pangloss

I had not heard that 'convergent mutation = synapomorphy' line before. That is a classic - a keeper - and a prime exmample of the cognitive dissonance that runs rampant in creationists....

Jobar

Hello CD; you haven't heard from me before, but I have followed with great interest the entire 25 pages of this thread, and I have a question, and an observation.

Back on pages 22 and 23, this exchange occurred:

Ken:
As a former missionary linguist-to-be-Bible translator in Africa, I was impressed by the similarities and differences between the language I studied and a neighboring related language. I often thought about the principles I had learned in my one historical linguistic class, and I was fascinated by the patterns I could uncover, and puzzled by the instances that ran counter to the rules. But I never once doubted that the two languages shared a common ancestor. The geographical and morphological proximity of the two languages made it impossible to argue otherwise, in spite of the puzzles. What really happened? In broad lines, they descended from a common ancestor. Exactly how it happened, I have no clue.

(Ken, I think that your contributions to this thread, as a former creationist who came to see the strength of evolution and the nonsensical implications of creationism, are at least as powerful as the voluminous technical information from our resident experts. Bravo!)

[color=dark red]CD:
Nor do I doubt that two languages can share a common ancestor. So what? You are not invoking spectacularly unlikely events. A people group split up and their once common language became two different languages. You are making a strawman argument. Creationists don't doubt such events. Or to put it another way, doubting the evolutionary process is not at all tantamount to doubting such events as language evolution.[/color]

Now, from this, I gather that you are not so much the Biblical literalist as to claim that the differing languages of humanity are the result of God passing a miracle to prevent the construction of the Tower of Babel. You say flat out that "Creationists don't doubt such events."

Charles, I was in elementary school when Watson and Crick determined the structure of DNA. I recall very clearly the achievement being called deciphering the LANGUAGE of genetics.

You admit that languages can evolve. Yet you try to claim that the genetic code cannot! Tell me, just how do you conclude this? Is there some reason that speech (a way of communicating information) can change to such a degree that two or more wildly varying languages can sprout from one language, while the genetic code (also a way of communicating information) cannot change to such a degree that two or more wildly varying species cannot sprout from one?

That's the question; the observation:

As far as I can see, as a highly-informed layman (my degree is in physics, but I once taught high school biology, and also was once a mod on this forum for a short while), the only real 'problem for evolution' you have shown in these pages has been the 2 missing HERVs in the human genome. Charles, claiming that this constitutes any sort of spoiler for the fact of evolution, is akin to claiming that small unexplained variations in the measured surface gravity of the Earth, constitutes a 'spoiler' to the fact of geosphericity.

Despite the fact that, IMO, you have utterly failed to show any significant flaw in the concept of evolution, I want to thank you for coming here and arguing; because thanks to your addlepated and silly objections, I have received a refresher course in the science of biology, and the theory (which explains the fact) of evolution.

Charles Darwin

Thank you for the citation. I'd seen that paper, but forgot that they had sequenced several gibbon genes. Let's look at what the paper really says, but first, you are wrong if you think I am "clutching at straws trying to avoid a conclusion" I don't like. That is simply not the case. Now on to the paper.

Earlier I pointed out that, even if one accepts evolution, there are pseudogenes that coincidentally contain identical yet independent mutations. This undercuts the evolutionary reasoning that pseudogenes, such as this urate oxidase pseudogene, must have a common ancestor because they share common crippling mutations. This paper contains yet more examples of this.

For instance: "The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation."

And then there is this apparent multiple event: "One exceptional change is a duplicated segment of GGGATGCC in intron 4 which is shared by the gorilla and the orangutan. However, because this change is phylogenetically incompatible with any of the three possible sister-relationships among the closely related trio of the human, the chimpanzee, and the gorilla, it might result from two independent duplications. Alternatively, though less likely, ...".

Next there is this "coincidence": "it is interesting to note that the exon 2 nonsense mutation (CGATGA) is the same as that found in psi-Uox in the human and the great apes. One possibility for such coincidence may be attributed to a high transition rate from C to T in a CGA codon." But the authors then discuss why this is not likely."

And here is a conflicting phylogeny within the Gibbons: "The splice donor site mutation at intron 3 is shared by gibbons, except H. syndactylus (data not shown). This and other substitutions in the gibbon Uox gene support that H. syndactylus is the most distantly related species in the family (fig. 3 ). This conclusion is different from that of Roos and Geissman (2001) , who studied the mitochondrial control region and Phe-tRNA."

