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

[Mercer (John Mercer)]

@Ashwin_s

He mentioned Graur’s paper was “independent of teh theory of evolution”… How should I take that?

As it was offered. The paper was independent of evolutionary theory. What is being assessed in the paper, which you didn’t understand, is based on direct observation. It’s relevant, yet independent, an important distinction you have utterly failed to grasp, despite the explanation he offered.

@Ashwin_s

I don’t have any problem with the above comment.

They are scientifically equivalent, so there’s no reason for you to object to one and not the other.

@Ashwin_s

I hope you have the habit of reading everything on a subject and understand teh context before you butt in.

I still maintain that you misrepresented @Faizal_Ali. “Independent of” is not logically equivalent to “nothing to do with.”

@Ashwin_s

What is my hypothesis here exactly?

You’re all over the place:

@Ashwin_s

I am sure they think it’s also significant in terms of design… but it’s also an argument against the current understanding of common descent.
There are good reasons based on evolution why more than 10% or 25% of the human genome should not have functional significance (depending on the paper you go by). So a higher amount of functionality will be significant.

@Ashwin_s

I would start with the hypothesis that scientists don’t really understand much about genes and how they effect the organism to start with.

A larger percentage of genes in human beings having function could.mean that mutations are not as random as currently supposed.

@Ashwin_s

Do you expect the majority of neutral mutations to be selected for or against? If not, the vast part of the genome will be non functional.
Especially in more recent species like human beings.
I don’t see why that would be wrong.

@Ashwin_s

My only point that finding function for larger percentages of the human genome would be a problem in light of these studies.

[John_Harshman]

You don’t seem to be engaging with the questions. Perhaps we could start with the hypothesis that you don’t really understand much about genes or about how much scientists understand.

What does “mutations are not random” mean? Are genetic diseases somehow intended? Why do deleterious mutations occur with high frequency in sequences known to be functional? Why would you suppose the frequency would be different in sequences not known to be functional? If you want to present a hypothesis, you should actually do so rather than just supposing that other people might. I don’t think there’s any sort of reasonable hypothesis, whether including God or otherwise, that fits your vaguely expressed ideas.

[John_Harshman]

@Ashwin_s

All I will say is that I was not proposing God directly working on mutations as a solution.

Ah, but what are you proposing? You’re quite vague about that.

[Ashwin_s]

@Mercer

As it was offered. The paper was independent of evolutionary theory. What is being assessed in the paper, which you didn’t understand, is based on direct observation. It’s relevant, yet independent, an important distinction you have utterly failed to grasp, despite the explanation he offered.

It’s based on premises that are based on evolutionary theory. The paper would be impossible without the framework of evolution.

I don’t see how it’s independent.

@Mercer

They are scientifically equivalent, so there’s no reason for you to object to one and not the other.

Once again
Which comment did I object to?

@Mercer

I still maintain that you misrepresented @Faizal_Ali. “Independent of” is not logically equivalent to “nothing to do with.”

The concept of function used by Dan Graur is totally dependent on the theory of evolution.
Once again, read the thread and what was being discussed.

@John_Harshman

Ah, but what are you proposing? You’re quite vague about that.

Wasn’t proposing anything. Read the thread.

I was making an observation.

[Ashwin_s]

@Mercer

What is my hypothesis here exactly?

You’re all over the place:

Actually you are … @Faizal_Ali claimed I made an argument which I did not… in fact if you had read the beginning of the thread, you would have seen that…

Now that you have quoted me below .read in context and understand what I wrote… it shouldn’t be tough.

[John_Harshman]

@Ashwin_s

I was making an observation.

But it was a nonsensical observation that you apparently have no interest in supporting or even discussing. Your “observation” has implications that you will not confront. If you won’t talk about it, why bring it up in the first place?

[Mercer (John Mercer)]

@Ashwin_s

It’s based on premises that are based on evolutionary theory. The paper would be impossible without the framework of evolution.

False. It’s based on short-term population genetics and directly-measured mutation rates. It applies whether people evolved or were specially created.

@Ashwin_s

I don’t see how it’s independent.

You also don’t see how someone who has held faculty positions in both the US and India would have a far better basis than you would for comparing and contrasting the two educational systems.

You’re just not seeing.

