I am sure I missed a step in the growth of this theory. I remember when the chemical analysis was very new and the chemical version of the phylogenetic tree diverged from the physiological version of the phylogenetic tree and there was a battle royale within the scientific community as to which was correct. The scientists had lots of evidence, but the interpretation of the evidence was in question. I am not sure that the issue was so much resolved as it was abandoned.
That's the problem with the modern approach to science. We tend to ignore the factors behind the interpretative decisions made that are not necessarily related to the data available.
Just recently (today or yesterday) I read that some analysis had found stubby fingers in very old fish fossils, which completely turns upside-down the notion that digits formed after fish had "crawled out onto the shore" (in the vernacular of the non-scientific). Since the interpretative paradigm is fixed we will turn the entire process on its head rather than ask the basic question, has our paradigm been wrong?
And the interpretation of common descent to explain the data of ERV’s and the nested hierarchies of DNA similarity and divergence is the only operative interpretation, nobody has offered a compelling explanation for the data other than common descent. Moreover it is a replicable and predictive science in that given two species molecular evolution can estimate a time of most recent common ancestry that comports well with the fossil record.
So what are your assumptions and your interpretation that makes sense of the data? Will you be the first to give an actual “Creation Science” explanation for this data?