I was listening a highly interesting talk about viruses in Helsinki by Dr. Matti Jalasvuori, a molecular biologist working in the University of Jyväskylä as a researcher (see this
). He has published a book about viruses in finnish titled "Virus. Elämän synnyttäjä, kuoleman kylväjä, ajatusten tartuttaja" (see this
I learned an extremely interesting new-to-me fact about viruses. They might be far from a mere nuisance, In TGD Universe they could be quantum memes, short pieces of a code of quantum computer code, wandering around and attaching to the existing quantum computer code represented by DNA! Replication of viruses would be replication of memes. If the infected organism survives the virus attack by taming the virus and making it part of its non-coding DNA, it will gain more strength! If my computer survives the updating of the operating system, it works better!
Some basic facts
Viruses are very small, few nanometers is the size scale. Virus contains short pieces of RNA or DNA coding for the virus, in particular the protein shell around it, which virus must have in the "non-living" state outside the host cell to which it can penerate. Inside its host this shell melts and virus attaches to DNA and is able to to replicate. The copies of virus leave the host cell to search for their own host cells.
Usually viruses are regarded as a nuisance. But a new more holistic vision is evolving about viruses and their actual role. Viruses have been present perhaps even before the cell was present in its recent form, they might have been crucial for the emergence of life as we know it and would be also now. The system would consist of various kinds of cells, not necesary those of single organism. The contain several kinds of DNA and RNA: cell nucleus and mitochondria contain their own genomes; there are circular plasmids, and also viruses.
There is a continual exchange of information between cells including viruses as form form of information exchange. In this framework virus represents a meme represented by its DNA ,which does not code for protein shell. This meme wants to replicate and must use the genetic machinery to achieve this. But does virus do this to only replicate and produce more nuisance?
The organism manages to survive the virus attack if it is able to transform the virus so that it cannot replicate. One manner to achieve this would be transformation of the DNA portion due to the attached virus DNA (possible reverse transcribed from the RNA of virus) to a non-coding DNA often referred to as "junk" DNA. Non-coding DNA includes both intragenic regions - introns - and intergenic regions containing for instance promoters and enhancers crucial for the control of gene expression as proteins (see this). Introns are portions of genes, whose contribution to mRNA is sliced away in translation to proteins. The decomposition to introns and translated regions is dynamical, which gives rise to a rich spectrum of different translations of the gene.
In fact, most of non-coding DNA might be due to viruses! The portion of non-coding DNA increases for speciei at higher evolutionary level. For our species it is estimated to be 98 percent! Most of our genome is "junk" as many biologists still would put it. But can this really be the case? On might think that immune system would have invented some mechanism to prevent the infection of DNA by junk DNA? The size of the trash bin cannot be a measure for evolutionary level! It is also known that virus infections force the organism to change and in some cases to become a better surviver. Viruses would drive evolution.
One can speculate that during the very early period in evolution there were only viruses and proto-cells. There is no need for them to be coded by genes. Self-organization can produce cell membrane like structures: soap films represent an example. The DNA fragments could survive inside these proto-cells but according to simulations done by the Jyäskylä group in which Matti Jalasvuori is working, eventually the evolution would lead to the emergence of parasitic DNA strands, which would soon begin to dominate and kill the protocell.
Viruses might solve the problem. Viruses would attract DNA fragments and replicate with themto build a protein wall around the fragment containg also a piece of DNA of proto-cell. Viruses would leave the proto cell before its death and find another protocell. Gradually genome would be formed as viruses would steal pieces of DNA fragments from protocells. One step in the later evolution could be the elimination of the part of virus coding for the protein shell and the use of the rest as protein coding DNA. For eukariotes the transformation to non-coding DNA including intronic and intergenic DNA becomes possible.
Viruses as pieces of quantum computer code?
Computational thinking would suggest that viruses might make possible the emergence of new biological program modules allowing to use existing program modules coding for proteins more effectively. The different slicings of mRNA dropping some pieces away would correspond to different manners to transform DNA sequences to proteins. But what about intragenic portions of DNA: are they just junk?
Could the non-coding DNA and viruses have a much deeper purpose of existence than mere replication? In TGD Universe this kind of purpose is easy to imagine if the system formed by DNA - say intragenic portions of DNA - and nuclear membrane (or cell membrane) system serves as a topological quantum computer. DNA codons would be connected to lipids of the lipid layer of cell nucleus by magnetic flux tubes carrying dark charged particles. These connections could be also to cell membrane and even to cell membranes of other cells.
The braiding of the flux tubes would define the space-time realization of a quantum computer program. This would represent a new expression of DNA and would explain why so small differences between our DNA and that of our cousins give rise to so huge differences. What is important that genetic code would not be terribly important: it is braiding that matters now. The realization as quantum computer programs would give rise to cultural evolution, the realization as proteins to biological evolution. There would be a transition from the level of genes to that of memes.
Viruses would correspond to pieces of quantum computer code - memes. They would be wandering between cells and infecting them to get fused to the DNA. If DNA is able to transform them to introns it gets the code. Otherwise it dies. Infection is the necessary price for achieving meme replication. Living cells could be seen quantum computer programs updating them continually. Sounds somehow familiar!
See the chapters DNA as topological quantum computer, Three new physics realizations of the genetic code and the role of dark matter in bio-systems, and More Precise TGD Based View about Quantum Biology and Prebiotic Evolution of "Genes and Memes".
For a summary of earlier postings see Latest progress in TGD.
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