It was called junk:
Years ago, when it was first proposed to map out every base pair in the human genome, the decision was made to map out not just the genes but the entire genome.  Dogma, ever since Watson and Crick made their (and that of Rosalind Franklin public there has been the Standard Dogma.  One gene makes one strand of RNA makes one polypeptide which alone or with others makes one protein with one function.  Just about every step along the way has proven to be an approximation, but the dogma is a good place to start.

Franklin did not live long enough to receive the Nobel prize as Watson and Crick did.  Her contribution was not trivial.  It was she who first suggested, “The skeleton is on the outside.”  That is true.  The structural elements of DNA coil around the elements that encode the information, for instance if it is a gene coding for a polypeptide three pairs of bases code for one amino acid, and their order encodes for the order of the amino acids.  Those bases are tucked away inside.  Also it was Franklin alone who was able to make DNA into crystals.  Once you have a crystal, the elements are arranged in a standard rigid pattern.  If two nuclei are separated every time by the same distance an x-ray of the appropriate wavelength will be deflected as it squeezes between.  Knowing the angle and direction of the deflection and the wavelength of the x-ray tells you a lot about what the possible forms of the crystal are.  It was her crystallography that gave the critical lengths that could then be combined with the known dimensions of elements of DNA to come up with the fundamental shape of DNA. 

A rather small fraction of DNA encodes for proteins.  The rest used to be called “junk.”  (Elizabeth Pennisi ENCODE Project Writes the Eulogy For Junk DNA SCIENCE vol. 337 no. 6099 September 7, 2012 page 1159)  Now my memory fails me.  I do remember learning for the first time that the junk DNA was going to be analyzed and thinking, “Why, for goodness sake?  It doesn’t do anything.”  And I do remember seeing the term “junk” and thinking, “What do you know?  That stuff may be doing something you cannot imagine.”  I just don’t remember which came first.  At all events, when the time came to decide, the decision was made that now seems to have been the wise one. 

The model of infertility from lack of consanguinity I have put together works with genes alone.  One need only invoke known epigenetic events.  (And of course one must invoke hitherto unknown biochemical events leading to the ultimate effect. 

But I always wonder whether the secret of the mechanism lies not in the genes but in the masses of DNA that are not genetic and that are not yet understood.  (Some bits are understood, such as the code to begin transcribing the DNA into RNA and the code for when to stop.)

The first clue that something important was going on in the non-gene DNA was when they noticed that some parts of DNA changed very little over time.  Species would share the same gene and that gene would be identical or very similar between the species.  Evidently organisms with a faulty copy were being eliminated.  Other areas showed much more rapid change.  And there were areas “conserved” between species that changed as little as genes changed.  Evidently organisms with a faulty copy there were also being eliminated so there had to be something important going on. 

Knowledge of functions of the “junk” is accumulating to the point that 80% seems to have a function.  The term “junk” is going the way of the dodo. 

I look at it and think, “And I suppose this non-gene DNA also has its function modified by epigenetic effects.  I wonder where that fits in.”  But no answer comes.

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