You have no evidence that the proteins eukaryotes use are the only proteins that can work with a genome that has introns.
Yes, it is. The entire point is that the bullet could have landed elsewhere.
Which paper shows that PRPF8 is required for a functioning genome with introns?
Your argument is based on the assumption that no simpler life forms existed. You need to support this assumption.
A solid lack of evidence for this speculation.
I am finished with this discussion at this point thank you for the interesting engagement.
Sometime in the future we can engage. Thanks for the discussion.
Supposing that is true, how does that rule it out? If we put that into the argument, the conclusion still doesn’t follow, or is it even implied.
Premise 1: PRPF8 is highly conserved. Check!
Premise 2: Sequence space for proteins of that length is 20^L, which is a very large number. Check!
Premise 3: The total number of functional sequences is less than the total sequence space. Check!
Premise 4: There is no evidence of lower fitness PRPF8 alleles.
Conclusion: Therefore it is highly doubtful, or impossible, that PRPF8 could have evolved.
Still an invalid argument. The conclusion of that argument still does not follow from those premises.
If you’re going to bow out now, then we are forced to conclude that you have failed to argue your case. The conclusion you have sought has not been validly supported.
It’s time to take a break as I have got business issues to deal with. Time will bring more evidence to the table.
Apologies if these papers have already come up in the discussion (it’s hard to keep track), but they seem relevant to the discussion of PRPF8 origins:
Prp8 is the largest and most highly conserved protein of the spliceosome, encoded by all sequenced eukaryotic genomes but missing from prokaryotes and viruses. Despite all evidence that Prp8 is an integral part of the spliceosomal catalytic center, much remains to be learned about its molecular functions and evolutionary origin. By analyzing sequence and structure similarities between Prp8 and other protein domains, we show that its N-terminal region contains a putative bromodomain. The central conserved domain of Prp8 is related to the catalytic domain of reverse transcriptases (RTs) and is most similar to homologous enzymes encoded by prokaryotic retroelements. However, putative catalytic residues in this RT domain are only partially conserved and may not be sufficient for the nucleotidyltransferase activity. The RT domain is followed by an uncharacterized sequence region with relatives found in fungal RT-like proteins. This part of Prp8 is predicted to adopt an α-helical structure and may be functionally equivalent to diverse maturase/X domains of retroelements and to the thumb domain of retroviral RTs. Together with a previously identified C-terminal domain that has an RNaseH-like fold, our results suggest evolutionary connections between Prp8 and ancient mobile elements. Prp8 may have evolved by acquiring nucleic acid–binding domains from inactivated retroelements, and their present-day role may be in maintaining proper conformation of the bound RNA cofactors and substrates of the splicing reaction. This is only the second example—the other one being telomerase—of the RT recruitment from a genomic parasite to serve an essential cellular function.
Crystal structure of Prp8 reveals active site cavity of the spliceosome
The active centre of the spliceosome consists of an intricate network formed by U5, U2 and U6 snRNAs, and a pre-mRNA substrate. Prp8, a component of the U5 snRNP, crosslinks extensively with this RNA catalytic core. We present the crystal structure of yeast Prp8 (residues 885-2413) in complex with the U5 snRNP assembly factor Aar2. The structure reveals new tightly associated domains of Prp8 resembling a bacterial group II intron reverse transcriptase and a type II restriction endonuclease. Suppressors of splice site mutations and an intron branchpoint crosslink map to a large cavity formed by the reverse transcriptase thumb, endonuclease-like and the RNaseH-like domains. This cavity is large enough to accommodate the catalytic core of group II intron RNA. The structure provides crucial insights into the architecture of the spliceosome’s active site and reinforces the notion that nuclear pre-mRNA splicing and group II intron splicing have a common origin.
Yes. Much of similar evidence has been brought up before. It is interesting to know how the catalytic core of the spliceosome essentially IS a group II intron. There are literally hundreds of articles detailing the connections. None of it matters to Bill of course, because he’s somehow convinced himself that because sequence space is big, then… something something because “substitutability”.
Also in an argument on The Skeptical Zone, Bill literally argued that when the sequences were highly similar this shows they couldn’t evolve, because change was selected against. Then we showed more dissimilar sequences from more distantly related eukaryotes (such as fungi) compared to vertebrate ones, and even more distantly related sequences (though still obviously similar) from group II introns, which then caused him to start arguing that their LACK of similarity was ALSO evidence against their evolvability, because now we had a big sequence gap we had to close.
Bill’s position has nothing to do with evidence. It fails at the level of reason. None of the claims he make even weakly implies the conclusion he apparently believes.