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The Human Genome Is Still Mostly Junk

Thermos aquaticus

Well-Known Member
Before we can delve too far into the debate about how much of the human genome is functional we first have to define what we mean by functional. The first question we have to ask is if there is a difference between doing something and being functional.

For example, your heart does many things. Your heart makes sounds, it adds 300 g to your body weight, it keeps your pericardium from collapsing, it causes your left lung to be smaller, and it moves blood through your body. Would you say that all of those properties are functions of the heart? If your heart were not pumping blood through your body but it was still adding 300 g to your body weight, would it be correct to say that your heart was still functioning?

The answer to the last question will say a lot about what portion of the human genome has function. If DNA just does something, is that enough to say that it is functional?

The ENCODE consortium famously concluded that around 80% of the human genome has function, but what did they mean by functional? As it turned out, their definition of DNA being functional was equivalent to your heart having function because it adds 300 g to your body weight. The ENCODE consortium considered DNA functional if it was transcribed, bound transcription factors, bound histones, or was methylated along with some other less important factors. The problem is that these are just examples of DNA doing something. Junk also does stuff, but that doesn't make it functional in the same way moving blood makes a heart functional.

The real problem for the ENCODE consortium is only 10% or so of the genome is conserved. In other words, 90% of the human genome is accumulating mutations at a rate consistent with neutral drift. If there really is important function in 80% of the human genome, then how is it that 70% of that function doesn't change no matter how many mutations we add to it? That makes no sense.

If we look beyond humans we find that the size of genomes in closely related species can differ by several fold. More distantly related species also provide insight. The bladderwort genome is just 0.083 billion bases with genes taking up more than 95% of the total genome. The human is 3 billion bases with about the same number of genes as the bladderwort genome, yet both function just fine. The bladderwort genome has had all of its junk DNA removed, and it does just fine. The onion genome has 16 billion bases, 5 times that of the human genome, yet it is no more complex than humans. The pufferfish genome is just 0.4 billion bases, about a 7th of the human genome, yet they aren't any less complex than a human and have about the same number of genes. What gives?

The only conclusion that makes sense is that the vast majority, about 90%, of the human genome does not have a vital function that affects human fitness. 80% of the human genome may do something, but that doesn't mean it makes a difference to human fitness which is the definition of function that most people use.
 

Kenny

Face to face with my Father
Premium Member
The way I view it, "junk DNA" isn't the correct wording. Perhaps a better wording would be "Science doesn't know the value of the function yet so we are going to call it 'unknown function DNA"

Granted, not all of them are necessary to live. We know we can live with just one lung, one kidney, one arm and one leg. But I wouldn't call the pair of those part "junk parts". :D
 

Thermos aquaticus

Well-Known Member
The way I view it, "junk DNA" isn't the correct wording. Perhaps a better wording would be "Science doesn't know the value of the function yet so we are going to call it 'unknown function DNA"

Science does know that 90% of the human genome is accumulating mutations at a rate consistent with neutral drift which indicates that it does not have function that affects human fitness. We also know how transposons are produced in the genome, and it has nothing to do with human fitness, it just has to do with how transposons like to copy themselves and create more insertions.

It isn't called junk because we don't know what it does. It is called junk because we do know what it does.

Granted, not all of them are necessary to live. We know we can live with just one lung, one kidney, one arm and one leg. But I wouldn't call the pair of those part "junk parts". :D

Would you say that the function of your arm is to add 15 lbs to your body weight?
 

Kenny

Face to face with my Father
Premium Member
Science does know that 90% of the human genome is accumulating mutations at a rate consistent with neutral drift which indicates that it does not have function that affects human fitness. We also know how transposons are produced in the genome, and it has nothing to do with human fitness, it just has to do with how transposons like to copy themselves and create more insertions.

It isn't called junk because we don't know what it does. It is called junk because we do know what it does.



Would you say that the function of your arm is to add 15 lbs to your body weight?
I'm not sure that everyone agrees with your position:

Scientific American: The ENCODE project has revealed a landscape that is absolutely teeming with important genetic elements—a landscape that used to be dismissed as “junk DNA.” Were our old views of how the genome is organized too simplistic?

BIRNEY: People always knew there was more there than protein-coding genes. It was always clear that there was regulation. What we didn’t know was just quite how extensive this was.


I think my position is more plausible. After all, science continues to rediscover truths and adjusts accordingly.

Hidden Treasures in Junk DNA

Should we be retiring the phrase “junk DNA” now?
Yes, I really think this phrase does need to be totally expunged from the lexicon. It was a slightly throwaway phrase to describe very interesting phenomena that were discovered in the 1970s. I am now convinced that it’s just not a very useful way of describing what’s going on
 

Thermos aquaticus

Well-Known Member
I'm not sure that everyone agrees with your position:

The majority of geneticists do.

I think my position is more plausible. After all, science continues to rediscover truths and adjusts accordingly.

One of those discovered truths is that 90% of the human genome is accumulating mutations at a rate consistent with neutral drift which is very strong evidence that it is junk. 50% of the human genome is broken pseudogenes and transposons. We already know what the function of transposons is, to copy themselves and create more transposon insertions.



Finding a tiny bit of non-coding DNA that has function does not mean all non-coding DNA has function.
 

Kenny

Face to face with my Father
Premium Member
The majority of geneticists do.



