The Human Genome Is Still Mostly Junk

[Kenny]

`23w

**sigh**

You still can't address the evidence.

You have ignored the evidence... can't help you.

 

[Thermos aquaticus]

`23w

You have ignored the evidence... can't help you.

I addressed the evidence. Only a small portion of the genome is made up of satellite DNA. Finding function for a tiny portion of the junk DNA does not evidence all junk DNA having function. It's a simple concept.

 

[Kenny]

I addressed the evidence. Only a small portion of the genome is made up of satellite DNA. Finding function for a tiny portion of the junk DNA does not evidence all junk DNA having function. It's a simple concept.

So... let me just take it one step at a time...

At one point, did they use to believe that all Junk DNA was just that, junk?

And did they discover later, that some of the Junk DNA was actually needed and not really Junk?

 

[Thermos aquaticus]

At one point, did they use to believe that all Junk DNA was just that, junk?

They never believed that all non-coding DNA was junk, if that's what you mean.

And did they discover later, that some of the Junk DNA was actually needed and not really Junk?

They have found tiny bits and pieces of non-coding DNA that was once junk DNA but now think that it is functional DNA. We are talking a few percentage here and there, a tiny fraction of the 90% of the human genome thought to be junk. It's like finding one functioning TV in a massive landfill. Just because you find one functioning TV does not mean that everything in the landfill is functional.

 

[Kenny]

They never believed that all non-coding DNA was junk, if that's what you mean.

They have found tiny bits and pieces of non-coding DNA that was once junk DNA but now think that it is functional DNA. We are talking a few percentage here and there, a tiny fraction of the 90% of the human genome thought to be junk. It's like finding one functioning TV in a massive landfill. Just because you find one functioning TV does not mean that everything in the landfill is functional.

OK... so let me explain what I am saying:

"And then–like crossing the streams in Ghostbusters–junk DNA and non-coding DNA got mixed up. Sometimes scientists discovered a stretch of non-coding DNA that had a function. They might clip out the segment from the DNA in an egg and find it couldn’t develop properly. BAM!–there was a press release declaring that non-coding DNA had long been dismissed as junk, but lo and behold, non-coding DNA can do something after all."

http://phenomena.nationalgeographic.com/2014/05/09/the-case-for-junk-dna/

My point is that it is simply still "in flux" and we cannot arbitrarily or definitively say we completely know whether the junk is junk.... yet!!!

again:

"To Britten and Kohne, the idea that repeating DNA was useless was “repugnant.”Seemingly on aesthetic grounds, they preferred the idea that it had a function that hadn’t been discovered yet."

I think that is a wise position.

 

[Thermos aquaticus]

OK... so let me explain what I am saying:

"And then–like crossing the streams in Ghostbusters–junk DNA and non-coding DNA got mixed up. Sometimes scientists discovered a stretch of non-coding DNA that had a function. They might clip out the segment from the DNA in an egg and find it couldn’t develop properly. BAM!–there was a press release declaring that non-coding DNA had long been dismissed as junk, but lo and behold, non-coding DNA can do something after all."

http://phenomena.nationalgeographic.com/2014/05/09/the-case-for-junk-dna/

If I pointed to a busted up TV and said it was junk DNA, would you think that I was trying to say that all TV's are junk? It's the same thing hear. No one is saying that all non-coding DNA is junk. However, all junk DNA is non-coding since if it coded for a protein then it wouldn't be junk. Do you understand the differences?

My point is that it is simply still "in flux" and we cannot arbitrarily or definitively say we completely know whether the junk is junk.... yet!!!

No one is arbitrarily labeling DNA as junk. There is tons of evidence demonstrating that it is junk.

"To Britten and Kohne, the idea that repeating DNA was useless was “repugnant.”Seemingly on aesthetic grounds, they preferred the idea that it had a function that hadn’t been discovered yet."

I think that is a wise position.

