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

[Rumraket (Mikkel R.)]

I rest my case.

[Giltil (Gilbert Thill)]

@swamidass

That number, tolerance of organismal fitness in humans to mutation, we already know by other means

How do we know that number by other means? If it is by considering the non conserved fraction of the genome, that would beg the question.

[John_Harshman]

@Ashwin_s

The third point I made was that the genome is more resilient in some parts

What does “resilient” mean in real terms?

@Ashwin_s

If the above are true, then it would mean that mutations are restricted

If. There is no evidence that mutations are restricted. They happen more in some regions than others, but they still happen everywhere, and there seems no other bias to where they happen. Where, then, can function be hiding in the junk DNA, so that it doesn’t experience mutations? And why should junk DNA be shielded from mutation when known functional DNA is not?

@Ashwin_s

This would mean that there is a limit to how much an organisms genome can change. Thus putting a limit to the change possible through evolution.

And that’s fantasy. There is clearly no such limit unless you ignore all the data on mutation and on phylogenetics.

@Ashwin_s

This will have implications on common descent.

Your conclusion, however, follows neither from the data nor from your premises.

[Faizal_Ali]

@Ashwin_s

I think this could also mean that mutations aren’t uniformly spread across the genome (i.e some regions are more prone to mutations than others) or that the genome is more resilient and most mutations aren’t deleterious (i.e the genome is configured in such a way that mutations are always neutral in some regions ).

This remains consistent with what Graur is saying, though his explanation is more reasonable than yours because he actually understands genetics.

There are regions of the genome in which mutations are unlikely to be observed in the genome of a living popuattion because these regions are subject to strong purifying selection and, therefore, mutations in these areas will be immediately removed thru the non-viabilty of the organism.

Other regions are more tolerant of mutations, and the most tolerant are those in which any mutation at all may occur because they are junk.

We continue to await your alternative explanation for these observations that has at least a modicum of scientific evidence to support it.

[Faizal_Ali]

@Giltil

What Graur is rightly saying is that the more the fonctionnal fraction of the genome is growing the more implausible the idea that human and chimps evolved from a common ancestor by some undirected mechanisms becomes.

That is not what he is saying. I which Graur were here to tell you what he thinks of what he wrote, except I doubt it would comply with the community standards of this group.

[Giltil (Gilbert Thill)]

@Faizal_Ali

That is not what he is saying.

I am afraid you are wrong on this matter.

[Rumraket (Mikkel R.)]

@swamidass

Honestly, I don’t know about this.

ENCODE scientists were puffing their work using a profoundly ambiguous term, “function.” In terms of evolution, what really matters is tolerance to mutation, not the wide net catch all meaning “function” that the ENCODE scientists were playing with to boost their numbers.

That number, tolerance of organismal fitness in humans to mutation, we already know by other means So was ENCODE right or wrong or in conflict with evolution? I think it should be stupidly obvious that they were using different definitions for “function” than would be important for determining the plausibility of evolution.

I agree, but it is in their public grandiose pronunciations they are wrong. In declaring the death of junk-DNA to the general public (not not in their publications), they are making a claim in the popular press that their work in the primary literature does not actually support. This is very misleading and really does a huge disservice to the public understanding of science. It should really not be a surprise that many, many scientists who know their stuff got pissed off about their popular press claims.

Among them biochemists who understand the implications of the ENCODE claims for decades of work in understanding the mechanisms of transcription, protein-DNA interactions, regulation and so on(hence Larry Moran says a lot of biochemistry would have to be re-thought), and the population geneticists who understand the implications for beneficial/neutral/deleterious mutations, and genome size evolution(hence, c-value paradox and genetic load). Dan Graur graciously acknowledges to Larry Moran that Larry was right that this is what Graur meant.

Unfortunately that short sentence of Dan Graur’s(“if ENCODE is right, then evolution is wrong”) is being blown out of proportion by creationists like Gilbert Thill who seem to think it means something else than what it does. They seem to think Dan’s statement means that suddenly all the evidence from the fossil record, nesting hierarchies, consilience of independent phylogenies and so on is all magically going to no longer be valid. That’s simply not the case, this evidence isn’t mysteriously going to disappear or fail to be evidence.

But Gilbert and like-minded creationists have a vested interest in making Graur’s words have wider implications because they think they can turn it into a battle of scientific authority. Blow up the authority of ENCODE “hands-on lab researchers” and contrast it to some group of diehard evolutionary “armchair theoreticians”. I’ve seen people like Sal Cordova push this exact line of argument multiple times.

[Faizal_Ali]

@Giltil

I am afraid you are wrong on this matter.

If you sincerely believe that Graur’s position is that the recent trend of evidence from genomics is against the idea of common ancestry between humans and other apes, I really don’t know what to say. You could not possibly be more wrong.

[Giltil (Gilbert Thill)]

@Faizal_Ali

If you sincerely believe that Graur’s position is that the recent trend of evidence from genomics is against the idea of common ancestry between humans and other apes, I really don’t know what to say. You could not possibly be more wrong.

I am not saying that at all. I perfectly know that Graur isn’t questioning the idea of common ancestry between human and apes. What I say is that his position is that if the fonctional fraction of the human genome is above a certain threshold that he considers to be 25%, then common ancestry between human and apes would be impossible. This is why he said that if ENCODE is right, then evolution is wrong. As whether ENCODE is right, I don’t know yet. Time will tell. But it would be better for evolutionists if ENCODE is wrong.

[T.j_Runyon]

@Giltil

I am afraid you are wrong on this matter

Graur said you are wrong…

[scd]

@John_Harshman

And how do you fit so many non-deleterious mutations, around 100 per person, into all those functional sequences?

its also possible that this suppose junk has a rule in the creature complexity. take a look at fig 2 in this paper:( A meta-analysis of the genomic and transcriptomic composition of complex life)

you can clearly see a correlation between the amount of junk and creature complexity in general (note that i said “general”).

[John_Harshman]

@scd

A meta-analysis of the genomic and transcriptomic composition of complex life

Congratulations. You have discovered what is formally known in the field as the “dog’s ass plot”.

[Faizal_Ali]

@Giltil

What I say is that his position is that if the fonctional fraction of the human genome is above a certain threshold that he considers to be 25%, then common ancestry between human and apes would be impossible.

He never said this. Quote where you believe he did.

[Giltil (Gilbert Thill)]

@Faizal_Ali

He never said this. Quote where you believe he did.

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?

[Rumraket (Mikkel R.)]

@Giltil

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%.

[Giltil (Gilbert Thill)]

@Rumraket

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.

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.

[Rumraket (Mikkel R.)]

@Giltil

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.

[Giltil (Gilbert Thill)]

@Rumraket

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

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

[Rumraket (Mikkel R.)]

@Giltil

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.

[scd]

@John_Harshman

Congratulations. You have discovered what is formally known in the field as the “dog’s ass plot”

are you talking about the onion test?