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

[Faizal_Ali]

Just click on the link.

[John_Harshman]

@scd

are you talking about the onion test?

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.

[Faizal_Ali]

@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?

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:

No Junk DNA vs. Rarity of Function

In my most humble opinion you either misunderstand or misrepresent the ID argument. It would perhaps be helpful if you could quote an actual argument. I would be very interested to see where any high profile ID figure makes the argument that function is rare in DNA sequence space.

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.

In Arguments for Intelligent Design, Definitions and Assumptions Are Important...

[glipsnort (Steve Schaffner)]

@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.

What is your evidence that this is his position?

[glipsnort (Steve Schaffner)]

@Giltil

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.

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).

[Ashwin_s]

@glipsnort

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).

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.

[John_Harshman]

@Ashwin_s

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.

[glipsnort (Steve Schaffner)]

@Ashwin_s

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

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.

@Ashwin_s

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

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

[Ashwin_s]

@John_Harshman

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

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

@glipsnort

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

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.

[Giltil (Gilbert Thill)]

@glipsnort

What is your evidence that this is his position?

His paper at 26.

[Giltil (Gilbert Thill)]

@glipsnort

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).

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.

[Faizal_Ali]

@Giltil

His paper at 26.

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

[Faizal_Ali]

@Ashwin_s

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.

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

[glipsnort (Steve Schaffner)]

@Ashwin_s

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.

There is tremendous merit to learning the mechanistic basis for biological function. That’s why the ENCODE project exists, that’s why our lab here is part of it, and that’s why lots of other researchers are studying the same kind of thing (and would be doing so regardless of whether ENCODE had ever existed). But none of it is a test of evolution.

[Giltil (Gilbert Thill)]

@Faizal_Ali

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

Please read again the abstract of Graur’s paper below. By doing so, you will understand Graur’s view on the topic and see that I am not mischaracterising him.

Abstract

For the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 25%, and is probably considerably lower.

[glipsnort (Steve Schaffner)]

@Giltil

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.

Then why are you discussing ENCODE in connection to function at all? Whatever Dan Graur does or doesn’t think, ENCODE doesn’t tell us anything about function in the sense you’re talking about, right? And it doesn’t tell us anything about the plausibility of evolution, agreed? So what is the point of this exchange?

[Faizal_Ali]

@Giltil

Please read again the abstract of Graur’s paper below. By doing so, you will understand Graur’s view on the topic and see that I am not mischaracterising him.

That abstract you quoted does not say that if the functional portion exceeds 25% evolution is false. It does say that the evidence shows that the functional portion cannot exceed 25% based on available evidence. But that is obviously not the same thing.

Are you prepared to admit that you have mischaracterized Graur’s position? Or a you going to keep looking for something to prove you didn’t?

[pnelson (Paul A Nelson)]

Has Graur now disavowed his argument that “if ENCODE is right, then evolution is wrong”?

See slide 16 of his 2013 SMBE presentation:

[glipsnort (Steve Schaffner)]

@pnelson

Has Graur now disavowed his argument that “if ENCODE is right, then evolution is wrong”?

Do you agree that if ENCODE is right in its own terms (i.e. using their definition of function), then it tells us nothing about the reality of evolution?

[John_Harshman]

@Ashwin_s

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

Sorry, but that seems to be more of a generic complaint than any sort of reasoned response. Why should a definition of function include everything? Wouldn’t that make it useless?