Does Neo-Darwinian evolution require change ?

I think that we need to clarify the basics of Punctuated Equilibria (again).It is necessary to start with the fact that P.E. deals with evolution and Paleontology. The "species" of P.E. are paleontological species. Thus, changes which do not show in the fossil record or changes which cannot be distinguished from the normal variation within a species are all permitted within "stasis". Since we know of "cryptic species" - biological species which are morphologically identical - it is quite possible that some paleontological species would be considered two distinct biological species if we had living specimens - perhaps some would even be split into three or even more.The next important fact is that P.E. is a prediction of evolutionary theory - or to be more precise Mayr's theory of speciation (still felt to be the main mechanism by which new species form). Mayr's mechanism starts with a small population becoming isolated from the main body of a species. Large populations are slow to evolve, by drift or even selection - this smaller population can change far more rapidly. If this smaller population thrives and evolves to form a new species and if it is able to return it may overrun the territory of the ancestral population, giving the appearance of a change more sudden than it actually was. Since most of the evolution happens relatively rapidly (but still "gradually" by human standards) and in a small region it is not uncommon for it to be missed - either absent from the fossil record for one reason or another, or simply not found by us.Thus Eldredge and Gould's "stasis" is explained by gene flow acting as a stabilising force often restricting the change within successful species - while they remain successful ! - to change within the limits of paleontological species.

I'd say that you missed the point that gene flow reduces the rate of change. And I thought the point that stasis definitely does not mean "no change" was worth mentioning as well as the fact that biological species can be morphologically identical.I'd also say that it looks as if you are assuming that most mutations have visible morphological effects, which I rather doubt even of those mutations which do have effects - and your "high" mutation rate must be counting many more which have no effects whatsoever (by a large majority).

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I understand all these, but I don't see how it answers what I'm asking. Which is that given the high mutation rates, how can it stay at that optimal peak when every single offspring will have inherited so many mutation (the majority deleterious, most only very slightly). Whichever one natural selection ''chooses'', it will still be less fit then it's parents were.

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I think it's time you supported your claims. Please produce evidence that humans have a mutation rate of at least 50 mutations per individual per generation and that the majority are at least slightly detrimental.

However, if I understand correctly this measures the whole genome, most of which appears to have no function. If I am correct, a large majority of these mutations will be truly neutral having absolutely no effect whatsoever. Slevesque's argument requires the majority to be detrimental, so he needs to use the far smaller number of mutations within functional regions of DNA (genes, regulatory sequences and the like).

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And what % of the genome do you think has a function ? 5% ? 10% ? 30% ?

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The truth is we don't really know, but this has been an ever increasing number in the past couple of years. I think most geneticists today would say at least 30%, but the ENCODE project has opened the possibility that the entire genome would be functional, and even that some times both sides of the DNA strand is useful, putting it's functionality at over 100%.

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It doesn't matter what MY opinion is. The point is that you are assuming 100% (which even ENCODE did not show). And last I heard ENCODE was coming under heavy criticism for misinterpreting the data and badly overestimating the amount of DNA transcribed (not used - just transcribed).Another study using a more accurate methodology found: Most Dark Matter Transcripts Are Associated With Known Genes

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Ok I think I got misunderstood there. What I was saying was: The % of functioning genome has been ever increasing in the past few years, as I'm sure you know. Right now, anyone can safely say that at least 30% of the genome is functional.

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Is that really true ? I'd have thought that the discovery of fewer genes than expected by the Human Genome Project would have cut the amount of functional DNA, and I very much doubt that the relatively small number of regulatory sequences etc. discovered makes up the difference.So is the figure really 30% ? Do you have any evidence ?

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For example:

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Therefore, more than one third of the mouse and human genomes, previously thought to be non-functional, may play some role in the regulation of gene expression and promotion of genetic diversity.

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Junk DNA Guides Embryo Formation – SciScoop Scitext ChemSpy

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So all you've got is speculation ? I'd have thought that things would have moved on a bit since 2004. So much for your claim that practically all geneticists would agree with your 30% figure.

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I think that we are starting to see a paradigm shift in this field. The paradigm was that, DNa was mostly junk, and so it was a waste of time to try searching for it's use. Once more and more parts are being unravelled and found to have a use, I think an avalanche of discoveries in that field will come. But, as prof. John Mattick said:

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the failure to recognise the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology

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Wake up. The truth is that the existence of regulatory sequences has been known for a long time. And the search for function in non-coding sequences has been going on for quite a time too - where do you think all the results you use to try to "prove" that so much of the genome has a function come from ?