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Author Topic:   Molecular Population Genetics and Diversity through Mutation
Genomicus
Member (Idle past 400 days)
Posts: 852
Joined: 02-15-2012


Message 181 of 455 (785560)
06-07-2016 7:12 AM
Reply to: Message 180 by Faith
06-07-2016 3:07 AM


Re: Mt DNA and microsatellites as measures of genetic diversity
I know you don't like Wikipedia but here it comes...

Wikipedia isn't exactly a scholarly source. Anyway, here's Clark et al. who use single-nucleotide polymorphisms (= nucleotide diversity) as a measure of genetic diversity. Please don't cite Wikipedia when it comes to definitional terms as there is a robust scientific literature on the different ways of measuring genetic diversity.


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 Message 180 by Faith, posted 06-07-2016 3:07 AM Faith has not yet responded

  
herebedragons
Member (Idle past 190 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


(2)
Message 182 of 455 (785569)
06-07-2016 8:41 AM
Reply to: Message 180 by Faith
06-07-2016 3:07 AM


Re: Mt DNA and microsatellites as measures of genetic diversity
I appreciate your previous reply to me and I plan to go back and answer some of those questions, but I am at a conference this week and don't think I will have time to do so until the weekend. But I wanted to touch on a couple things in this post real quick (I hope)

Pretty standard definition here. Polymorphic loci, many alleles per locus I take into account as a matter of fact as where most loss of genetic diversity occurs; Heterozygosity, alleles per locus, exactly what I've been talking about.

True genetic diversity would need to be measured over the entire genome, not at just a few loci. Currently this is just not possible to do. So we need a measure - a proxy of genetic diversity. Heterozygosity is one proxy that is used for overall genetic diversity, but it needs to specify what loci it is measuring and then all it can really say is the amount of heterogeneity at those loci. If those loci are chosen properly, then it can represent the genetic diversity of the entire genome, but it is not the actual, true diversity.

Think about it... let's say an organism has 20,000 gene loci and 100 of them are fixed (homogeneous) while the remaining 19,900 are polymorphic (heterogeneous) - that's the true situation (but you don't really know this - it is what you are testing for). Now you choose 4 nDNA (nuclear DNA) loci that determine key characteristic traits of said organism and find that they are all monomorphic (homogeneous). What does that say about the genetic diversity of the organism?

Interesting that there's no mention here of MtDNA or microsatellites either.

Wikipedia is fine for general information or as a general reference, but it doesn't trump actual scientific articles. The journal article cited used mtDNA as a measure of genetic diversity, the fact that Wikipedia fails to mention that as a suitable measure does not make the use of mtDNA questionable. Can you cited a scientific article that questions the utility of using mtDNA as a proxy, or a measure, of genetic diversity?

These different measure of diversity tell us different things - they are not all measures of exactly the same thing. As my example above shows, even using nDNA can give misleading results. Understanding what the different measures tell you is key to understanding the results. I will try to come back to this point later (when this conference is over) and respond to your last reply to me.

Then it must agree with the normal ways of measuring genetic diversity or it's of no use anyway, and assuming it does agree I'll stick with heterozygosity and number of alleles per locus.

OK, you know what this sounds like? "I will stick with what agrees with me." Rather than that, you should try to understand how researchers use these different measures and what they mean.

Your reference on the elephant seals found high genetic diversity, which has to be some kind of delusion

Wrong. They did not find "high" genetic diversity. They found increasing genetic diversity. Big difference. The point of that citation was to illustrate that genetic diversity could increase despite isolation. Just because you don't accept mtDNA as valid is irrelevant. As I already pointed out, mtDNA diversity increasing while nDNA is not tells a story about what is going on with the population. The researchers were NOT suggesting that the population was not at risk because of low genetic diversity (however, northern elephant seals are not endangered they are on the 'Least Concern' list). Rather, they were studying the effects of a severe bottleneck and subsequent recovery. This same approach could be used to study the "flood bottleneck" right?

Or there's something wrong with the study

You don't make a case for that except to cite some facts that raise questions about it. Do you know or understand the data they analysed in order to come to that conclusion? Have you raised concerns about there methodology? No, you only doubt the study because the conclusions don't match what you think the conclusion should be. That is an insufficient reason to conclude "there's something wrong with the study."

