Christopher J Noble,
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Eleni Papadopulos-Eleopulos writes: "Again, suppose for the sake of argument that there are published papers with evidence (and not merely evidence in databases) which prove that in RNA viruses the nucleic acid "sequences differ by approximately 50%" ...... "
There is no need for supposition. Within influenza A subtypes, hemagglutinin sequences differ by up to 20%; between subtypes up to 60%. (1) Why do you continue to deny this? I asked you a specific question regarding the genomes of the Sabin polio strains. You have not answered. Why?
Eleni Papadopulos-Eleopulos continues: "The problem then is how loose the "leash" can be before you start asking questions in regard to: (i) protein function.."
It is your argument. Why don't you tell us? You are the one that has been saying that "the genomes of RNA viruses do not differ by more than 1%" and attempting to use this "fact" to argue against the existence of HIV.
The hemagglutinin gene in different influenza A subtypes differ by approximately 50% and yet the protein performs the same function in the virus. In fact, reassortment is a basic feature of influenza A evolution. When a host is infected with two different types of influenza A the hemagglutinin gene of one virus can be swapped with the hemagglutin gene of another. The hemagglutinin genes are interchangeable. They perform the same function.
Your argument concerning the genetic variation of RNA viruses is demonstrably false. For some reason you refuse to admit this.
Eleni Papadopulos-Eleopulos continues: "Since the human genome contains endogenous retroviruses which can be expressed especially in cultures under the conditions used by "HIV" experts, Christopher Noble then like us will conclude that such viruses may not be exogenous and in fact may not be present in the AIDS patients."
There is very little sequence similarity between human endogenous sequences and HIV sequences. Only short matches of around 18 base pairs can be found - a tiny fraction of the HIV genome. The same sort of matches can be found if we compare an influenza A genome and the human genome. For some reason you do not seem to be claiming that "influenza" virus sequences are endogenous. I presume this is because you do not have a competing theory for the causation of influenza.
If you want to you can purchase the cell lines, such as H9 ot HUT78 etc., used for growing HIV. (2) Now, "oxidise" these cells with PHA or want ever you want and get them to produce RNA that has even vaguely significant sequence similarity to HIV RNA. If you could get a sequence with open reading frames for gag,pol,vif,vpr,vpu, tat,rev,env,nef there might be a Nobel prize for you. The world is eagerly awaiting your contribution to science.
(1) Nobusawa,E., Aoyama,T., Kato,H., Suzuki,Y., Tateno,Y. and Nakajima,K. (1991) Comparison of complete amino acid sequences and receptor-binding properties among 13 serotypes of hemagglutinins of influenza A viruses. Virology, 182, 475-485
Competing interests: None declared