Adding information to the genome.

Actually, given that homeobox genes are being discussed here, loss-of-function was a bad choice of terms. Modification-of-function would be more appropriate. I don't mean "pre-existing" in the sense that the phenotype has existed before. I mean that the phenotype already exists in the form of a possible permutation of the downstream genes, just waiting for the appropriate modification of Dlx5 and/or 6. I was talking more about the "compensatory effect" needed for simultaneously growing the dentary while shrinking the malleus and incus. The fact that modification of Dlx5/6 resulted in upregulation of some genes and downregulation of others suggests that this is possible. I'm suggesting that the mammalian jaw may be the result of mutational modification of Dlx5 and Dlx6

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

Yes, this was always a high-risk strategy. Let me (somewhat hastily) explain myself. The fact that the mammalian jaw is largely under the control of two hox genes makes it a lot easier for RM/NS to achieve that particular configuration. But the presence of hox genes, and the genes they control, shouts "intelligent design".Let's forget the actual jaw, for a moment, and consider the genetic structure that expresses it. What evolved first? The hox genes? Nothing to control. The subordinate genes? Nothing to control them.It's another chicken-and-the-egg conundrum, like DNA and RNA or DNA and protein. Simultaneous and mutually-dependent cause and effect.So needless to say, rumours of my defection have been greatly exaggerated

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

It's only your side of the debate that considers them errors.For example, on Kimura you have insisted that he had no problem with natural selection. And while it is true that he suggested selection played a role at the phenotypic level, he also said this:"What I want to emphasize is that relaxation of natural selection is the prerequisite for new evolutionary progress. In other words, "liberation from selective constraint" enables extensive neutral evolution to occur, creating new variants,some of which turn out to be useful in a new environment...In conclusion, I would like to emphasize the importance of random genetic drift as a major cause of evolution. We must be liberated, so to speak, from the selective constraint posed by the neo-Darwinian (or the synthetic) theory of evolution."Do you agree with that, Percy? Are you convinced that relaxation of selective constraint is a prerequisite for evolutionary progress? Do you believe we must be liberated from the erroneous tenets of neo-Darwinism?I asked you (and Coyote, I think) to explain how the genome can evolve by one method and the phenotype by another. If I am wrong, then please forgive me, but I don't recall getting an answer on that one. No they are not. And unacceptance does not mean uncomprehension. Indeed. And if your opponent doesn't feel your rebuttal is effective, he's likely to keep using the same arguments.

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

It's only your side of the debate that considers them errors.For example, on Kimura you have insisted that he had no problem with natural selection. And while it is true that he suggested selection played a role at the phenotypic level, he also said this:"What I want to emphasize is that relaxation of natural selection is the prerequisite for new evolutionary progress. In other words, "liberation from selective constraint" enables extensive neutral evolution to occur, creating new variants,some of which turn out to be useful in a new environment...In conclusion, I would like to emphasize the importance of random genetic drift as a major cause of evolution. We must be liberated, so to speak, from the selective constraint posed by the neo-Darwinian (or the synthetic) theory of evolution."Do you agree with that, Percy? Are you convinced that relaxation of selective constraint is a prerequisite for evolutionary progress? Do you believe we must be liberated from the erroneous tenets of neo-Darwinism?I asked you (and Coyote, I think) to explain how the genome can evolve by one method and the phenotype by another. If I am wrong, then please forgive me, but I don't recall getting an answer on that one. No they are not. And unacceptance does not mean uncomprehension. Indeed. And if your opponent doesn't feel your rebuttal is effective, he's likely to keep using the same arguments.

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

It's only your side of the debate that considers them errors.For example, on Kimura you have insisted that he had no problem with natural selection. And while it is true that he suggested selection played a role at the phenotypic level, he also said this:"What I want to emphasize is that relaxation of natural selection is the prerequisite for new evolutionary progress. In other words, "liberation from selective constraint" enables extensive neutral evolution to occur, creating new variants,some of which turn out to be useful in a new environment...In conclusion, I would like to emphasize the importance of random genetic drift as a major cause of evolution. We must be liberated, so to speak, from the selective constraint posed by the neo-Darwinian (or the synthetic) theory of evolution."Do you agree with that, Percy? Are you convinced that relaxation of selective constraint is a prerequisite for evolutionary progress? Do you believe we must be liberated from the erroneous tenets of neo-Darwinism?I asked you (and Coyote, I think) to explain how the genome can evolve by one method and the phenotype by another. If I am wrong, then please forgive me, but I don't recall getting an answer on that one. No they are not. And unacceptance does not mean uncomprehension. Indeed. And if your opponent doesn't feel your rebuttal is effective, he's likely to keep using the same arguments.

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

Okay, I take it from that statement that you're suggesting the "subordinate" genes evolved first. Given that, as you say, these genes were already being regulated "some other way", can you explain the step-by-step causality of a new gene arising that 1) has the sole function of controlling other genes, b) knows exactly which genes to control and c) has a way of replacing or overriding their current form of regulation?

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

A caricature of Kimura? This is the sentence in question: Tell me, what is it that is posed by the neo-Darwinian (or the synthetic) theory of evolution and from which -according to Kimura- we must be liberated?

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

Fine. Good. Understood. So when Kimura writes:"The Neutral theory asserts that the great majority of evolutionary changes at the molecular level, as revealed by comparative studies of Protein and DNA sequences, are caused not by Darwinian selection but by random drift of selectively neutral or nearly neutral mutants."...you assert that the same must be true at the phenotypic level.Fair enough. Doesn't leave natural selection with much on its plate though, does it?