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 180 by Faith, posted 06-07-2016 3:07 AM Faith has responded

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Faith
Member
Posts: 35154
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 183 of 455 (785582)
06-07-2016 11:40 AM
Reply to: Message 182 by herebedragons
06-07-2016 8:41 AM


Re: Mt DNA and microsatellites as measures of genetic diversity
Pretty standard definition here. Polymorphic loci, many alleles per locus I take into account as a matter of fact as where most loss of genetic diversity occurs; Heterozygosity, alleles per locus, exactly what I've been talking about.

True genetic diversity would need to be measured over the entire genome, not at just a few loci. Currently this is just not possible to do. So we need a measure - a proxy of genetic diversity. Heterozygosity is one proxy that is used for overall genetic diversity, but it needs to specify what loci it is measuring and then all it can really say is the amount of heterogeneity at those loci. If those loci are chosen properly, then it can represent the genetic diversity of the entire genome, but it is not the actual, true diversity.

Yes, but if it shows reduced genetic diversity at those loci, or even homozygosity, after all the steps I've been talking about have been completed: daughter population with new gene frequencies, reproductive isolation, some number of generations during which those frequencies are worked through and a pretty stable phenotype emerges -- the reasonable conclusion would be that this reduction in genetic diversity is genome-wide, because it's the gene frequencies themselves brought about by the reduced number of individuals, that leads to that reduction, and you aren't going to get different results of the same processes in different parts of the genome. Check a hundred or a few dozen loci that form the main characteristics of the species or breed, in as many breeds or species as possible. The pattern should hold up. Other parts of the genome code for more hidden elements in the species or breed, internal systems and organs perhaps. but it's the main characteristics that establish the breed or species as what it is, so looking at those loci should reveal the pattern in question.

Think about it... let's say an organism has 20,000 gene loci and 100 of them are fixed (homogeneous) while the remaining 19,900 are polymorphic (heterogeneous) - that's the true situation (but you don't really know this - it is what you are testing for). Now you choose 4 nDNA (nuclear DNA) loci that determine key characteristic traits of said organism and find that they are all monomorphic (homogeneous). What does that say about the genetic diversity of the organism?

The thing is if I'm right the entire genome has to undergo reduced genetic diversity because it's also a product of the reduced number of individuals and the consequent new gene frequencies same as the main traits. Loci with a great number of alleles are still going to lose some of those alleles; homozygosity isn't always going to be the proof of this trend, but reduction will be. One thing is certain: there won't be a general increase in the genome, there could only be a general decrease. Because the whole genome has to be affected by the same processes, not different parts of it.

Interesting that there's no mention here of MtDNA or microsatellites either.

Wikipedia is fine for general information or as a general reference, but it doesn't trump actual scientific articles. The journal article cited used mtDNA as a measure of genetic diversity, the fact that Wikipedia fails to mention that as a suitable measure does not make the use of mtDNA questionable. Can you cited a scientific article that questions the utility of using mtDNA as a proxy, or a measure, of genetic diversity?

The writers for Wikipedia aren't babies in their field are they? Why would they leave out a common practice for assessing genetic diversity?

However, I'll provisionally take your word for it.

These different measure of diversity tell us different things - they are not all measures of exactly the same thing. As my example above shows, even using nDNA can give misleading results. Understanding what the different measures tell you is key to understanding the results. I will try to come back to this point later (when this conference is over) and respond to your last reply to me.

Yes, because it certainly remains inexplicable why you would choose a site that is known for accumulating mutations but has nothing to do with the genetic issues under discussion, doesn't even code for anything related to the discussion. But also I did defend the focus on heterozygosity above. More of the genome could be checked of course, even though a laborious undertaking, than just the characteristic traits of the organism, just to see if I'm right.

Then it must agree with the normal ways of measuring genetic diversity or it's of no use anyway, and assuming it does agree I'll stick with heterozygosity and number of alleles per locus.

OK, you know what this sounds like? "I will stick with what agrees with me." Rather than that, you should try to understand how researchers use these different measures and what they mean.

Well, efforts in that direction have yielded absolutely zip so far. Perhaps when you come back you'll do a better job of it. Meanwhile I KNOW heterozygosity measures the situation I'm talking about, and anything that contradicts it is suspect, to put it mildly. If you are going to try to convince me from MtDNA that the seals have increased genetic diversity I'm just going to wait for the reports of their going extinct.

Your reference on the elephant seals found high genetic diversity, which has to be some kind of delusion

Wrong. They did not find "high" genetic diversity. They found increasing genetic diversity. Big difference.