Finally, things became so confused that they resort to admitting that even the two independent events that are supposed to have caused the inactivation, probably, in fact, did not really do the job all by themselves. Rather, it must have been a progressive process of degradation: "Although dysfunctioning of the Uox gene in the human and great ape clade stems from a nonsense mutation in exon 2 or in the gibbon clade stems from a nonsense mutation in exon 2 or one-base indels, the promoter might have already been deteriorated by harmful mutations before Catarrhini and Platyrrhini diverged from each other. It therefore appears that the stepwise loss of Uox activity is more reasonable than the single step loss during primate evolution."

Then there is theh remarkable multiple CGA-TGA conversions: "Overall, it is remarkable that, except one CGA codon in exon 6, all the other four CGA codons are converted to the TGA termination codon in all or some of the hominoids."

Furthermore, you claim that the urate oxidase pseudogene phylogeny confirms the consensus phylogeny, but this is not the case. The latter has the gorilla splitting off first, and then chimp-human split occurring later. The urate oxidase pseudogene phylogeny has the human splitting off first. The authors are forced to resort to the claim that there must have been high levels of polymorphism in the ancestral species followed by random sorting of polymorphism in the descendant species.

I'm sorry, but these pseudogenes are simply not the unequivocal proofs of evolution and common descent as you claim. In fact, not only do they fail to provide such undeniable evidence, but they raise several problems.

markfiend

Coo-eee! Charles! Did you miss this? Still waiting for an answer!

Charles Darwin

Some species are more similar to each other than to others. Like two autos that are more similar, I am simply using the word "related" to describe this, not to suggest they have common ancestors. Species are not all equally different or similar.

Charles Darwin

No I did not define 'kind.' Why is it crucial?

Charles Darwin

Interesting point. I'm only able to find it in the human (D17461), chimp, orangutan and macaque. Also, see this paper for example. I have never seen a gorilla or gibbon sequence for this pseudogene. Is this evidence going to turn out like the urate oxidase pseudogene ?

Charles Darwin

Just to be clear, I did not claim the genetic code cannot evolve; I claimed it is highly unlikely. I'd prefer not to get into a lengthy discussion comparing it with the evolution of language. They are two different things and I think the analogy just won't get us very far. The reason teh evolution of the genetic code is so far-fetched has to do with physics and chemistry; the idea is simply unsupported by science. When you bring up human language you introduce a raft of complicating factors, such as they human brain, sociology, and so forth.

You next point out that aside from a couple of HERVs, there really aren't any evidential problems with evolution. You are certainly not alone here. This belief, along with the claim that evolution is a fact, are the telling parts of this tale. It isn't enough to posit a most bizarre theory; that the most complex things we know of arose all by themselves. But evolutionists next tell us with a straight face that the theory is a fact, and that there isn't any evidence to the contrary. You have no idea how the genetic code, echolocation, or a thousand other complexities could have evolved, but there isn't any evidence to the contrary. Adaptation is driven by a complex machine which evolution doesn't explain yet relies on, but there isn't any evidence to the contrary. Everything we know from breeding and mutation experiments is that change doesn't take you very far, but there isn't any evidence to the contrary. Homologies have different development patterns, but there isn't any evidence to the contrary. The Burgess Shale fossils look like they were planted there, but there isn't any evidence to the contrary. The fossil pattern looks like an inverted evolutionary tree, but there isn't any evidence to the contrary. Can you see why evolution is so problematic?

NottyImp

But doesn't going not very far over several billion years get you quite a long way? That's the point, isn't it?

Just to be clear though, Charles, how old do you think the earth is?

markfiend

Oh dear. Didn't we go over this (what feels like) several thousand posts ago? The point that "Species are not all equally different or similar" is what I was trying to explain to you in my posts about cladistics here, here, here, and here. You deny this in one post, then accept it several pages later.No. It is perfectly well-supported by science but denied by your theology. Argument from incredulity, now Charles? What??? Oh I cannot be bothered going through this thread again for the many hypotheses put forward for how echolocation could have evolved. But I know they are there, and if you are honest, so do you.It's called the environment, Charles. Ever heard of it? This is what drives evolution, adaptation to the environment. This is wrong, as has been explained to you on many occasions. No it doesn't. Can you not take on board a single correction of your misconceptions that any of us offer? Quite frankly, no. It is not problematic unless posed against your dogmatic unwillingness to accept it.