Junk DNA Lives

And takes a sledgehammer to creationist assertions ...

Incl. intelligent design, belief in divine creation

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Re: Junk DNA Lives

#21  Postby Rumraket » Jul 21, 2017 7:33 pm

DavidMcC wrote:
Rumraket wrote:David, have you ever wondered why you happen to end up in arguments like that so often?

I do not wonder, I think I know, because I am "big, bad dave", ever since I accused the site of having more opinions than ideas. This dates from the rather pathetic acceptance by all on this site, except me of Harold White Jr's FTL starship theories (the guy who got a job at the prestigious JPL, by virtue of his dad's influence).
Now, naturally, there is no shortage of posters trying to draw me into a big row, in which they hope I will lose my cool, make a mistake, and then can be suspended or even banned.

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Re: Junk DNA Lives

#22  Postby juju7 » Jul 24, 2017 7:39 am

DavidMcC wrote:
Rumraket wrote:David, have you ever wondered why you happen to end up in arguments like that so often?

I do not wonder, I think I know, because I am "big, bad dave", ever since I accused the site of having more opinions than ideas. This dates from the rather pathetic acceptance by all on this site, except me of Harold White Jr's FTL starship theories (the guy who got a job at the prestigious JPL, by virtue of his dad's influence).
Now, naturally, there is no shortage of posters trying to draw me into a big row, in which they hope I will lose my cool, make a mistake, and then can be suspended or even banned.


Why would they want to do that?
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Re: Junk DNA Lives

#23  Postby GrahamH » Jul 24, 2017 9:15 am

Rumraket wrote:
GrahamH wrote:
Rumraket wrote:
GrahamH wrote:

My point is that the logic may be unsound. That doesn't need examples, and your vague recollection hardly counts, but thanks anyway.

You are right that with multiple levels of redundancy this could suppress the effects of otherwise deleterious mutations. But that's a lot of DNA wasted on "redundancy", and it doesn't explain the so-called c-value paradox.

Whether redundancy is a waste comes down to it's effect on reproductive fitness, does it not? Generally redundant systems are more reliable than non-redundant systems and could therefre potentially have higher fitness. I don't think it can be called 'junk'. On that basis most digital communications and storage media have large amounts of 'junk data' because they use redundancy to achieve reliable transmission. But reliability is functional and the 'junk' is there by design to serve a purpose. You can scratch a CD and find it stills plays but that doesn't mean the bits the scratch obliterates were 'junk'. If we take playability as a metaphor for reproductive fitness can't we see redundancy as a potentially selectable trait?

Yes, and there are systems with redundancy known from biology, but it is a problem of scale. Natural selection could simply not maintain it at the level of extra DNA observed in most organisms, this is what the math shows.

Imagine you had eleven thousand redundant copies of the same gene, but only one of them is ever required at any single moment. And it's a functional gene.
What would happen if we speed up time? Genome is replicated, chances are one of those genes gets a mutation. But would natural selection remove that mutation? Probably not, after all, there are 10.999 gene copies left to take over it's function. That mutation would probably be entirely invisible to selection. Next generation, what happens? Same thing again. Another mutation creeps in. Would natural selection remove it? Probably not, there are 10.998 remaining functional copies that could take over. And so on and so forth. You would probably end up with over 10.990 junk-genes deactivated by deleterious mutations. Natural selection simply can't preserve all those genes if they don't all see active use. And they'd only see use if all the other ones are rendered nonfunctional or have significantly degraded functions, or if there is some extreme demand on the level of gene expression.

Now there are cases where having many copies of a gene is actually beneficial, because they all see use. One example is, IIRC, the ribosome which exists in some species in up to 700 copies (and that is the highest number known for any functional gene). But that's only because the ribosome is seeing constant use, and having a single gene for it would simply not allow enough expression of that single gene for enough new ribosomes to be biosynthetized.


I wasn't aware that 'junk DNA' being discussed was anything like 'eleven thousand redundant copies of the same gene'. I was thinking more of a few copies of thousands of genes, or possibly different collections of genes that had comparable phenotypic effects. To stretch the metaphor, we might not see how four byte sequenced encoded on a CD relate to musical notes or phrases, or how other different bytes contribute redundant error correction, but none of those bytes are 'junk'. We could delete or alter lots of bytes and detect no impact on the sound. That is not a valid test for junk data in that case. Is a selection process applied at the level of sound produced it would tend to preserve the CDs with redundancy rather than those without in real-world conditions with non-zero error rates.

