and Indiana University Bloomington are not sure, but they did find something surprising.  There seem to be hot spots for intron insertion.  Different organisms with different genotypes can end up with the same introns at the same places.  They call this “parallel intron gain”.  Michael Lynch at Indiana U said, “This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.”  If they did not evolve from common ancestry, how did they come about?  The team is testing a hypothesis: “Our molecular analyses have enabled us to reject a number of hypotheses for the mechanism of intron origins, while clearly indicating an entirely unexpected pathway — emergence as accidents arising during the repair of double-strand breaks.”
    A somewhat related story in PhysOrg reported an “inverse relationship between gene duplication and alternative splicing.”  Scientists at the University of Georgia, working with the lab plant Arabidopsis and with poplar trees, noted the difference in their degrees of duplication.  They believe they reflect “distinct defense strategies” due to different environmental threats.  “Alternative splicing is the molecular process that allows a single gene to produce many gene products or proteins with potentially different functions,” the article explained.  The fact that the large poplar tree has only 7,000 more genes than a tiny weed indicated to the team that it’s not the number of genes that matters in a genome, but how they are regulated.
    Gene regulation – including the regulation of introns and duplicates and alternative ways to splice exons together – is at the cutting edge of genome research.  Are these aspects of the evolutionary history of the organisms, or do they reflect underlying design strategies we do not yet understand?

The design hypothesis already has a superior track record in debunking much of the “junk DNA” notion (12/05/2009, 05/18/2009).  Here is a clear opportunity for design scientists to approach these puzzles with a different orientation than evolutionary biologists.  Rather than assuming these are all leftover relics of common ancestry, why not assume there is a method to the madness?  Already, “gene regulation” implies higher-order design that is not readily derivable from DNA itself.  And developmental biology is beginning to see levels of hierarchical design that are orders of magnitude more intricate than anything man has ever designed.
    Introns appear as nonsense to us right now.  Maybe that is because we just don’t understand the language yet.  Even if they turn out to be the accumulations of scars from repair of double-stranded breaks, that fact would presuppose repair systems that were robust enough to prevent genetic catastrophes.  Humans routinely discard much of the packaging of their inventions (crates, cardboard boxes, bubble wrap) without losing confidence that the goods were designed.  The hypothesis that introns leave a trace of common ancestry has just been challenged by the discovery of parallel intron gain.  Each new revelation in genomics, by contrast, underscores the elegance of the machinery that reads, transcribes and translates the genetic code.  And to think that elaborate proofreading and repair systems exist to protect the genome is mind boggling (see Science Daily 10/22/2009, for example).  With essential molecular machines like this required for reproduction, it seems impossible for evolution to even get started without the machinery already present and working – by design.
    Yet the mystery of introns remains unsolved (09/02/2003).  There are tantalizing clues of design to be discovered.  Already a functional intron has been reported (02/06/2008), or they may provide “handles” for transcription machinery (09/12/2003).  The sophistication of the spliceosome that cuts out introns and splices together the exons gives us cause to wonder why Darwinian natural selection would go to such trouble to keep them around.  Why isn’t evolution eliminating them from the genome?  Given Darwinism’s dismal record on vestigial organs, glial cells and junk DNA, will you trust them with this question?  It will be interesting to follow which approach – design or evolution – emerges as the fittest in explaining the puzzle of introns.

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