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

[Faizal_Ali]

@Argon

Professor Dan Graur (aka ‘Judge Starling’) has a helpful diagram:

Wow. That just lays it all out.

Here is the key to the numbers:

The genome (red) consists of functional DNA (blue) and junk DNA (yellow). Both functional DNA and junk DNA may be transcribed and translated. (1) Untranscribed functional DNA (e.g., DNA regulatory elements), (2) Transcribed but untranslated functional DNA (RNA specifying functional genes, e.g., tRNA, rRNA), (3) Translated functional DNA (protein-coding genes).

[Ashwin_s]

@Faizal_Ali

So does that mean humans evolved, but bacteria are being constantly created in new forms by a god?

Do you think that’s an intelligent question on your part?

[Faizal_Ali]

Yes.

Please answer. Then, the tricky part: If your answer is “No,”, show how this is compatible with your claim that evolved organisms must have large quantities of non-functional DNA and “designed” or “created” organisms must not.

If that is not your position, then explain why you have been writing things that strongly suggest it is.

Thanks in advance.

[Ashwin_s]

@Faizal_Ali

Please answer. Then, the tricky part: If your answer is “No,”, show how this is compatible with your claim that evolved organisms must have large quantities of non-functional DNA and “designed” or “created” organisms must not.

There is a paper published by evolutionary biologist Dan fraud which calculates the percentage of genes which are functional in the human genome as 25 % max. This is based on

1. The assumption that mutations are random and hence most mutations are neutral/deleterious.
2. Deleterious mutations are selected against. The higher the percentage of functional genes, the more the chances for a mutation to be deleterious and this the no: of viable off spring decreases.

This is a prediction based on evolutionary theory. So if it turns out to be wrong, then it’s a problem for the theory.

I don’t remember making any point about designed organism and how much non functional information they can have.

[Faizal_Ali]

@Ashwin_s

This is a prediction based on evolutionary theory. So if it turns out to be wrong, then it’s a problem for the theory.

No. As I have already mentioned, there are organisms with next to no Junk DNA. These pose no challenge to the theory of evolution.

The research you are citing, if I understand correctly, is based on the observed mutation rates, and how much of the genome can be functional in order to tolerate a given number of mutations without leading to mutational meltdown (The figure varies with the proportion of mutations that are assumed to be deleterious). This is independent of the theory of evolution, and could equally apply to a situation in which humans were specially created by God with genomes that are prone to mutation.

Also, this is not quite correct:

@Ashwin_s

There is a paper published by evolutionary biologist Dan fraud which calculates the percentage of genes which are functional in the human genome as 25 % max.

100% of genes are functional, by definition.

Who is “Dan fraud”, BTW? Perhaps you were thinking of “Dan Freud”, as in Freudian slip?

[Ashwin_s]

@Faizal_Ali

The research you are citing, if I understand correctly, is based on the observed mutation rates, and how much of the genome can be functional in order to tolerate a given number of mutations without leading to mutational meltdown. This is independent of the theory of evolution.

It’s not. You can track and read the paper.

@Faizal_Ali

Who is “Dan fraud”, BTW? Perhaps you were thinking of “Dan Freud”, as in Freudian slip?

No, that was Google correcting my spelling… it seems to think Graur us spelled better as fraud.

Edit: I think I typed fraur instead of Graur… and ended up with fraud.

[Faizal_Ali]

@Ashwin_s

It’s not. You can track and read the paper.

If this is the paper (and I am pretty sure it is), you are wrong. You did not understand what you read. Thankfully, there are many people in addition to myself who do understand it and can explain it to you better than I just tried to.

An Upper Limit on the Functional Fraction of the Human Genome

[Faizal_Ali]

I edited my earlier post while you were responding so you might have missed this: Graur’s argument would apply equally well if humans has been specially created by God with genomes that are prone to mutations.

[Ashwin_s]

@Faizal_Ali

If this is the paper (and I am pretty sure it is), you are wrong. You did not understand what you read. Thankfully, there are many people in addition to myself who do understand it and can explain it to you better than I just tried to.

If you think the paper has nothing to do with the theory of evolution, then you are wrong.

[Faizal_Ali]

See my last comment above.

[Mercer (John Mercer)]

@Ashwin_s

If you think the paper has nothing to do with the theory of evolution, then you are wrong.

Please explain why you reached that conclusion.

Also, you are grossly misrepresenting what @Faizal_Ali wrote, which was:

@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 hope that your misrepresentation was not deliberate…

[Mercer (John Mercer)]

@Ashwin_s

So does that mean humans evolved, but bacteria are being constantly created in new forms by a god?

Do you think that’s an intelligent question on your part?

It follows logically from your hypothesis, does it not?

[John_Harshman]

@Ashwin_s

There is a paper published by evolutionary biologist Dan fraud

What is this paper, and who is “Dan fraud”, which seems like an unfortunate name?

@Ashwin_s

This is a prediction based on evolutionary theory.

No, it’s based on observation. And note that the only evolution involved here, if you want to call it evolution, is mutation and selection within species. That’s the sort of thing that creationists generally claim to accept. What’s your alternative? Do you think that God actively curates our genomes to prevent deleterious mutations from happening? If so, then why do we observe so many deleterious mutations in non-junk DNA? Does he only prevent deleterious mutations in supposed junk DNA? And how do you fit so many non-deleterious mutations, around 100 per person, into all those functional sequences?

[Ashwin_s]

@Mercer

Please explain why you reached that conclusion.

Also, you are grossly misrepresenting what @Faizal_Ali wrote, which was:

@Faizal_Ali wrote as below-

@Ashwin_s

The research you are citing, if I understand correctly, is based on the observed mutation rates, and how much of the genome can be functional in order to tolerate a given number of mutations without leading to mutational meltdown. This is independent of the theory of evolution.

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.

@Mercer

I hope that your misrepresentation was not deliberate…

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

@Mercer

It follows logically from your hypothesis, does it not?

What is my hypothesis here exactly?
What you quoted was something @Faizal_Ali wrote.

Can you quote exactly what you are referring to?

[Ashwin_s]

@John_Harshman

No, it’s based on observation. And note that the only evolution involved here, if you want to call it evolution, is mutation and selection within species. That’s the sort of thing that creationists generally claim to accept. What’s your alternative? Do you think that God actively curates our genomes to prevent deleterious mutations from happening? If so, then why do we observe so many deleterious mutations in non-junk DNA? Does he only prevent deleterious mutations in supposed junk DNA? And how do you fit so many non-deleterious mutations, around 100 per person, into all those functional sequences?

My only point that finding function for larger percentages of the human genome would be a problem in light of these studies. The issues that could arise (as far as I understand) if larger parts of the genome have function are as below-

1. The evolutionary definition of function will have to cede ground to a definition based on whether the gene actually possess an useful function.

2. The classification of genes as “junk” itself might have to be relooked at.

[Ashwin_s]

@T_aquaticus

At some point, you will have to look at function in real terms. If most of the genome turns out to have some function (I am using the word here as it is used in English), then you will at the least have to redefine the word function in neutral theory… or perhaps explain why some useful traits are selected for while others (perhaps the vast majority) are not selected for.
Do you predict a vast difference between functions that are selected for vis a vis functions(english word again) that are useful to the organism. If not, I don’t see why you are protesting.

@John_Harshman… I have requoted my last comments on this subject above…
I don’t know where @Faizal_Ali got the creationist argument from.
And of course @Mercer jumped in without reading anything.

[John_Harshman]

@Ashwin_s

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

Is that your only point? Well, of course. Finding that large portions of the moon were made of Wensleydale would be a problem too. Do you expect either of these things to happen?

Now, if it did somehow turn out that most of the genome was functional, that would tell us that population genetic theory (not evolutionary theory, precisely) had some basic lack, somewhere. What do you suppose that lack could be? The only thing I can think of is what I proposed, that God (or something else) acts to prevent deleterious mutations from happening in the parts of the genome currently considered junk while freely allowing them in the parts currently considered functional. Does that seem like a reasonable hypothesis to you? If not, can you think of another? Or is considering the implications of your ideas not something you’re into?

[John_Harshman]

@Ashwin_s

I have requoted my last comments on this subject above…

I’m not sure what that is supposed to mean. If I speculate on its meaning, it seems to miss all the real potential points.

[Ashwin_s]

@John_Harshman

Now, if it did somehow turn out that most of the genome was functional, that would tell us that population genetic theory (not evolutionary theory, precisely) had some basic lack, somewhere. What do you suppose that lack could be? The only thing I can think of is what I proposed, that God (or something else) acts to prevent deleterious mutations from happening in the parts of the genome currently considered junk while freely allowing them in the parts currently considered functional. Does that seem like a reasonable hypothesis to you? If not, can you think of another? Or is considering the implications of your ideas not something you’re into?

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.
I don’t see why God would be the only explanation. I am sure people can make other hypothesis.

[Ashwin_s]

@John_Harshman

I’m not sure what that is supposed to mean. If I speculate on its meaning, it seems to miss all the real potential points.

Just read the thread if you are so interested. All I will say is that I was not proposing God directly working on mutations as a solution. I don’t know why you are harping on that point.