@John_Harshman, please take this as a good-faith question, I’m not trying to prove a point or argue, just get some clarity.
Partially because of what I learned about genetic ghosts, etc. reading GAE and partially because of my own view of how science operates (absence of evidence isn’t evidence of absence), I’m a bit suspicious about the idea that we know scientifically that common descent is completely universal. Is it not possible to have, suspending the question of God’s existence for a minute, special creation of individual organism and perhaps lineages, that would not be observable to us today in the DNA we have access to? I would guess it would have to be limited, but it seems like it would be impossible to rule it out completely, right?
Maybe another way to put it is that we see the signal of common descent in the DNA we have access to, but since we don’t have the DNA of all organisms throughout time, what limitations might there be on the universality of common descent?