Adding information to the genome.

So the genotype evolves by one method, the phenotype by another? But didn't you just write: Were you wrong then? Or now?

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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 I'll put to you the same question I've just put to Coyote: do you believe the genotype evolves by one method, the phenotype by another?

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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 we can say with stone-cold certainty that cynodonts did not bear live young? It's such an attractive idea, isn't it? You can just see the animation; the malleus and incus falling back, shrinking down as the dentary gets bigger and bigger, and then the two small bones eventually disappear into the ear, to play a brand new role there.But if this actually happened, let's consider for a moment what is required in terms of known evolutionary mechanisms.For each small, incremental step in this process:1. At least three simultaneous mutations must occur, two to diminish the malleus and incus, one to enlarge the dentary.2. The mutations must be perfectly complementary, i.e. the shrinkage of the malleus and incus must be perfectly offset by the growth of the dentary, otherwise a misshapen jaw will result- clearly a survival disadvantage.3. A survival advantage must be conferred, significant enough to reach fixation.Remember, these requirements are for each incremental step. Anyone feel up to doing the maths? The probability would obviously run into the trillions-to-one against, but that shouldn't be a problemAs long as there were trillions of therapsids.

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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 in the case of the cynodonts, you're invoking the hopeful monster?

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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

The literature I have been reading doesn't mention the "nature" of the protein, but does mention the location and occasion of expression (e.g. in the leaf, on the application of heat). Can you explain the effect the promoter has on the "nature" of the protein more fully? Then what does specify these considerations? So you are saying that the evolutionary modification of the malleus, incus and dentary was not genetic in nature? Then what on earth caused it? Obviously not mutation. A dance the genes were sitting out, apparently. Just out of interest, what was controlling "the timing and concentrations of proteins"?

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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, so genes are the controlling elements. If, however, they do not specify the position, shape, size and orientation, then what does? Fine. Then how are the parameters specified?

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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

One bone is getting larger, while two bones are getting smaller. You believe this can happen through a single mutation? It is precisely this "sequence of changes" that requires detailed methodological explanation. Do you agree with Percy that the size, shape and orientation of jaw components are not decided by genes? No. The growth of the dentary must be perfectly matched by the shrinkage of the malleus and incus or a misshapen jaw -and a severe survival disadvantage- results. Unless you can show how a single mutation can shrink and reposition two bones while growing another at a compensatory rate, you need multiple simultaneous mutations.

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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 the shrinkage of the malleus and incus and their migration back into the inner ear didn't happen through gene expression? Then it wasn't evolution. And it isn't heritable.Curiouser and curiouser.

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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, I picked up on that. "Slowly I turned, step by step" suggests he's accepting multiple mutations.However, I still insist on simultaniety (try pronouncing that ). The shrinkage of the malleus and incus must happen at the same time as the expansion of the dentary, otherwise a misshapen jaw results (e.g. an overbite or an underbite).Edited by Kaichos Man, : smiley trouble

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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

G'day Ned. Yes, that seems to be what Percy's getting at. However, we are learning more and more about DNA every year. It was only about five years ago that scientists were suggesting only 2% of the human genome codes for anything. Now, with the discovery of regulatory pathways etc. the figure seems to have grown to around 10%.So I wouldn't be surprised if the "blueprint" does exist, and we just haven't worked out how to read it yet.

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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

As you well know, the rule with stepwise mutations is that each must confer a survival advantage (in order to become fixed in the population). An overbite or underbite, severe or not, is never going to be a survival advantage.What you're suggesting is reminiscent of Kimura's "survival of the luckiest". Though this particular cynodont would have to be extra lucky to a) survive being selected out with a misshapen jaw, and b) have progeny that possess a compensatory mutation.

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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

Anyone who knows me will assure you that I don't have to play dumb The fact that I understood it doesn't mean that I considered it an adequate answer. The "recipe" doesn't specify shape, size or orientation- so I pressed you to say what does.

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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

Well it's funny you should ask that, Percy. For better or worse, I'm about to radically change my position. (Takes a deep breath).What if the development of the mammalian jaw, far from being too complex for evolutionary processes, is actually too simple to require them? What if the pattern for the mammalian jaw is already in the genome, and requires very few mutations to be activated?"Is he mad?", I hear you ask. Consider this:"Therefore, the `Dlx codes' appear to regionalize the jaw primordium such that Dlx1/2 regulate upper jaw development, while Dlx5/6 confer the lower jaw fate. Towards identifying the genetic pathways downstream of Dlx5/6, we compared the gene expression profiles of the wild-type and Dlx5/6-/- mouse mandibular arch (prospective lower jaw). We identified 20 previously unrecognized Dlx5/6-downstream genes, of which 12 were downregulated and 8 upregulated in the mutant.The full paper is available here:Dlx genes pattern mammalian jaw primordium by regulating both lower jaw-specific and upper jaw-specific genetic programs | Development | The Company of BiologistsOkay, what do we have here? It appears two genes, Dlx5 and Dlx6 are largely responsible for lower jaw development in mammals. Fascinatingly, when both are inactivated, we see a marked downstream effect on no fewer than 20 genes, and of those genes 12 are downregulated and 8 upregulated. Now, I am obviously not saying that the downregulation and upregulation applies directly to the shrinking of the malleus and incus and the growth of the dentary, but it does suggest that such a twofold effect is possible. It certainly shows that widespread effects on jaw development are possible with very few mutations, and that the "compensatory" effect needed may actually be built in.So where does that leave us? It suggests that the development of the mammalian jaw may rely on simple loss-of-function mutations to existing control genes. Which makes the whole process so simple that one might expect it to have occurred more than once. And that appears to be the case:"We report a Cretaceous trechnotherian mammal with an ossified Meckel’;s cartilage in the adult, showing that homoplastic evolution of the DMME occurred in derived therian mammals, besides the known cases of eutriconodonts. The mandible with ossified Meckel’;s cartilage appears to be paedomorphic. Reabsorption of embryonic Meckel’;s cartilage to disconnect the ear ossicles from the mandible is patterned by a network of genes and signaling pathways. This fossil suggests that developmental heterochrony and gene patterning are major mechanisms in homoplastic evolution of the DMME."
(Luo et al 2007)DMME refers to the mammalian middle ear. Homoplasy, or convergence, is mentioned often in connection to mammalian middle ear and jaw development. Exactly what you would expect if the information for the organs was already in the genome, waiting for the very few mutations needed for activation.

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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

That is a most disturbing notion, given your avatar

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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

Percy, it's not a request, it's an explanation. You accused me of "playing dumb", and subsequently revealing myself in an exchange with NosyNed. I pointed out that I was not playing dumb, I understood your answer perfectly, and I felt that Ned's suggestion of a "recipe" rather than a "blueprint" pretty well summed up what you were saying.Understanding an explanation does not imply its acceptance. The fact remains that your answer(s) pertain more to what genes don't do, leaving the question of specification of the size, shape and orientation of the jaw bones unanswered. It never was.

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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