One of those discovered truths is that 90% of the human genome is accumulating mutations at a rate consistent with neutral drift which is very strong evidence that it is junk. 50% of the human genome is broken pseudogenes and transposons. We already know what the function of transposons is, to copy themselves and create more transposon insertions.




Finding a tiny bit of non-coding DNA that has function does not mean all non-coding DNA has function.
But it did mean that what they used to call Junk is not longer Junk which leads to the "possibility" that maybe most of the rest of the genome may actually have a purpose if but to create the rest of the genome or some other use. Who would know for sure? Science certainly hasn't plumbed the depths of all the uses of the genome.
 

Thermos aquaticus

Well-Known Member
But it did mean that what they used to call Junk is not longer Junk . . .

It is still junk. Junk can do something and still be junk. Doing something is not the same as having function.

which leads to the "possibility" that maybe most of the rest of the genome may actually have a purpose if but to create the rest of the genome or some other use. Who would know for sure? Science certainly hasn't plumbed the depths of all the uses of the genome.

Nature would know if it had function. If it did have function then there would be conserved sequence.
 

Kenny

Face to face with my Father
Premium Member
It is still junk. Junk can do something and still be junk. Doing something is not the same as having function.



Nature would know if it had function. If it did have function then there would be conserved sequence.
Have at it, my friend.
 

Kenny

Face to face with my Father
Premium Member
Would you agree that some mutations in functional DNA would be detrimental?

Would you also agree that such detrimental mutations would be selected out of the population through natural selection?
Yes... Down's syndrome or jacobsen syndrome are both detrimental. Apparently they don't get selected out because they continue to happen.
 

tayla

My dog's name is Tayla
The only conclusion that makes sense is that the vast majority, about 90%, of the human genome does not have a vital function that affects human fitness.
I am surprised. I was under the impression that all this so-called junk DNA was used in DNA's role in controlling cell functioning and in utilizing DNA's instructions. I don't remember the terminology for all this.
 

Subduction Zone

Veteran Member
I am surprised. I was under the impression that all this so-called junk DNA was used in DNA's role in controlling cell functioning and in utilizing DNA's instructions. I don't remember the terminology for all this.
So far it appears that that was an over-statement. One must remember that the world of science is not perfect. The people behind Project ENCODE were looking for more funding, as research projects always are. They may have overstated their case just a little bit (in other words quite a bit).
 

Thermos aquaticus

Well-Known Member
Yes... Down's syndrome or jacobsen syndrome are both detrimental. Apparently they don't get selected out because they continue to happen.

If they weren't selected out then they would be as common as A type blood or any other common allele. Obviously, they aren't as common as what we consider to be harmless changes in DNA. Therefore, they are being selected against. That these mutations keep occurring spontaneously does nothing to change the fact that they are selected against once these mutations do occur.

It seems that you don't understand how selection works.
 

Thermos aquaticus

Well-Known Member
I am surprised. I was under the impression that all this so-called junk DNA was used in DNA's role in controlling cell functioning and in utilizing DNA's instructions. I don't remember the terminology for all this.

That is a false impression created by people who want to give a false impression. Some people will use the terms "non-coding DNA" and "junk DNA" interchangeably, as if they are the same thing. They aren't the same thing. Non-coding DNA can be broken up into functional and non-functional (i.e. junk) DNA. Even some coding DNA is junk since not all proteins derived from DNA have function.

It is important to remember that junk DNA refers to stretches of DNA that do not affect fitness. DNA that is transcribed into RNA or even translated into proteins can still be junk. DNA that binds transcription factors can still be junk if that binding does not affect fitness.
 

Twilight Hue

Twilight, not bright nor dark, good nor bad.
That is a false impression created by people who want to give a false impression. Some people will use the terms "non-coding DNA" and "junk DNA" interchangeably, as if they are the same thing. They aren't the same thing. Non-coding DNA can be broken up into functional and non-functional (i.e. junk) DNA. Even some coding DNA is junk since not all proteins derived from DNA have function.

It is important to remember that junk DNA refers to stretches of DNA that do not affect fitness. DNA that is transcribed into RNA or even translated into proteins can still be junk. DNA that binds transcription factors can still be junk if that binding does not affect fitness.
Wouldn't "junk" dna be regarded as random givin it can be broken up and used?
 

Thermos aquaticus

Well-Known Member
Wouldn't "junk" dna be regarded as random givin it can be broken up and used?

Pseudogenes are junk DNA, but they can have non-random features like we see in genes. Transposons are definitely non-random since they have repetitive DNA that is easily detected by algorithms, but they are still junk. Junk DNA can accumulate mutations to the point where it doesn't have any signatures that we would recognize, but it isn't a requirement for DNA to be junk.

As to being "broken up and used", I'm not sure what you are referring to.
 

Twilight Hue

Twilight, not bright nor dark, good nor bad.
Pseudogenes are junk DNA, but they can have non-random features like we see in genes. Transposons are definitely non-random since they have repetitive DNA that is easily detected by algorithms, but they are still junk. Junk DNA can accumulate mutations to the point where it doesn't have any signatures that we would recognize, but it isn't a requirement for DNA to be junk.

As to being "broken up and used", I'm not sure what you are referring to.
I just wanted a little clarification on non coding dna per your post 16, but I see now what you said there. I read the post wrong.
 
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