A long-shot this question is, pertaining more generally to any informational structure (like a symbol sequence) and that such are, in and of themselves, interpretable in any number of ways, each interpretation therefore being the yield of the interpreter; rather Peircean in threeness. So, perhaps DNA, or RNA, is interpreted not just in terms of the mechanics of transcription and translation.
Perhaps there is value to discussion of how a unit of information can simultaneously support (especially where evolutionary pressures come to bear) two different interpretations, in two different domains.
There has never been just one interpreter. One example, during synapsis of homologous chromosomes in meiosis, the sequence of the DNA must have provided the basis for synapsis, which unlikely uses the same information structure as used in transcription/translation. Similarly, the DNA repair process may also use a different informational structure in the DNA comparing to the transcription/translation process.
I do not think that can anwer the question, but it seems that it has some relation to the phenomenon of new genes appeared due to frameshift (for instance described in "Using Triplet Periodicity of Nucleotide Sequences for Finding Potential Reading Frame Shifts in Genes" by F.E. Frenkel, and E.V. Korotkov at DNA RESEARCH 16, 105–114, (2009))
The words of Peter R. Wills, in his 2013 Biosemiotics paper, having the title:
Genetic Information, Physical Interpreters and Thermodynamics; The Material-Informatic Basis of Biosemiosis
bear consideration. To wit,
"...an individual human organism as a particular interpretation of some selected body of information of size ~6×109 bits embedded in DNA sequences. However, there exists a multitude of other interpretations of the information in the human genome, the range of which is restricted only by the ingenuity of whoever wishes to build a device capable of giving effect to their potentially perverse imaginings."
It seems pretty clear that one may construct interpreters of any desired nature (however perverse) by which to give meaning to some unit of information.
So, my question becomes, why should we in science expect that there is only one interpreter of the genome; i.e., the biochemistry of the ribosome, the synthase and transferase and RNAs?
Even if DNA has but one interpreter (the well known biochemical system of gene duplication, repair and translation into RNA and protein), the concept bears analysis, for doing so may given insight into the nature of interpretation.
You have mentioned at least two known other levels of "reading and correcting" genetic information before ribosome (enzymes and small RNAs). But, I see that you look at the huge amount information encoded in genome without any obvious purpose (considering the only one "interpreter"). Recent study on correlation between genome size and evolution rate show that large genomes are changing faster (http://www.nature.com/nrg/journal/v13/n3/full/nrg3192.html). Some researchers have tried to assign special physical properties like unique electromagnetic fields to DNA sequence . But it was not accepted by majority of scientists.
EV Koonin in his work describes early mechanisms of biologic evolution (http://arxiv.org/ftp/q-bio/papers/0701/0701023.pdf). If it was the first "interpreter" in RNA world, and ribosomal protein synthesis was the second one, it might be the third, etc.
There has never been just one interpreter. One example, during synapsis of homologous chromosomes in meiosis, the sequence of the DNA must have provided the basis for synapsis, which unlikely uses the same information structure as used in transcription/translation. Similarly, the DNA repair process may also use a different informational structure in the DNA comparing to the transcription/translation process.
I think the interpreters are the molecular machineries which deal with the information and not us. As stated by Ming Yang, each one of the machineries recognize different bits of information. That’s what we learn from Biology.
In case you’re referring to something else, then just as an example, the DNA can be physically used to store digital information with unimaginable capacity. It is conceivable then, that all forms of DNA-based life have extra information stored in them either randomly or by somewhat unknown being (s). How to decode it?
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