@Ashwin_s

The concept of function used by Dan Graur is totally dependent on the theory of evolution.

Was the concept of function used by the ENCODE Consortium similarly dependent?

@Ashwin_s

Once again, read the thread and what was being discussed.

I am. It is clear that you don’t understand.

@Ashwin_s

Now that you have quoted me below .read in context and understand what I wrote… it shouldn’t be tough.

It’s not tough. You don’t understand.

[Ashwin_s]

@John_Harshman

But it was a nonsensical observation that you apparently have no interest in supporting or even discussing. Your “observation” has implications that you will not confront. If you won’t talk about it, why bring it up in the first place?

Actually, I don’t think you have read the thread. You are responding to something which I have never said, i.e that having large percentage of functional genes in the human genome indicates design.

In such a scenario, why should I treat you as anything other than an internet troll who happens to have a PhD?

[Faizal_Ali]

@Ashwin_s

He mentioned Graur’s paper was “independent of teh theory of evolution”… How should I take that?

Later on he edited his comment to add the below which I missed.

Faizal_Ali:

Graur’s argument would apply equally well if humans has been specially created by God with genomes that are prone to mutations.

I don’t have any problem with the above comment.

Those two statement amount to the same thing. If Graur’s paper remains no less relevant and accurate in a creationist scenario, then it is independent of the theory of evolution.

I don’t know how much more clearly I can explain this.

[Ashwin_s]

@Faizal_Ali

Those two statement amount to the same thing. If Graur’s paper remains no less relevant and accurate in a creationist scenario, then it is independent of the theory of evolution.

The definition of function would change radically in a scenario involving design.

Do you know how biologists define function in the genome? The definition used by Graur depends totally on the concept of evolution.

[John_Harshman]

@Ashwin_s

You are responding to something which I have never said, i.e that having large percentage of functional genes in the human genome indicates design.

No, that’s not at all what I was responding to. Perhaps you’re the one who hasn’t read.

[Ashwin_s]

@John_Harshman

No, that’s not at all what I was responding to.

Why don’t you start by acknowledging I did not make any claim about creationism and then move on to the next issue.
And I will respond.

[John_Harshman]

@Ashwin_s

Why don’t you start by acknowledging I did not make any claim about creationism and then move on to the next issue.

Sure. I’ve never said you did. Now would you care to engage?

[Ashwin_s]

@John_Harshman

Now would you care to engage?

Sure. What’s the point you want to make.

[Faizal_Ali]

@Ashwin_s

Do you know how biologists define function in the genome? The definition used by Graur depends totally on the concept of evolution.

Only if you include under “evolution” any process in which organisms inherit their genetic material from their ancestors, and in which this genetic material is subject to mutations which can be neutral, detrimental or beneficial to the organism. Most people who consider themselves creationists accept that this process occurs (it’d be very hard not to) and yet still reject evolution, so I don’t think it can be reasonably argued that this alone constitutes evolution.

Graur’s paper does not employ any particular definition of function. That is part of what makes it such a powerful argument. It works no matter how one defines function.

[Ashwin_s]

@Faizal_Ali

Only if you include under “evolution” any process in which organisms inherit their genetic material from their ancestors, and in which this genetic material is subject to mutations which can be neutral, detrimental or beneficial to the organism.

Evolution involves heritable change. It’s a vital part of the theory.
I don’t know anybody who doesn’t include inheritable traits and change in these traits as a fundamental part of evolution.

@Faizal_Ali

Most people who consider themselves creationists accept that this process occurs (it’d be very hard not to) and yet still reject evolution, so I don’t think it can be reasonably argued that this alone constitutes evolution.

This is not accurate. These creationists do not reject evolution. In fact they acknowledge it. They reject what they call “macro evolution” and universal common ancestry.

@Faizal_Ali

Graur’s paper does not employ any particular definition of function. That is part of what makes it such a powerful argument. It works no matter how one defines function.

Graur’s paper defines function as something that effects reproductive fitness.
So a functional gene undergoing a mutation would lead to fitness loss…
This is a common definition based on the theory of evolution. In his paper, under the segment definitions, he defines his usage of function as below-

Throughout this paper, the term “function” is used to denote selected effect function, that is, a capacity that has been shaped by and is maintained by natural selection (Wright 1973; Graur et al. 2013, 2015; Brunet and Doolittle 2014). The selected effect function stands in contradistinction with the causal role function (or activity), which is ahistorical and nonevolutionary, and merely describes what an entity does.