OK, but increasing genetic diversity is also delusional questionable.

The point of that citation was to illustrate that genetic diversity could increase despite isolation.

Yes, but this is some kind of joke if that diversity is increasing by useless mutations in a location that has absolutely nothing to do with the genetic problems the animal is facing, or even the benign loss of genetic diversity I keep describing as a result of population splits.

OK, OK, I'll TRY to think maybe there could be a reasonable explanation for this... Oy

Just because you don't accept mtDNA as valid is irrelevant.

This isn't just some bias of mine, I haven't yet seen the slightest reasonable explanation for using it.

As I already pointed out, mtDNA diversity increasing while nDNA is not tells a story about what is going on with the population. The researchers were NOT suggesting that the population was not at risk because of low genetic diversity (however, northern elephant seals are not endangered they are on the 'Least Concern' list). Rather, they were studying the effects of a severe bottleneck and subsequent recovery. This same approach could be used to study the "flood bottleneck" right?

So is Scientific American out to deceive the public by telling us the seals are genetically in bad shape?

I have yet to see any reason to think increasing diversity at MtDNA is anything more than accumulation of useless mutations. That's not genetic diversity. And that's a separate issue from how an increase in MtDNA could say anything at all about the losses of diversity we've been discussing all along.

Recovery of population isn't recovery of genetic diversity, as that Scientific American article made clear.

The genetic situation on the ark would have been enormously more diverse and variable than it is today after so many generations of population splits.

Did you read that article about the Jutland cattle by the way? There is concern by conservationists about farm animals in general, including cattle, because of hundreds of years of fragmentation, meaning population splits, and a growing number of extinctions of breeds.

Or there's something wrong with the study

You don't make a case for that except to cite some facts that raise questions about it. Do you know or understand the data they analysed in order to come to that conclusion? Have you raised concerns about there methodology? No, you only doubt the study because the conclusions don't match what you think the conclusion should be. That is an insufficient reason to conclude "there's something wrong with the study."

Sure, but it's a reasonable wild guess from where I sit that there's something weirdly wrong about using MtDNA, microsatellites and nucleotides to measure genetic diversity. I've gone from total inability to understand any of it to suspicions born of a bit of knowledge. Now I'm suspecting too much trust in the ToE as the cause of such a weirdness. But yes, this is just my own ponderings, you can ignore me for now, carry on.

Edited by Faith, : No reason given.


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Replies to this message:
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14174dm
Member
Posts: 155
From: Cincinnati OH
Joined: 10-12-2015


Message 184 of 455 (785587)
06-07-2016 12:16 PM
Reply to: Message 104 by New Cat's Eye
06-01-2016 10:24 PM


Re: Was Adam Human?
Stumbled across an old reply I thought I would poke at.

Do humans live 900 years?

I've always wondered if the long lives were due to genetics or lifestyle or environment or what.

I lean towards the very few long lived people listed in the bible were actually closer to God and he chose to allow them long life. Their names and ages are highlighted as special cases rather than the norm for the time.

Edited by 14174dm, : No reason given.


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Faith
Member
Posts: 35154
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 185 of 455 (785588)
06-07-2016 12:29 PM
Reply to: Message 184 by 14174dm
06-07-2016 12:16 PM


Why they lived longer then
Before the Fall all living things were immortal, human beings as well as animals. After the Fall all died, but not immediately. They still had a great deal of vitality in them that allowed them to live enormously long lives by our standards. Before the Flood the environment would also have contributed to their vitality. After the Flood the world was less hospitable to life, but it is sin that kills us and we inherit the propensity to sin and that's why we all die. After the Flood people still lived long lives by our standards but over time the length of life was shortened until God decreed a limit or average around seventy years. People may live much longer even now both because of good genes and because of living good lives.

Edited by Faith, : No reason given.


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NoNukes
Inactive Member


(2)
Message 186 of 455 (785589)
06-07-2016 1:05 PM
Reply to: Message 185 by Faith
06-07-2016 12:29 PM


Re: Why they lived longer then
Before the Fall all living things were immortal, human beings as well as animals. After the Fall all died, but not immediately.

So what was the 'Tree of Life'? Genesis 3:21 says that eating from the Tree of Life produces immortality and that after Adam sinned, that he must be prevented from eating from the tree of life. Given that Adam was originally allowed to eat from that tree, it seems that Adams immortality must have been bound up in eating from the tree.