And what you think is wrong, as shown by something as simply as mutational load.

• Genetic Load
  Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.

You can check out the science here:

"Let us now see what happens if we assume that 80% of the diploid human genome is functional, as was claimed by The ENCODE Project Consortium (2012). By using the lower bound for the deleterious mutation rate (4 × 10−10 mutations per nucleotide per generation), the mean individual fertility required to maintain a constant population size would be F = 7.14. For 80% of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce."
Upper Limit on the Functional Fraction of the Human Genome | Genome Biology and Evolution | Oxford Academic

This is just one piece of evidence out of many.

 

[Thermos aquaticus]

The problem of genetic load is one of the more compelling pieces of evidence for most of the human genome being junk. The most compelling piece of evidence, IMHO, is the lack of sequence conservation for the majority of the human genome.

If a stretch of DNA has function that depends on the sequence of bases within that stretch of DNA then there will be changes to that sequence which will remove that function. These are called deleterious mutations, and they are removed by natural selection since individuals with deleterious mutations tend to have fewer offspring than those without the deleterious mutation. Therefore, functional DNA sequences should change at a slower rate than non-functional DNA sequences because some of the mutations in functional DNA are removed over time. This is known as sequence conservation.

As it stands now, there is only evidence for sequence conservation in about 10% of the human genome (which is also in agreement with the argument from genetic load). If nearly 100% of the human genome is functional, then how is it that no mutation in these regions is deleterious? Anyone who argues for most of the human genome being functional needs to explain how deleterious mutations do not occur in 90% of the human genome or how DNA can be changed at any base without losing its function.

I don't see any way that 90% of the human genome keeps its function no matter how many changes are made to it. I have yet to see anyone who is able to address this evidence and still be able to support a human genome with nearly 100% function.

"A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect."
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. - PubMed - NCBI

 

[ScottySatan]

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.

Science is not so black and white.

I've heard a proposition to create a microbial cell without junk DNA. Synthetic Biology. It's extremely expensive to do and doesn't have enough funders to get the job done, because it has no immediate payback.

There are many ways to define what junk DNA means. The example above that I heard was to make a yeast strain with no introns and see what happens. You could also define it as intergenic spaces. You could also define it as non-coding spaces unbound by transcription factors. No one definition is "correct". Correctness depends on what you're interested in. Just like in physics, if you ask "what is the radius of a hydrogen atom?", the answer is really, "It depends, what aspect of the atom are you looking at?". Each definition (for genetics) is an important and impossibly expensive experiment with today's technology.

However, being scientists, we can't say what the purpose of junk DNA is in life unless we can see what life is like without it, by doing an experiment that removes it. With a possible exception for experiments like seeing what happens if you double the junk DNA. Until this happens, no one can say what junk DNA is for, if anything.

Historically, organisms stop producing energy intensive structures like billions of base-pairs of DNA per cell, with no purpose because it reduces fitness. So that junk DNA exists at all is a clue that it's there for a reason.

 

[Guy Threepwood]

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".

exactly

I am old enough to remember when ALL non coding DNA was still confidently declared 'junk', we have come a long way! But the 'junk' label lingers as an argument from the ever shrinking gaps. 'I still don't understand this part, so it must be pointless'

A caveman randomly extracting components from a modern car could make similar claims, it still drives just fine without the air bags!

But we are gaining an appreciation for DNA as being akin to a vast array of archives, sub routines, modules, applications, that can be called upon where and when needed, just as our own software, the implications of which can be a little uncomfortable in certain circles.

 

[Subduction Zone]

exactly

I am old enough to remember when ALL non coding DNA was still confidently declared 'junk', we have come a long way! But the 'junk' label lingers as an argument from the ever shrinking gaps. 'I still don't understand this part, so it must be pointless'

A caveman randomly extracting components from a modern car could make similar claims, it still drives just fine without the air bags!