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

So our thinking was erroneous with regard to the part they played. That's because the answers given did not, in my opinion, deal with my arguments, so I am well within my rights to ignore them.Huntard, do me the honour of not considering me a complete idiot. You will know when I believe my argument has received a mortal blow (or been manoeuvred into apparent deadlock) because I'll probably stop talking about it and change the subject. In the overall battle between Creationism and evolution, this could be termed retreating and attacking on another front. No, quite the reverse. Have you seen the last few exchanges between myself and Wounded King? That discussion has changed markedly...

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

Agreed. But you seem to have left out the most important reason- that the majority of variation evident at the molecular area is in the functionally less important areas, namely junk DNA. One of Kimura's 5 principles is:"(ii) Functionally less important molecules or parts of a molecule evolve (in terms of mutant substitutions) faster than more important ones."Kimura's take on the macroevolutionary process is illuminating:"(i) A population is liberated from the preexisting selective constraint. (ii) There is a sudden increase or boom of neutral variations under relaxed selection. In this stage, gene duplication in addition to point mutation must play a very important role in producing genetic variations. Needless to say, their fate is largely
determined by random drift. (iii) The latent selection potential
of some of the neutral mutants is realized. In other words, some of the accumulated neutral mutants (at the phenotypic level) turn out to be useful in a new environment, which the species then exploits. (iv) Intergroup competition and individual selection lead to extensive adaptive evolution, creating a radically different taxonomic group adapted to a newly opened ecological niche."It's interesting that Kimura sees natural selection as an essentially conservative force, from which "liberation" is required before evolution is possible (step i). This is relevant to the parallel discussion on stasis.But even more important is his view on variation (step ii). Notice that it requires a relaxation of selective pressure accompanied by random drift acting on gene duplication and point mutation. Natural selection's only role at this stage is to get out of the way.Notice also that it isn't until (step iv) that selection enters the equation- after gene duplication, point mutation and random drift have created phenotypic variations able to exploit the new ecological niche.So where does that leave us? Do the genome and phenotype evolve by different methods? Kimura asks the same question:"Finally, I would like to discuss briefly the problem How
can we understand evolution at two levels-that is, molecular
and phenotypic-in a unified way?And then he answers it:" It is generally believed that, in contrast to the neutralist view of molecular evolution, evolutionary changes at the phenotypic level are almost exclusively adaptive and caused by Darwinian positive selection. However, I think that even at the phenotypic level, there must be many changes that are so nearly neutral that
random drift plays a significant role"Emphasis added. Carefully worded, but I think we can all (if you'll excuse the terrible pun) catch his drift.Edited by Kaichos Man, : italic problems

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

Huntard's question related to the evolution of the mammalian jaw. I was referring to the exchange between WK and myself regarding hox genes.

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

I fail to see how selection can play two roles in the process. Perhaps you can? Well, not really. This is a transcript of Kimura's appearance on a BBC documentary:"Kimura [standing beside a pond of colored carp]: As between the carp and me, there are many [genetic differences], but the surprising fact is that most of these mutations do nothing to help establish the differences between a human being and a fish. The carp and I both need hemoglobin to do exactly the same job of carrying oxygen around the body. Yet one half of all the chemical units in my hemoglobin molecules are different from the carp's. That unnecessary sort of evolution, and my studies of its rate and pattern, suggest to me that natural selection has had no reason for preferring one variant of the molecule over another. I think chance plays a much greater part in evolution, and natural selection a lesser part, than biologists supposed a few years ago."So according to Kimura, the evidence for Natural Selection is non-existent in the evolution of hemoglobin.And when you say: You're half right. He didn't "actually reject natural selection", but he certainly was considered controversial: Dobzhansky: "It took a century to show that [objections to Darwinism] are devoid of foundation. But now Dr. Kimura and his followers claim evolution to be due to changes which are neither useful nor harmful to their possessors. They are simply neutral and are established merely by chance. If that were so, evolution would have hardly any meaning, and would not be going anywhere in particular. All that we knowall that we observe both in nature and in the laboratoryseems, I believe, to contradict this contention. This is not simply a quibble among specialists. To a man looking for the meaning of his existence, evolution by natural selection makes sense."It seems Dobzhansky was considerably less comfortable with Kimura's theory than you are, Percy.

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

Really? Consider:The second is the "conservative nature" of the changesi.e., functionally less important molecules, or portions of molecules, evolve faster than more important ones"And"As to the second feature (i.e., the conservative nature), it can easily be understood from the neutral theory, because the less drastic or more conservative the mutational change, the more likely it is to turn out to be nondeleterious, and therefore selectively neutral."As well as:"What I want to emphasize is that relaxation of natural selection is the prerequisite for new evolutionary progress. And your opinion is not a good predictor of who's opinion is being stated.Edited by Kaichos Man, : typo

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

I don't see two, hence the question. You have pointed out that steps 3 and 4 both require natural selection. How so?

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

I have changed my position on mammalian jaw evolution, as a result of my own research into hox genes Dlx5&6. You can claim some credit for forcing me to undertake this research. I no longer believe that simultaneous and compensatory mutations are needed, and that these are impossible by evolutionary mechanisms. I now believe that the creation of hox genes and their subordinate genes are impossible by evolutionary mechanisms.As for lactation, that remains one of the worst examples of an evolutionary "just so" story I've ever come across. Some guy points at a fossil and says "I think those bones and teeth are too well developed for a creature that I don't think was old enough to feed itself". Next thing you know we've got a permeable egg being clasped to a hair follicle. Viola! Lactation has evolved.Any self-respecting science-fiction writer would screw that one up and toss it at the waste paper basket with a sigh and "No-one's going to buy that". And yet this rubbish is probably just a heartbeat away from finding it's way into the next high school biology textbook. As a "fact", no doubt.It's not good science, RAZD.It's not even good fiction.

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"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin