I apologize in advance if I’m just making things worse and/or wasting time spelling out what is obvious and well understood by everyone else. But to me it seems like something needs to change if this thread is going to go anywhere. And I am curious what would count as evidence against common ancestry.
The most concrete point I can find & wrap my head around is this one:
First: The human sequence and the Dictyostelium discoideum sequence are ~80% identical over ~2330aa, not 100% identical.
Nevertheless, I think the point here is that in roughly 1 billion years of exploring protein sequence space, no alternative was found for most of the amino acids. So how were the ~1800 conversed amino acids found in the preceding 1.5-2 billion years (from the prokaryote-eukaryote divergence to the human-slime mold divergence)? And that’s a generous time frame, since Prp8 goes back before slime molds. Is that a fair rephrasing?
Since that point, we’ve had a lot of back-and-forth about what pertains to common descent and what pertains to guided and unguided evolution. I think it is clear, at least to me, that if God is guiding which mutations happen in a series of generations such that Prp8 is incrementally assembled, then that is just as much common descent as if the mutations were unguided. But what if there is a massive influx of sequence change in a single generation? Since we likely talking about single-celled organisms, does it make sense to say one descended from the other if the genome of one is not a replicant of the genome of the other, even if some of the atoms and molecules were sourced from the latter? (There is possibly some analogy here to asking if Eve is a descendant of Adam if she is literally formed from his rib/side.)
Now, that’s probably more of a philosophical question. But, if I’m representing things fairly, it is to me the most concrete way to express how the guided/unguided evolution rubber is meeting the common descent road.
Of course, there are a variety of ways we could proceed from there. We can note that the Saccharomyces cerevisiae Prp8 is only 60% identical to the human and slime mold versions, so the sequence is not quite so constrained. We can note that some portions of Prp8 have potential prokaryotic antecedents as discussed in this paper:
We can also note that Prp8 has some modularity, which would make it easier to construct incrementally (Garside et al 2019).
But those are irrelevant if I’ve misunderstood the key points. Are the issues really that (1) at some points there are significant chunks of functionality that seem (to @colewd) to represent a horizon beyond which the convergence-of-ancestral-sequence style evidence for common descent is not available and thus (2) there are large enough single-generation changes that the concept of ancestors and descendants breaks down regardless of how the atoms and molecules were shuffled?