Thanks for your replies.
Anyway,
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Re: Junk DNA Lives

#24  Postby Rumraket » Jul 24, 2017 10:05 am

To pick a really extreme example, there are over one million ALU insertions in the human genome, for example. They're old copies of the gene for 7SL RNA.

A tiny fraction of these are known to be functional as transcription factors for known genes. Another small fraction are implicated in disease because of their effect on trancription some times causes them to mess up normal gene expression (usually because mutations have made them "active" again after having previously deactivated to deleterious mutations). The vast majority are degraded retrotransposons.

I think what you're missing is that we actually have a pretty good estimate of the fraction of mutations that are deleterious, as in cause a reduction in fitness. With this variable in hand (and others such as mutation rate, genome size, population size and average fecundity) it can actually be calculated how big the mutational load will be from deleterious mutations, which in turn will tell us how big a fraction of the genome can be functional.

What I've been trying to get across is that even if we disregard the math, we can see on the actual DNA what kinds of genetic elements our genome consists of, and it is consistent with the results implied by genetic load calculations.
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Re: Junk DNA Lives

#25  Postby GrahamH » Jul 24, 2017 10:10 am

Rumraket wrote:To pick a really extreme example, there are over one million ALU insertions in the human genome, for example. They're old copies of the gene for 7SL RNA.

A tiny fraction of these are known to be functional as transcription factors for known genes. Another small fraction are implicated in disease because of their effect on trancription some times causes them to mess up normal gene expression (usually because mutations have made them "active" again after having previously deactivated to deleterious mutations). The vast majority are degraded retrotransposons.

I think what you're missing is that we actually have a pretty good estimate of the fraction of mutations that are deleterious, as in cause a reduction in fitness. With this variable in hand (and others such as mutation rate, genome size, population size and average fecundity) it can actually be calculated how big the mutational load will be from deleterious mutations, which in turn will tell us how big a fraction of the genome can be functional.

What I've been trying to get across is that even if we disregard the math, we can see on the actual DNA what kinds of genetic elements our genome consists of, and it is consistent with the results implied by genetic load calculations.


Got it and thanks again. My point was only ever a very narrow one and you have provided a good explanation of the wider context. :thumbup:
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Re: Junk DNA Lives

#26  Postby DavidMcC » Jul 24, 2017 11:38 am

Rumraket wrote:
GrahamH wrote:
Rumraket wrote:
GrahamH wrote:

My point is that the logic may be unsound. That doesn't need examples, and your vague recollection hardly counts, but thanks anyway.

You are right that with multiple levels of redundancy this could suppress the effects of otherwise deleterious mutations. But that's a lot of DNA wasted on "redundancy", and it doesn't explain the so-called c-value paradox.

Whether redundancy is a waste comes down to it's effect on reproductive fitness, does it not? Generally redundant systems are more reliable than non-redundant systems and could therefre potentially have higher fitness. I don't think it can be called 'junk'. On that basis most digital communications and storage media have large amounts of 'junk data' because they use redundancy to achieve reliable transmission. But reliability is functional and the 'junk' is there by design to serve a purpose. You can scratch a CD and find it stills plays but that doesn't mean the bits the scratch obliterates were 'junk'. If we take playability as a metaphor for reproductive fitness can't we see redundancy as a potentially selectable trait?

Yes, and there are systems with redundancy known from biology, but it is a problem of scale. Natural selection could simply not maintain it at the level of extra DNA observed in most organisms, this is what the math shows.

Imagine you had eleven thousand redundant copies of the same gene, but only one of them is ever required at any single moment. And it's a functional gene.
What would happen if we speed up time? Genome is replicated, chances are one of those genes gets a mutation. But would natural selection remove that mutation? Probably not, after all, there are 10.999 gene copies left to take over it's function. That mutation would probably be entirely invisible to selection. Next generation, what happens? Same thing again. Another mutation creeps in. Would natural selection remove it? Probably not, there are 10.998 remaining functional copies that could take over. And so on and so forth. You would probably end up with over 10.990 junk-genes deactivated by deleterious mutations. Natural selection simply can't preserve all those genes if they don't all see active use. And they'd only see use if all the other ones are rendered nonfunctional or have significantly degraded functions, or if there is some extreme demand on the level of gene expression.

