It is much easier these days to invoke informational models of DNA as a kind of encoding. Just consider that real working DNA computers have been successfully designed and built. But biological DNA evolves, the genes are a relatively small number of bases compared to large sections which don't appear to encode genes, but do have some use. This partly-useful DNA has to be evolutionary, an advantage, or it wouldn't be (even partly) useful. Moreover, the DNA replication process has viruses to contend with, and here again evolution has produced cells that survive by integrating the viral gene advantageously. Evolution also steps in when errors aren't repaired, these ones might be a bad mutation and die out, a good mutation and survive, or have no effect. But we still don't know much about this so-called "junk DNA" except it isn't junk, and there's a lot of it. I speculate that it's connected to the way viral resistance evolves which is basically cells learning to slow single-gene replication and preventing the formation of viral particles. So the virus "family" is actually a major evolutionary driver, it "infects" all other forms of life from bacteria to us mammals. I think that understanding junk DNA is going to show that it's really about how what we call life, processes genetic information, and that viruses that can invade the system and hijack the code will be shown to be absolutely necessary for life to exist as we know it, Jim. Which is to say, viral forms of "encoding", are advantageous for evolution in general. Otherwise they would have died out and we wouldn't find much evidence in the DNA record.
In your view , is the virus part of an existing life or something that just popped out from nowhere ? In my view a virus is a leftover of some existing life that have lost its cytoplasm . Do all viruses have to penetrate into the nucleus to make alteration for evolution to take place ? I suppose the virus who do not penetrate into the nucleus and use the ribosome for multiplication will not help to evolve into other form because it will burst the cytoplasm and the cell will die.
Well, my argument is speculative, to understate the obvious. There are various possibilities. One is that the virii evolved after viable cellular life did as the prokaryotes. That would mean the existence of viral genes, is because of some kind of failure in the evolution of prokaryotes, which sounds reasonable because infection requires existing viable cells. Or, the virii and prokaryotes co-evolved; we would need to understand a lot more about how cellular life first appeared to be able to eliminate possibilities. Nonetheless, viral infections are part of evolution, they constitute a selection process--cells that can stop or slow viral replication by learning to do something about it will survive. How they learn is (again, speculatively) tied to the junk DNA. This could just be a defence against viral infection--the virus has a greater chance of splicing its DNA into a non-coding part of the host DNA, simply because there is a lot more non-coding DNA generally. Or, successful virus forms have learned how to splice their DNA into regions which contain the host genes and the host has to somehow evolve a defence. Perhaps the junk is a way the cell can do this, since if it can encode some kind of enzyme, but in a very distributed way, almost random, then that might represent the same kind of "fast evolution" the virii seem to have. But I think as we learn more about the ancient viral genes in DNA and RNA across the spectrum of lifeforms, we will understand evolution better, and maybe understand how it got started, eventually. Or maybe not.
Are viruses encoded with polyhistidine in order to decrease the size of the unit ? ( folded and packed )
I'm not sure about polyhistidine. It does appear that histones are associated with the viral genome. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4478594/
A lot of it may really be useless junk. At least initially, like ALU elements and gene duplications. But evolution has a way of generating new functions for those kind of things. I think that a lot of the 'junk DNA' produces non-coding RNAs that don't produce proteins in the ribosomes. Nobody is currently sure what all that non-coding RNA is doing. There's a lot of it though. Some of it probably is doing nothing, other bits are probably doing a whole variety of often necessary things. (It's highly conserved and some of it is seemingly very ancient.) I suspect that a lot of it is regulatory, helping to control when genes are and aren't expressed. https://en.wikipedia.org/wiki/MicroRNA Very possible.
