I have a rather stupid question 
I was debating with one of the creationists in the Retrovirus Handbook and he told me that the word “orthogonal” does not necessarily mean that the retroviruses are in the exact same place or the same base, is there a source that indicates that the use of the word orthogonal means the same place?
Do you perhaps mean “orthologous”?
Is it possible the word was actually “orthologous”?
Did you/he mean “orthologous”?
Never heard the expression orthogonal in relation to retroviral insertions or their positions. Could he have been referring to orthologous?
If the retroviral insertion is known to be in identical positions in the different species in question, and their sequences are sufficiently similar, that is evidence they derive from the same common ancestral insertion event and thus common ancestral insertion is inferred.
If the location is not the same, then common descent of one ancestral insertion is not inferred.
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Evidence, but not perfect evidence. There are occasional, very rare homoplasious insertions.
Those are transposons, not ERVs, but the principle is the same.
Yes, that’s the word I mean, my English isn’t my native language. I’m going to adjust it
I meant the word “orthologous” rather than orthogonal
I guess the admins have been a bit overworked lately. 
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Hello @Islam,
Comment moderation is turned on, and you posted the same comment several times since I last checked. I will remove the extra comments soon
Dan
The arrival rate of new comments is non-normal and highly dependent on context. This might be a good situation to apply a Bootstrap. 
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In case nobody else has answered your question clearly: orthologous retroviruses must be in the same place, in exactly the same spot, because in order to be orthologous they must descent directly from the same insertion event. Orthologous sequences are homologous, meaning that they are similar by descent from a common ancestor. Paralogous sequences are homologous, but must descend from separate copies of an original sequence due to duplication, transposition, or some similar event.
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