Now there are cases where having many copies of a gene is actually beneficial, because they all see use. One example is, IIRC, the ribosome which exists in some species in up to 700 copies (and that is the highest number known for any functional gene). But that's only because the ribosome is seeing constant use, and having a single gene for it would simply not allow enough expression of that single gene for enough new ribosomes to be biosynthetized.

Rumraket, I'm sure you know this, but a ribosome is not a gene! Nor is it a single RNA, expressed by a gene. Rather, it is a complex of several RNAs (and a few proteins):
https://en.wikipedia.org/wiki/Ribosome

Ribosome
From Wikipedia, the free encyclopedia
The ribosome (/ˈraɪbəˌsoʊm, -boʊ-/[1]) is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules. Ribosomes consist of two major components: the small ribosomal subunit, which reads the RNA, and the large subunit, which joins amino acids to form a polypeptide chain. Each subunit is composed of one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.
...

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Re: Junk DNA Lives

#27  Postby Calilasseia » Jul 24, 2017 4:05 pm

Actually, the ribosome is itself the product of gene expression, viz:

The rRNA is transcribed, at a high speed, in the nucleolus, which contains all 45S rRNA genes. The only exception is the 5S rRNA which is transcribed outside the nucleolus.


The above applies to eukaryotes. A related (but in detail, substantively different) mechanism performs the task in prokaryotes.

In the case of eukaryotes, we have this exposition:

In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats; in humans approximately 300–400 repeats are present in five clusters (on chromosomes 13, 14, 15, 21 and 22). Because of their special structure and transcription behaviour, rRNA gene clusters are commonly called "ribosomal DNA" (note that the term seems to imply that ribosomes contain DNA, which is not the case).


The point being made in Rumraket's post, is that many copies of the genes encoding for ribosome components exist. Because of the ubiquity of ribosome usage, having many copies of the genes in question allows for mass production of ribosomes, that would not be possible if only one copy of the genes in question were present. Moreover, because all of those genes are in use, and are frequently essential, they tend to be subject to purifying selection, hence the high degree of conservation thereof across lineages. Though gene deletion experiments in various model organisms have alighted upon some that are apparently non-essential, the majority are essential, and deletion of those genes is invariably lethal.
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Re: Junk DNA Lives

#28  Postby Macdoc » Jul 24, 2017 4:17 pm

Where would that lethality show up ....

Prior to conception?

After conception??

Both?
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Re: Junk DNA Lives

#29  Postby Rumraket » Jul 24, 2017 6:38 pm

DavidMcC wrote:Rumraket, I'm sure you know this, but a ribosome is not a gene!

Yes I should have written that genes encoding ribosomal RNA and proteins exist in many copies. And the highest I've heard of is 700 for one of the proteins IIRC.

Any particular cell might contain millions of ribosomes at any point in time. Which is one of the reasons so many genes encoding ribosomal components are required, because those millions of ribosomes are all constantly in use, and they break down and need to be replaced. So the genes that encode the components of ribosomes can't be transcribed and translated fast enough to replace the rate of breaking down ribosomes if there was only one.
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Re: Junk DNA Lives

#30  Postby Rumraket » Jul 24, 2017 6:39 pm

Calilasseia wrote:Actually, the ribosome is itself the product of gene expression, viz:

The rRNA is transcribed, at a high speed, in the nucleolus, which contains all 45S rRNA genes. The only exception is the 5S rRNA which is transcribed outside the nucleolus.


The above applies to eukaryotes. A related (but in detail, substantively different) mechanism performs the task in prokaryotes.

In the case of eukaryotes, we have this exposition:

In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats; in humans approximately 300–400 repeats are present in five clusters (on chromosomes 13, 14, 15, 21 and 22). Because of their special structure and transcription behaviour, rRNA gene clusters are commonly called "ribosomal DNA" (note that the term seems to imply that ribosomes contain DNA, which is not the case).


