Genes are Fine Tuned:
In the computer program that I presented, most of the things in the program are very easy to accept.  A population consists of a number of individuals.  The size of the population is finite one way or the other.  Generation succeeds generation.  There are recessive lethal mutation, mutations that do little or no harm if one has a single copy but are incompatible with life if one has two copies. 

There is, however, one assumption that might cause a reasonable and prudent person to raise and eyebrow.  Genes are tuned to each other.  We will look at that idea again soon.  Mutations can degrade that fine tuning.  That seems inevitable.  Detuning mutations occur in many parts of the genome.  Certainly.  No problem with that.  The impact, in terms of the number of potential offspring lost because of a single increment of detuning can be anything from trivial to immediately lethal.  That is axiomatic.  The trivial one we ignore.  The devastating ones we ignore.  So far so good.  But the model specifies that every incremental step of detuning has the same impact as every other incremental step.  Oops.  We have a problem.  How can I postulate that?  One imagines the genome built by evolution to be sort of a wickiup built of twigs, random branched twigs knitted together with care to support a thatch.  It may work, but it seems unlikely that breaking one twig will do the same amount of damage as breaking any other twig.

I postulated it because it was simple, and I kept it because it worked so spectacularly well.  But it could still make you squirm.

Not so many years ago, as they were understanding and analyzing DNA, they discovered the not all DNA was coding for proteins.  Generally we are taught that DNA is replicated when a cell divides.  The DNA is transcribed into RNA that then codes for the proteins that contribute so much to the capability and complexity of living tissue.  They had the code for translating DNA sequence into the sequence of amino acids in proteins, but not all the DNA translated.

There were many sections of this non-coding DNA even within proper coding genes.  These are called “introns.”  Together with non-coding DNA they were called “junk DNA.”  With the benefit of hindsight, that seems like a rash term.  Much junk DNA consisted of long repeats of a few base pairs.  The observation was, “See.  They couldn’t possible have any function.  There is no information, just nonsense repeated again and again.”

Of course over time these long repeating sequences would have been degraded by mutations if they indeed had no function.  They would have been very handy for predicting things like how long since two species had separated.  In order not to be degraded, they would have had to have been preserved by, you guessed it, eliminating offspring in the form of fertilized eggs that did not develop.  It is now known that they have something to do with regulation.  A burning question is how much of evolution has consisted of mutations of genes and how much of fine tuning of the function of those genes.  (Elizabeth Pennisi, Deciphering the Genetics of Evolution SCIENCE vol. 321 no. 5890 page 760)  And it seems to be clear that the regulatory elements, specifically something called cis-regulatory elements, are in fact capable of fine tuning gene expression.  A current advocate of this as being an important part in evolution (and the I think an important part of the mutations that unwind prior evolutionary gains) is Sean Carroll of the University of Wisconsin.

Now it looks like we have it in the crosshairs.  If the function of non-coding conserved DNA is the regulation of gene expression, and if much of this non-coding DNA consist of long strings of identical repeated units, then mutations in one of those units might quite possibly have the same impact as mutations in others.  The assumption is not a total flight of fancy.

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