Twin-Nested Heirarchy

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.

That validates it in the case of the gophers and their lice, but that does not immediately validate any phylogenetic tree constructed with cladistic techniques. Ok...that requires me to accept the existence of DNA that has no effect on morphology.As a creationist, I'm afraid I can't do that.But, because I am trying to be a reasonable one, I'll have to provide a source for that. Fortunately, there is a researcher at my university who specialises in just this issue:John S. Mattick "Non-coding RNAs: the architects of eukaryotic complexity" European Molecular Biology Organization Reports 2(11):986-991, November 15 2001

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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.

Nonsense. Rather, it's like a scale that reads those gram weights accurately, and then you start to use it to weigh beached whales.Microevolution of lice and gophers within a kind is one thing, but that doesn't validate the technique for use on every living creature at once. There is evidence aplenty. I just used a nice summary article because it was available for free. Besides, science is ever changing. You can't assume that the protein-centric view is right when for the past 5-10 years much evidence is suggesting that it is too limited.Even in E.Coli, RNA encoded by non-coding regions (such as the 3' untranslated region) has been shown to have a function in stabilising mRNA (). I may suggest that you pick up a recent textbook on genetics and look up ncRNA/functional RNA or RNA regulation.But, to discuss it in-depth would be out of the realms of this topic, I fear.Edited by Goddy, : url tags

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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.)

Well of course we don't tell people that, it's not true.We are under no obligation to recite your propaganda for you.

No.Common descent (plus what we know from the fossil record) makes certain predictions about what we should see if we applies these techniques. We can, of course, test these predictions without assuming common descent to be true. In fact, when these techniques were developed, the creationist response should have been: "Whoopee! Those evilutionists predict that birds should have genes closer to crocodiles than to anything else --- now we're gonna show em! To the laboratory!"

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For some reason this didn't happen, possibly because of intellectual cowardice but most likely because they don't actually have laboratories.Now, once one has been convinced by this and all the other evidence that evolution is correct, then one can use it to construct cladograms. It is not the cladograms themselves which are offered as proof of common descent, but rather that the theory predicts the data on which the cladograms are based.

Try:Hedges, S. B., and L. L. Poling. 1999. A molecular phylogeny. Science 83:998-1001Kumazawa, Y., and M. Nishida. 1999. Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink, statistical evidence for archosaurian affinity of turtles. Mol. Biol. Evol. 16:784-792Summary: birds are closer genetically to crocodiles and turtles than to anything else; crocodiles and turtles are closer genetically to each other and to birds than to other reptiles.---Here's another example. Evolutionary theory predicts that lobe-finned fish should be genetically closer to humans than to ray-finned fish.Guess what, it's true!

Have those studies been confirmed? It is a very surprising result: it has long been believed that the split between anapsids (turtles) and diapsids (the other reptiles) occurred very, very early.Color me skeptical, at least until further studies confirm this one.Added by edit:I should add the classical phylogenic tree from Palaeos. It shows the split between anapsids and diapsids occurring very early in the reptile lineage -- not long after the split between reptiles and synapsids (mammal ancestors) in fact. In fact, if I recall, it was debated for a short time whether the synapsids or the anapsids were the first to split from the main amniote line.Of course, our understanding of the evolution of any taxon is subject to change as new information comes to light. I was just under the impression that the classical understanding of the diapsid/anapsid split was pretty well established by palaeontology.Edited by Chiroptera, : No reason given.

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Computers have cut-and-paste functions. So does right-wing historical memory. -- Rick Perlstein

It's just lice losing information as they evolve within the lice kind, and likewise for the gophers. No macroevolution involved. I have no reason to believe you when you continually assert that simply because you can use molecular techniques accurately on some piece of microevolution, that it will automatically work on a broader scale too. But while the assumption of common descent may actually be true for different lice species and different gopher species, you have to make a leap to assume it will be true for all life. I know that (well, at least Doddy knew that)! But the example is still valid because it shows that short sequences of non protein-coding RNA, even in the simple prokaryotes, can regulate morphology. Do you have some reason to think that it won't be the same in the more complex eukaryotes? The idea that they are immediately digested and thus play no functional role is being challenged! At the very least, some introns do persist long enough to either interfere with or stabilise mRNA, thus affecting their translation.Here is recent review: Rana T " Illuminating the silence: understanding the structure and function of small RNAs" Nature Reviews Molecular Cell Biology 8, 23-36 (January 2007)For God's sake, just go to Google Scholar, PubMed or Web of Science and look up 'miRNA', 'siRNA' or 'RNA interference'! Surely, if I can come up with papers that suggest that introns are actually functional, some professional geneticist would have published a rebuttal to denounce such talk.

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But, why couldn't common design also result in such a pattern in the data?

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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.

By "common design" I had understood you to mean designs for a common purpose having common features. As you put it in your OP: And if that is your reasoning, then we should be surprised that the lobe finned fish are closer to humans than to the ray-finned fish, shouldn't we? Unless we are evolutionists, in which case that's exactly what we should expect.---If you just mean that perhaps God decided to make all the creatures in such a way that their genes would conform exactly to the theory of evolution, then he might have done, in the same way that he might have appointed angels to push the planets round in exact conformance to the theory of gravity.But you cannot claim the conformity of genetics to the theory of evolution as evidence of common design, any more than you can claim the conformity of planetary orbits to the theory of gravity as evidence for angels.Because the hypothesis: "All creatures has a common designer" does not predict the observation: "All their genes will conform exactly to the predictions of the theory of evolution." Whereas the theory of evolution does predict that.Hence, the observation that all creatures' genes conform to the predictions of the theory of evolution is evidence for the theory of evolution and is not evidence for "common design". Compatible with it, yes, under the additional hypothesis that God made the world as a big hoax to fool scientists, something that, I think, neither of us believes."Raffiniert ist der Herr Gott, aber boshaft ist Er nicht", said Einstein --- "The Lord God is subtle, but He is not malicious."Edited by Dr Adequate, : No reason given.

Yes, the birds-and-turtles thing was something of a poor choice of example on the part of mark24, because the place of turtles within Reptilua has long been controversial --- not enough fossils, you see.On the other hand, the crocodile-bird affinity is, from the fossil record, indubitable --- they're both definitely archosaurs, and if turtles aren't archosaurs, then they're the only living archosaurs.

Something that creationists have proved by a rigorous process known as "wishful thinking". As I have pointed out, we do not have to assume common descent in order to use these genetic similarities as evidence for common descent. Rather, we have to observe that common descent (together with the fossil record) predicts the nature of these similarities. Accurately. But not that all of them do! Non-coding sections of DNA that have a function tend to be highly conserved. Most eukaryote DNA is not.This seems to be something of a side-issue.