The point being made in Rumraket's post, is that many copies of the genes encoding for ribosome components exist. Because of the ubiquity of ribosome usage, having many copies of the genes in question allows for mass production of ribosomes, that would not be possible if only one copy of the genes in question were present. Moreover, because all of those genes are in use, and are frequently essential, they tend to be subject to purifying selection, hence the high degree of conservation thereof across lineages. Though gene deletion experiments in various model organisms have alighted upon some that are apparently non-essential, the majority are essential, and deletion of those genes is invariably lethal.

Yes exactly.
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Re: Junk DNA Lives

#31  Postby Rumraket » Jul 24, 2017 6:45 pm

Macdoc wrote:Where would that lethality show up ....

Prior to conception?

After conception??

Both?

That can't really be said without knowing the extent of the damage to ribosomal biosynthesis. Functional cells could probably persist and divide with a very low level, but they could not go on to build large multicellular organisms as these would detoriate faster than new cells could be made to replace dying cells.

So it could really be anywhere between lethal at binary fission (as in the offspring cell at cell division cannot live because it can never produce enough proteins to replace those that break down from wear and tear), to only showing up as a genetic disease that results in decreased healing and growth abilities in developing and maturing multicellular organisms.
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Re: Junk DNA Lives

#32  Postby Macdoc » Jul 24, 2017 8:12 pm

I would yhink the major choke points are in order of frequency due to numbers

Viable sperm

Viable egg

Viable zygote...

My point being those filters have to catch an awfully high percentage of the "defects".
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Re: Junk DNA Lives

#33  Postby Wortfish » Jul 25, 2017 4:19 pm

Manticore wrote:How can you read it from a creationist perspective when it contains maths and words with more than three syllables?


The mutational load problem has, ironically, been used by creationists to try and show that evolution cannot work. This paper may show that a maximum limit of 25% of the genome has a bearing on the phenotype but it can't show that 75% of the genome is junk. There may be vast swathes of the genome that are functional but relatively unaffected by mutation or which is functionally redundant.
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Re: Junk DNA Lives

#34  Postby Rumraket » Jul 25, 2017 9:20 pm

Wortfish wrote:
Manticore wrote:How can you read it from a creationist perspective when it contains maths and words with more than three syllables?


The mutational load problem has, ironically, been used by creationists to try and show that evolution cannot work. This paper may show that a maximum limit of 25% of the genome has a bearing on the phenotype but it can't show that 75% of the genome is junk. There may be vast swathes of the genome that are functional but relatively unaffected by mutation or which is functionally redundant.

It is true some have tried to bring up so-called "spacer DNA" or "bulk DNA" hypotheses, which circumvent the mutational load argument by arguing it is the length of sequence that matters, not the sequence itself (so it can mutate all it wants, as long as there's enough of it the sequence doens't matter).

For those arguments, there are the c-value paradox and the onion test.

It is not that any particular pro-junk-DNA argument can't be rationalized away with some ad-hoc hypothesis, but it is the totality of the evidence for junk, that shows it really is junk.
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Re: Junk DNA Lives

#35  Postby Wortfish » Aug 02, 2017 1:24 pm

Rumraket wrote:
It is not that any particular pro-junk-DNA argument can't be rationalized away with some ad-hoc hypothesis, but it is the totality of the evidence for junk, that shows it really is junk.


We know only 5% of the genome is conserved by selection but for the other 95% the sequence itself may not be so important. I find it totally plausible that sequence spacers allow transcription factors to avoid colliding with each other and causing congestion.
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Re: Junk DNA Lives

#36  Postby Rumraket » Aug 02, 2017 6:32 pm

Wortfish wrote:I find it totally plausible that...

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Re: Junk DNA Lives

#37  Postby Wortfish » Aug 04, 2017 5:11 pm

You may ask why it is that organisms that code for fewer transcription factors have less "junk" DNA.
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Re: Junk DNA Lives

#38  Postby Rumraket » Aug 05, 2017 10:06 am

Wortfish wrote:You may ask why it is that organisms that code for fewer transcription factors have less "junk" DNA.

I reject the premise outright.
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