But we are gaining an appreciation for DNA as being akin to a vast array of archives, sub routines, modules, applications, that can be called upon where and when needed, just as our own software, the implications of which can be a little uncomfortable in certain circles.

How is 20% tops of noncoding DNA having even the least of functions "coming a long way"?

Of course creationists still can't answer why the genome of an Amoeba can be one hundred times as long as man's:

Sizing up genomes: Amoeba is king

If there is no such thing as 'Junk DNA" then are you arguing that an amoeba's genome has one hundred times the information that a man's genome has?

 

[Thermos aquaticus]

I've heard a proposition to create a microbial cell without junk DNA. Synthetic Biology. It's extremely expensive to do and doesn't have enough funders to get the job done, because it has no immediate payback.

Luckily, nature has already done the experiment for us. The bladderwort genome is just 83 million bases large, but it has about the same gene content as the human genome which is 3,000 million bases large. The bladderwort genome is thought to be more than 95% functional with little to no junk, and the bladderwort does just fine.

Architecture and evolution of a minute plant genome

There are many ways to define what junk DNA means. The example above that I heard was to make a yeast strain with no introns and see what happens. You could also define it as intergenic spaces. You could also define it as non-coding spaces unbound by transcription factors. No one definition is "correct". Correctness depends on what you're interested in. Just like in physics, if you ask "what is the radius of a hydrogen atom?", the answer is really, "It depends, what aspect of the atom are you looking at?". Each definition (for genetics) is an important and impossibly expensive experiment with today's technology.

The earliest examples of junk DNA I have seen are spacers between transcription units and pseudogenes. From the start the concept of junk DNA was DNA you could throw away without impacting the fitness of the organism. That still ties in well with current views, as well as current methods such as sequence conservation.

However, being scientists, we can't say what the purpose of junk DNA is in life unless we can see what life is like without it, by doing an experiment that removes it. With a possible exception for experiments like seeing what happens if you double the junk DNA. Until this happens, no one can say what junk DNA is for, if anything.

Why can't we use neutral drift as evidence for lack of function? If there is DNA sequence specific function then deleterious mutations should occur in that DNA and you should see evidence of negative selection (i.e. sequence conservation).

Historically, organisms stop producing energy intensive structures like billions of base-pairs of DNA per cell, with no purpose because it reduces fitness. So that junk DNA exists at all is a clue that it's there for a reason.

What is the energy budget for DNA replication? I suspect it makes up a very, very tiny percentage of energy consumption in the cell. RNA Transcription far, far outweighs DNA replication. Protein translation is also energy intensive and will far outweigh DNA replication. This is before we get to actual cellular activity, such as muscle contractions. I highly doubt there is any selective pressure for decreasing the size of genomes down to the bare minimum in most species.

The one interesting case is the bladderwort. It lives in phosphorous poor environments which would put selective pressure on phosphorous conservation, not necessarily energy conservation. Therefore, a smaller genome may be preferred in those cases.

 

[Thermos aquaticus]

exactly

I am old enough to remember when ALL non coding DNA was still confidently declared 'junk', we have come a long way!

That was never the case.

But the 'junk' label lingers as an argument from the ever shrinking gaps. 'I still don't understand this part, so it must be pointless'

That's not what is going on. We understand what is happening in DNA which is why we conclude that it is junk. We know that transposons copy themselves and produce new copies in the genome. They are junk. We know that genes which are no longer needed accumulate knockout mutations which results in pseudogenes. We know that about 90% of the human genome is accumulating mutations at a rate consistent with neutral drift. This is positive evidence for DNA being junk, and no scientist is arguing that DNA must be junk because we don't know anything about it.

But we are gaining an appreciation for DNA as being akin to a vast array of archives, sub routines, modules, applications, that can be called upon where and when needed, just as our own software, the implications of which can be a little uncomfortable in certain circles.

What are you talking about?

