Twin-Nested Heirarchy

The correlation in phylogeny between simultaneously-speciating organisms like pocket gophers and their pubic lice prove that molecular phylogeny accurately reconstructs real ancestral relationships regardless of morphological similarity.You'll have to try harder, Goddy.Edited by crashfrog, : No reason given.

You don't have to assume anything to use the methods; neither the DNAEasy kit, nor the PCR, nor the electrophoretic gel, nor the computational analysis methods require that you, personally, hold the assumptions that validate those tools.I wonder if you read the thread. If you had you would have seen that, indisputably, the convergence in phylogenetic topology can only be explained if the assumption of common ancestry is true.Otherwise there's no other explanation. If the "phylogenies" were just badly interpreted genetic noise - like seeing Abraham Lincoln's head in a cloud - then there's absolutely no reason for a convergence in their topology. The likelihood is the same as two frames of television static being exactly the same.And it can't be morphological similarity, right? I mean, there's nothing the same about a pocket gopher and a louse, right? Between gophers and lice? What could possibly be similar about those organisms, Goddy? Obviously, because the chance of random convergence of phylogenetic topology is very low. It's the same odds that any two random persons have a family tree with precisely the same number of "leaves" on every branch.The only pattern is one of inheritance. Morphology can't be the explanation because its hard to imagine two creatures more dissimilar than pocket gophers and their lice.Perhaps maybe you don't understand what's being compared, here. I'm not saying that this is a family tree that includes gophers and lice, together. I'm not saying that at all.I'm saying that if you take the molecularly inferred phylogeny of the pocket gopher species complex, and the molecularly inferred phylogeny of the gopher pubic lice species complex, and printed them out on transparencies, you could overlay them and they would match. Not the names of the individuals, but the trees themselves.It makes sense under evolution, because we know by observation that the pubic lice only mate when the pocket gophers do and therefore they speciate at the same time. But it can't be explained by any recursion to mere morphological similarity, because there is none, and that's not what we're comparing.The odds that we'd see this kind of topological symmetry is the same as if we were to compare our family trees, and see that we both had two (and only two) sisters, one brother, three uncles on mom's side, two on dad's, and a grand-uncle who never married. That kind of convergence would have absolutely nothing to do with whether or not we both had brown hair. It would have everything to do with the patterns of mating in our families. In our case it would be coincidence. In the case of the gophers, it's because their lice can only mate when they do, and therefore their populations wind up structured exactly the same way. And we see that similarity in their genetic code.If we see their population structure in their genetic code, then it stands to reason that we're seeing it when we look in everybody's code; thus, the example of pocket gophers vs. their lice settles the issue. Phylogeny detects real ancestry, not just created morphological differences.

The validity of the analysis relies on common decent being actually true, of course. But there's nothing stopping you from running the analysis without holding that position. Nobody's going to prevent you from doing so.But it's not an assumption. It's a conclusion validated by the topological phylogenetic convergence of pocket gophers and their pubic lice. The topological convergence is there regardless of what assumptions you hold. It verifies that the molecular techniques used actually do establish real patterns of inheritance. You need not assume anything - the convergence is real and it verifies the techniques.Let me repeat - because of the pocket gopher/pubic lice convergence, the molecular techniques are no longer based on any assumption. They're based on the verified fact that these tools correctly identify real evolutionary relationships. Yes. Generally, because all organisms are inheriting more genetic sequences from their ancestors than they're creating, on their own, through mutation. Specifically, because the gene sequences that are being used to develop these relationships are non-coding sequences that have nothing to do with morphology (they are introns that are spliced out after RNA transscription.)Verified, because the only possible explanation for the topological convergence we've been referring to is if pocket gophers and their lice speciate simultaneously, which we know is what's happening, therefore the molecular techniques are verified to be producing genuine phylogenetic histories, not just noise.

It's the exact same techniques, therefore they are validated.Pocket gophers and their lice are not the only two species that show this sort of convergence, incidentally. Nonetheless - same techniques, therefore the gopher situation validates them across the board - just like weighing a scale against a known weight validates it for all weights within its range. You wouldn't have any basis to say "well, sure, it reads accurately for the 1g, 2g, and 5g certification weights; but how do we know that the weight of this object is actually 1.2g?"You know that it's actually 1.2g because it accurately weighed the 1, 2, and 5g tests. That's the principle of measurement verification. Similarly, the gopher situation validates the same molecular tools for everything else. Well, you wouldn't be a creationist if you weren't simply ignoring evidence that you found inconvenient. Nonetheless if you're not aware of the existence of things like introns and microsatellites, then might I suggest a course in remedial genetics? Your paper is interesting, but it's just speculation. They don't present any evidence. That an alternate explanation for introns is presented doesn't challenge the consensus view that these sequences are not related to morphology.

Why do you say that? What's your evidence that the pocket gopher species complex is so much simpler than any other species complex assessed with molecular phylogeny? That's exactly what it does, as I've proved. You can continue to assert that it doesn't prove anything, but there's no reason to believe you. Prokaryotes such as E. coli don't have introns in their protein-encoding sequences, as someone who actually knew something about genetics would know, so your example is irrelevant.We're talking about eukaryotes, which do have introns - regions of DNA that, when transcripted to hnRNA, are spliced out and digested. Since they're neither used a signaling molecules nor translated into proteins, they simply don't persist long enough as RNA to have any effect on morphology. Thus, similarities between intron sequences must reflect shared ancestry (or random chance, of course.)

What's your evidence for that? And are you aware that this is a dodge? I've given you ample reason to believe me - the topological convergence of phylogenies we've been talking about. It settled the issue two pages ago but you don't seem to get that, yet. By no evidence. You haven't presented any such evidence, because the papers you're presenting aren't talking about introns. They're talking about non-coding RNA, but we already knew that stuff had a function, for instance tRNA.

The same way that calibrating a scale to a known weight confirms its ability to measure other weights, as I explained. Are you going to ape creationist to the extent of asking questions already answered? (It would be nice if creationists could be shown how to address the arguments of evolutionists honestly, instead of with a never-ending series of dodges.) How about a research article that's actually relevant? We're not doing phylogeny on "mirtrons" or short introns, they're too short. Indeed most of the phylogeny we're doing is based on mitochondrial sequences, not nuclear sequences, with lots of repetition (to generate sufficiently long sequences when restricted.)

Why not, if it's species to species at every step?

I hope you'll feel free to quote or paraphrase anything I've said, even without attribution.Good show, though. Well done.