Pls read his paper.

[John_Harshman]

@Ashwin_s

What’s the point you want to make.

Please go back and respond to what I actually say in previous comments.

[Faizal_Ali]

Here is where I think you are confused.

It is true that one means of determining whether a particular DNA sequence if “functional” is by determining the degree to which it is conserved (i.e. subject to selection). Note that, strictly speaking, this is not a means of defining function, but rather of measuring it.

You would be correct if your position is that this is a method that relies on accepting evolution and, in particular, the concept of common ancestry between different species.

Dan Graur may well favour this as a means of determining whether a sequence is functional. However, this is not germane to the particular paper we are discussing. He does not compare sequence conservation in the human line to that of other lineages.

Here is what his paper did: He starts from the premise that, the higher the number of detrimental mutations occurring in a population, the greater the number of offspring must be produced in order to prevent extinction due to the poor fitness of offspring affected by detrimental mutations. This is non-controversial.

The average number of detrimental mutations per offspring can be estimated by knowing 1) the overall mutation rate; 2) the percentage of mutations that are detrimental if they occur in a sequence that is functional and 3) the percentage of the genome that is functional.

So, to use some hypothetical numbers to illustrate:

If the mutation rate is such that 100 mutations occur a generation, 10% of these are detrimental (in functional sequences) and 50% of the genome is functional, this will produce 5 detrimental mutations per generation. But if only 10% of the genome is functional, that number goes down to 1.

Is that clear? If not, let us know and someone I’m sure can explain further.

Graur then went on the calculate the numbers for a range of mutation rates and ratios of detrimental to neutral mutations as applied to various proportions of the genome that could be functional.

He found that at any levels of function >25%, unrealistic numbers of offspring per couple would be required to prevent the population from going extinct from the genetic load of deleterious mutations.

Now, the point is that this has nothing to do with evolutionary concepts such as common ancestry. As I said, it only requires acceptance of the existence of genetic inheritance and mutations, which applies to every single creationist I can think of. Graur’s argument is independent of evolution. If he was wrong, evolution could still be true. And if he is correct, evolution could still be wrong

[Faizal_Ali]

@Ashwin_s

Evolution involves heritable change. It’s a vital part of the theory.
I don’t know anybody who doesn’t include inheritable traits and change in these traits as a fundamental part of evolution.

Which is besides the point. I also do not know any creationist how does not include these as part of their understanding of creation.

@Ashwin_s

This is not accurate. These creationists do not reject evolution. In fact they acknowledge it. They reject what they call “macro evolution” and universal common ancestry.

Well there you go. You just agreed with the essence of what I wrote. The only disagreement is over the semantics of how creationists try to use weasel words like “micro-evolution” and “macro-evolution.”

@Ashwin_s

Graur’s paper defines function as something that effects reproductive fitness.
So a functional gene undergoing a mutation would lead to fitness loss…
This is a common definition based on the theory of evolution. In his paper, under the segment definitions, he defines his usage of function as below-

It is also consistent with what creationists call “microevolution”, as you just admitted. So, again, Graur’s paper is equally applicable whether one accepts evolution or believes in creationism. It is independent of the theory of evolution.

@Ashwin_s

Graur’s paper defines function as something that effects reproductive fitness.
So a functional gene undergoing a mutation would lead to fitness loss…
This is a common definition based on the theory of evolution.

Now, please show how using a different definition would affect the analysis of his paper as I have given above.

[Mercer (John Mercer)]

@Faizal_Ali

Now, the point is that this has nothing to do with evolutionary concepts such as common ancestry .

Exactly. This does not seem to be complex to me, but then again, I’m a geneticist.

@Faizal_Ali

As I said, it only requires acceptance of the existence of genetic inheritance and mutations, which applies to every single creationist I can think of.

Well, if @Ashwin_s does not accept the existence of genetic inheritance and mutations, that certainly would be interesting.

@Faizal_Ali

Graur’s argument is independent of evolution. If he was wrong, evolution could still be true. And if he is correct, evolution could still be wrong

Again, exactly correct. @Ashwin_s, do you disagree?