Arabidopsis thaliana, which is model plant organism that is widely studied, has revealed a relationship between RNA and methylation that sustains epigenetic changes. This is one of the pathways that allow changes to DNA that are not inherited in the usual way.
It is the general assumption that much of the DNA holds no meaning because it is repetitive and exists as the result of retroviral inclusions and transposons.
The idea that as much as 90% of the genome is junk is an absurd concept. Those genes that have been identified to code for an effect are perhaps 14,000 different sites and though that does describe virtually all of the visible properties, the additional DNA can be a participant in a yet to be discovered cycle that operates at such a high level of complexity that it not possible to measure its effect without understanding and excluding the other more common elements of the process.
I can generate a type of electromagnetic signal that is undetectable by conventional means and does not interfere with radio signal reception. I can also generate this signal as a continuous pure sine wave and, if received, would seem to contain no information whatsoever. How could a sine wave that contains a sequence that repeats forever 010101 contain information? It can and does. I am sure that nearly every person who works in data transmission, radio, or signal processing would say that this is inherently impossible and yet I do it. This is the same reason why I assume that though the DNA may appear to be repetitive, it is not. Where there is change, there is information.
There are some very elegant and effective mathematical and computational algorithms which go into the process of determining if a region is "conserved" and I trust that math and method, however they may be making assumptions about one location and attempting to apply that conclusion to all similar regions and that is not valid, IMHO.
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