 

[Audie]

Luckily, nature has already done the experiment for us. The bladderwort genome is just 83 million bases large, but it has about the same gene content as the human genome which is 3,000 million bases large. The bladderwort genome is thought to be more than 95% functional with little to no junk, and the bladderwort does just fine.

Architecture and evolution of a minute plant genome



The earliest examples of junk DNA I have seen are spacers between transcription units and pseudogenes. From the start the concept of junk DNA was DNA you could throw away without impacting the fitness of the organism. That still ties in well with current views, as well as current methods such as sequence conservation.



Why can't we use neutral drift as evidence for lack of function? If there is DNA sequence specific function then deleterious mutations should occur in that DNA and you should see evidence of negative selection (i.e. sequence conservation).



What is the energy budget for DNA replication? I suspect it makes up a very, very tiny percentage of energy consumption in the cell. RNA Transcription far, far outweighs DNA replication. Protein translation is also energy intensive and will far outweigh DNA replication. This is before we get to actual cellular activity, such as muscle contractions. I highly doubt there is any selective pressure for decreasing the size of genomes down to the bare minimum in most species.

The one interesting case is the bladderwort. It lives in phosphorous poor environments which would put selective pressure on phosphorous conservation, not necessarily energy conservation. Therefore, a smaller genome may be preferred in those cases.

I wonder if some of the junk DNA hangs in there, even if it costs something
to keep it going, because it is 'smart enough" to make sure it gets copied.

You can guess I am not a geneticist.

 

[Audie]

That was never the case.



That's not what is going on. We understand what is happening in DNA which is why we conclude that it is junk. We know that transposons copy themselves and produce new copies in the genome. They are junk. We know that genes which are no longer needed accumulate knockout mutations which results in pseudogenes. We know that about 90% of the human genome is accumulating mutations at a rate consistent with neutral drift. This is positive evidence for DNA being junk, and no scientist is arguing that DNA must be junk because we don't know anything about it.



What are you talking about?

(I think he is talking about computers)

 

[Thermos aquaticus]

I wonder if some of the junk DNA hangs in there, even if it costs something
to keep it going, because it is 'smart enough" to make sure it gets copied.

There is DNA that copies itself and then inserts those copies elsewhere in the genome. These are called transposons. A few may end up close to genes and alter gene expression, but the vast majority of transposon insertions are simply selfish DNA whose sole function is to make more copies of itself. Transposons make up nearly half of the human genome.

 

[Audie]

There is DNA that copies itself and then inserts those copies elsewhere in the genome. These are called transposons. A few may end up close to genes and alter gene expression, but the vast majority of transposon insertions are simply selfish DNA whose sole function is to make more copies of itself. Transposons make up nearly half of the human genome.

Hm, ok so my guess makes sense, they exist as parasites.

 

[Thermos aquaticus]

Hm, ok so my guess makes sense, they exist as parasites.

Many scientists have described transposons as parasites, so give yourself a gold star.

 

[whirlingmerc]

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.

Actually what is called junk is just things that the use isn't discovered yet
same with so called vestigial organs

There is all kinds of purpose one being error checking

“Junk” DNA Is Not “Junk”
“Junk” DNA Is Not “Junk”
by Dr. David A. DeWitt on June 26, 2012

 

[Subduction Zone]

Actually what is called junk is just things that the use isn't discovered yet
same with so called vestigial organs

There is all kinds of purpose one being error checking

You do not seem to even understand what a vestigial organ is. The appendix is still a vestigial organ.

 

[Thermos aquaticus]

Actually what is called junk is just things that the use isn't discovered yet
same with so called vestigial organs

Already covered this several times. If junk DNA had sequence specific function then there would be evidence of sequence conservation. That evidence isn't there. We know that it is junk DNA because of what we have discovered, not because of a lack of discoveries.

Also, vestigial organs are still vestigial. Finding rudimentary or secondary functions does not change the fact that they lack other functions. The human appendix does not help us digest cellulose, as one example. That is why it is vestigial.