As far as I can tell, there is no direct language about animals living forever, and I believe the idea that no animals died prior to the fall is doctrinal.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


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caffeine
Member
Posts: 1790
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 3.3


(2)
Message 187 of 455 (785593)
06-07-2016 3:13 PM
Reply to: Message 183 by Faith
06-07-2016 11:40 AM


Re: Mt DNA and microsatellites as measures of genetic diversity
Sure, but it's a reasonable wild guess from where I sit that there's something weirdly wrong about using MtDNA, microsatellites and nucleotides to measure genetic diversity. I've gone from total inability to understand any of it to suspicions born of a bit of knowledge. Now I'm suspecting too much trust in the ToE as the cause of such a weirdness. But yes, this is just my own ponderings, you can ignore me for now, carry on.

Whilst something completely different I stumbled across something relevant to this thread. The article was talking about testing the hypothesis of population bottlenecks by comparing heterozygosity and total allele diversity - the idea being that if the former was higher in proportion to the latter it implied a bottleneck. A reduction in population would eliminate rare alleles but not common ones; so heterozygosity may not be affected if there was more than one common allele, but total diversity would.

Ignoring whether this is a good test for a moment, the logic does make a good point that heterozygosity is not necessarily a good test of genetic diversity. Consider the two very small populations of five individuals below, with each pair of letters representing on diploid individual, and each different letter being a different allele:

Population 1:

AB AB AB AB AB

Population 2:

AC DB AE FG FH

Both populations are equally heterzygous at this locus, but population 2 is clearly much more genetically diverse.


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Faith
Member
Posts: 35154
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 188 of 455 (785597)
06-07-2016 4:25 PM
Reply to: Message 186 by NoNukes
06-07-2016 1:05 PM


Re: Why they lived longer then
So what was the 'Tree of Life'? Genesis 3:21 says that eating from the Tree of Life produces immortality and that after Adam sinned, that he must be prevented from eating from the tree of life. Given that Adam was originally allowed to eat from that tree, it seems that Adams immortality must have been bound up in eating from the tree.

Certainly must have had a part in sustaining their immortal life. We'll have the Tree of Life again in the New Jerusalem. Couldn't eat from it as sinners or we'd be immortal sinners, incapable of salvation. Not a good idea.

As far as I can tell, there is no direct language about animals living forever, and I believe the idea that no animals died prior to the fall is doctrinal.

Christian doctrine is always derived from the Bible, and I think animal immortality IS based on the Bible because the phrasing is "By one man sin entered the world, and death by sin." So it didn't exist at all in the world until then. It also wouldn't make sense for anything to die if all things were made good. But I know some believe animals died, mostly believing that because it fits with evolution though. I don't believe it myself but I'm not going to argue with you about it.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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Faith
Member
Posts: 35154
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 189 of 455 (785599)
06-07-2016 4:38 PM
Reply to: Message 187 by caffeine
06-07-2016 3:13 PM


Re: Mt DNA and microsatellites as measures of genetic diversity
I think Population 2 falls under the first of the three measures of genetic diversity I found at Wikipedia:

  • Gene Diversity is the proportion of polymorphic loci across the genome.
  • Heterozygosity is the fraction of individuals in a population that are heterozygous for a particular locus.
  • Alleles per locus is also used to demonstrate variability.

Polymorphous loci means many alleles per locus. A change in that number between populations is what you'd look for to check for increase or decrease. Not easy I suppose.


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Genomicus
Member (Idle past 400 days)
Posts: 852
Joined: 02-15-2012


Message 190 of 455 (785600)
06-07-2016 5:02 PM
Reply to: Message 189 by Faith
06-07-2016 4:38 PM


Re: Mt DNA and microsatellites as measures of genetic diversity
Just FYI, "polymorphic loci" also often refers to the nucleotide sequence variation among the alleles at a locus. Highly polymorphic loci have highly variable nucleotide sequences. This meaning of "polymorphic loci" goes way back to the dawn of the genomics revolution; see, e.g., this 1975 paper.

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Faith
Member
Posts: 35154
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 191 of 455 (785602)
06-07-2016 7:11 PM
Reply to: Message 190 by Genomicus
06-07-2016 5:02 PM


Re: Mt DNA and microsatellites as measures of genetic diversity
Just FYI, "polymorphic loci" also often refers to the nucleotide sequence variation among the alleles at a locus. Highly polymorphic loci have highly variable nucleotide sequences. This meaning of "polymorphic loci" goes way back to the dawn of the genomics revolution; see, e.g., this 1975 paper.

