November 3, 2008 | David F. Coppedge

Biological Complexity Continues to Astound

There’s more going on in your thinking apparatus than you think.  New scientific discoveries continue to unfold new layers of complexity and control.  Here are a few examples:

  1. Meta-code:  Your body has codes directing codes.  Geneticists were initially dismayed to find only 20,000 to 30,000 genes in the human genome.  “We were expecting that something as sophisticated, complex and intelligent as ourselves would have about a hundred thousand genes at least,” said one geneticists quoted in Nature News.  Something has happened since, “restoring the dignity of complexity to the human genome.”  It’s called alternative splicing.  A given gene can produce multiple RNA transcripts, depending on how the pieces are assembled.  These, in turn, can produce vary different protein machines: “This process, called alternative splicing, can produce mRNA molecules and proteins with dramatically different functions, despite being formed from the same gene.”  The report on Science Daily that two proteins coming from the same gene can have opposite functions, depending on how they are spliced and in what cells they are expressed.
        The potential for expansion of the DNA code is huge; one gene in fruit flies, reported Nature News, is thought to generate over 38,000 protein products.  Only about 6% of human genes, it turns out, produce a transcript from a linear strand of DNA.  Most others put together parts from different locations on the chromosome.  With alternative splicing, it’s possible that dozens, or hundreds, or thousands of different products can be produced from the same gene.  This begs another question: what code is directing the assembly of these pieces of DNA code?
  2. Motor memory:  Your long-term memory may depend on little cellular trucks that run on cellular highways.  These trucks haul neurotransmitters to the junctions between neurons, keeping the junctions active.  Read all about Science Now.  This begs a question: who is the dispatcher?
  3. Rewind repair:  Another molecular machine has been discovered that fixes unwound DNA.  “When your DNA gets stuck in the unwound position,” an article on Science Daily says, “your cells are in big trouble, and in humans, that ultimately leads to death.”  This “rewinding machine” takes a damaged portion of DNA and rewinds it into the familiar double helix.  In effect, it does the opposite of the helicase machine that unwinds DNA for transcribing.  The machine, named HARP, uses ATP, the universal energy currency of the cell.
        The UCSD scientists were “astounded” to find out how this little machine works.  “It didn’t occur to us that such enzymes even existed,” they said.  “In fact, we never knew until now what happened to DNA when it got stuck in the unwound position.”  Good thing the machine knows what to do.  Failure to heal unwound DNA leads to fatal diseases; yet it cannot interfere with the other helicases that legitimately unwind DNA for transcription.  This begs another question, though: what tells this machine where the damage is and how to fix it?

The last article said that the discovery is spurring the scientists to look for more DNA-healing machines.  Here was a whole class of proteins they didn’t even know about.  “This will open up a whole new area of study,” said one team member.  “There are very few enzymes known that alter DNA structure.  And we’ve discovered an entirely new one.  This was not expected to happen in the year 2008.  We should have found them all by now.”  Young scientists should take encouragement: “The field potentially can be fairly large.  And as more and more people discover additional annealing helicases, this field will expand.”
    The palpable excitement in their tone required a look at the original paper in Science.1  Yusufzai and Kadonaga called their machine a “molecular zipper” and said, “the pleiotropy of HARP mutations is consistent with the function of HARP as an annealing helicase that acts throughout the genome to oppose the action of DNA-unwinding activities in the nucleus.”  By pleiotropy, they mean that mutated HARP genes can cause problems all over the place.  They identified one disease, SIOD (Schimke immuno-osseous dysplasia), that can actually be traced to mutations in HARP.  The genetic disorder leads to dwarfism, a damaged immune system and early death.
    The HARP machine is ubiquitous in the nucleus, they said, because the possibilities for DNA winding errors are ubiquitous.  Helicases might fail, or bubbles in double-stranded DNA might form spontaneously.  Without repair machinery available, the DNA transcribing and duplicating machines could fail.  “In this manner, HARP would be able to promote the proper functioning of the cell by catalyzing the rewinding of the stably unwound DNA,” their paper ended.  “More generally, HARP would serve as an opposing force to the numerous DNA-unwinding activities in the nucleus.”


1.  Timur Yusufzai and James T. Kadonaga, “HARP Is an ATP-Driven Annealing Helicase,” Science, 31 October 2008: Vol. 322. no. 5902, pp. 748-750, DOI: 10.1126/science.1161233.

None of these articles needed, referred to, or owed anything to evolutionary theory.  This was the good old science at work: uncovering the mechanisms of the world, as if it were designed, and seeking to understand the workings of nature.  In fact, the third article says this: “The discovery represents the first time scientists have identified a motor protein specifically designed to prevent the accumulation of bubbles of unwound DNA.”  If that does not presuppose intelligent design, what does?  And how did cells get along before chance found a way to invent a powered repair machine for DNA?
    Earlier scientists like Leeuwenhoek and Pasteur would have been pleased and thrilled to learn about the levels of complexity being revealed in the cells they only knew as black boxes.  There is plenty of work for design-motivated scientists to discover.  We will all benefit from their grand openings of the black box.

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