How Much of Genome is "Functional" or "Neutral"?

I didn’t say that Graur said « this » but that his position was « this ».
Anyway, are you contesting that as the fonctionnel fraction of the human genome grows, the plausibility of the idea that human and chimps evolved from a common ancestor by some undirected mechanisms decreases?

No, the plausibility of that common ancestry having occurred undirected would go down(we’d still share common ancestry though). There would likely have to be some mechanism that was extremely efficient at weeding out deleterious mutations, and you could call that a sort of “directing” mechanism. We could imagine all sorts of ways that was possible.

Of course, it’s also possible what Larry Moran says, that if the functional fraction of the human genome really is very high, 80% or more, that our understanding of population genetics, or the biochemistry of DNA-protein interactions and transcription, are wrong.

There is however no good evidence that these things are wrong, or that the functional fraction of the human genome is higher than 10%.

Assuming common anscestry between man and chimps, I pretty much agree with all you are saying here. However, assuming that future discoveries will substantially expand the fonctional fraction, then all that you are proposing as a mean to save common ancestry would look like as new epicycles.

Heh, no epicycles would be what you’d have to come up with to explain away why the independent evidence for common ancestry suddenly no longer counts. I know that’s where you want this to go, but I’m pretty sure you don’t really understand what that would require.

The functional fraction of the human genome has no bearing on the reality that there is nesting hierarchical structure in anatomical and molecular data, for which common descent is the only sensible explanation. You’re still an ape, and you’ll have genealogical cousins crawling around in trees even if ENCODE is right contrary to all available evidence.

Here is an alternative explanation to common descent for the nesting hierarchical pattern you are pointing to:
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2018.3/BIO-C.2018.3

That paper has been discussed on this very site, for example here: Winston Ewert: The Dependency Graph of Life

Ewert hasn’t shown what you think he has, but that has not been advertised on the typical ID propaganda outlets I guess.

are you talking about the onion test?

Just click on the link.

No. Like Faizal Ali says, click on the link. It’s true that T. Ryan Gregory came up with both of them, and they’re both connected to genome size. But then Gregory is an expert on genome size and curates the genome size database. You might pay attention to him.

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Yes, I am.

Something being overlooked here: It is ID Creationism, and not evolution, that is threatened by the idea of a genome that is largely functional, as @T_aquaticus discussed here on this thread:

This ultimately led Ann Gauger to admit what evolutionists had been trying to explain to her for years: That ENCODE’s identification of biochemically active sites in the genome did not translate to biological function.

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What is your evidence that this is his position?

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We should be more precise here, rather than just quoting Dan Graur’s comment. ENCODE could be entirely right in everything they published, and 80% of the human genome could be functional (in the sense they defined it), and it would have no effect at all on evolutionary biology or the plausibility of common descent. That’s because the ENCODE definition of “function” doesn’t imply anything about the actual functionality of sequence, i.e. it doesn’t tell us anything about the effect of changing that sequence on the fitness of the organism (or on what it looks or acts like).

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Change in reproductive fitness is not a complete description of what an organism looks or acts like.

So defining function based on Change in fitness misses out on a lot of what makes an organism what it is.

Yes, and a definition of function has no reason to include everything that makes an organism what it is.

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I know. That’s why I said that the ENCODE definition of function doesn’t tell us about either reproductive fitness or about what an organism looks and acts like. “Or” connects two different things in that sentence.

And the ENCODE definition of fitness tells us about none of those things.

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That’s a viewpoint that developed because of a commitment to evolution. To me it sound more about ideology than facts.

True. But there is merit to a more causal approach to function. Especially in the medical field. ENCODE seems to have opened the door to such an approach.

His paper at 26.

I agree. But note that when Graur said that « if ENCODE is right, then evolution is wrong », he had in mind the following definition of function for a genomic segment: « A genomic segment is considered to possess a selected effect function if at least one out of all the possible mutations that can affect its sequence is deleterious. » IOW, a genomic segment has fonction if it contributes to the fitness of the organism. It is in that sense that I used the word function in all this conversation.

Quote exactly where he says that in the paper, please.

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We’ll see, I guess. That has no bearing on the current discussion, though, does it?

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