I looked, read the abstract. One thing you may need to know is that my eyes can't take much glare of white backgrounds, which is the reason I often don't read linked papers or only read small parts of them. It's always a big help if someone puts the gist of it into their own words. Just writing a post in this white box is hard on my eyes.

Abstract
It is possible to define a strategy for experimentally demonstrating that natural selection acts directly on a particular polymorphic locus, rather than on other loci in linkage disequilibrium with it.

It's an interesting proposal since I find it difficult to believe that natural selection could act on a single locus and not affect others, just because it usually works on the individual as a whole. But I won't be reading the paper to find out how they arrived at this conclusion. Also, the term "linkage disequilibrium" is one of those jargon terms that are meaningless to me. As is the rest of the abstract. Oh well.

However, I think I do get your statement that polymorphic loci refers to "nucleotide sequence variation among the alleles at a locus. Highly polymorphic loci have highly variable nucleotide sequences." I could be wrong I suppose but variation in the sequence would be expected from allele to allele, wouldn't it? I mean they are different and do different things. The only problem is when you've got a mutation that doesn't do anything instead of an allele that does. This is where the idea of nucleotide diversity loses me.

Edited by Faith, : No reason given.


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AdminAsgara
Administrator (Idle past 761 days)
Posts: 2073
From: The Universe
Joined: 10-11-2003


Message 192 of 455 (785603)
06-07-2016 7:39 PM
Reply to: Message 191 by Faith
06-07-2016 7:11 PM


quick off topic help
Faith, there is a Chrome extension called High Contrast that lets you change the view of the page. There is a normal setting, an increased contrast setting, grey scale, inverted color, inverted grey scale, and yellow on black. I'm sure you can find a setting you like for different applications. I found the inverted grey scale gives me light writing on a dark background. This might help you with reading some of the abstracts and papers being linked.

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 Message 191 by Faith, posted 06-07-2016 7:11 PM Faith has responded

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Faith
Member
Posts: 35154
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 193 of 455 (785604)
06-07-2016 7:40 PM
Reply to: Message 192 by AdminAsgara
06-07-2016 7:39 PM


Re: quick off topic help
That's good to know, thanks!

I've got some issues with Chrome I have to iron out first but that sounds like a great solution to this problem.


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NoNukes
Inactive Member


Message 194 of 455 (785605)
06-07-2016 8:00 PM
Reply to: Message 188 by Faith
06-07-2016 4:25 PM


Re: Why they lived longer then and dragging this onto the topic
"By one man sin entered the world, and death by sin." So it didn't exist at all in the world until then."

The scope of the term 'death' is certainly not clear. I am pretty sure from past discussions that you will agree that the term death as used in that text did not include the passing away of microbes like the ones in Adam's gut or in that of cattle, or the passing away of the plants Adam ate. Did the enterring of death via sin then apply also to animals other than Man? There is no explicit confirmation that it did, and plenty of reason to doubt that it did. There Bible describes no salvation plan for any animals other than humans. Seriously, if eating animals by other animals is evil behavior, what would you call wearing their hides on your feet?

Secondly, the Bible does not suggest that death entered the world because God messed with either Adam's physiology or his genome. The text says that God exiled Adam from the garden for the specified purpose of separating him from the Tree of Life and immortality. God then sent an angel with a flaming sword to block access to the Tree of Life.

So, if you are making up stuff about the human genome based on the Fall, then your argument is not strongly supported by the Bible alone, but is subject to your interpretation of the Bible. After all, even if evolution and mutation were not involved in the creation of humanity, there is still no Biblical reason that variations since then did not include mutation at least for powering microevolution, and thus no reason to separate the scientific and Biblical explanations based on mutation. Extra-Biblical doctrine is required to make such arguments.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


This message is a reply to:
 Message 188 by Faith, posted 06-07-2016 4:25 PM Faith has responded

Replies to this message:
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Genomicus
Member (Idle past 400 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 195 of 455 (785607)
06-07-2016 10:37 PM
Reply to: Message 183 by Faith
06-07-2016 11:40 AM


Re: Mt DNA and microsatellites as measures of genetic diversity
The writers for Wikipedia aren't babies in their field are they? Why would they leave out a common practice for assessing genetic diversity?

Check out the Wikipedia entry on measuring genetic diversity again


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Replies to this message:
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