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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
Taq
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Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 121 of 518 (808747)
05-12-2017 1:35 PM
Reply to: Message 120 by Faith
05-12-2017 1:30 PM


Re: Getting from the super genome to two alleles per gene
Faith writes:
Why so many alleles? Aren't they just mutations? Mutations don't normally do anything good. Parker showed how the whole range of human skin colors can be produced in one generation by only two genes with two alleles each according to standard Mendelian principles. That's a LOT of variation in one generation. And if there are yet more genes for skin color there's a lot more than that and without any extra alleles.
The main problem with this very narrow argument is that you are extrapolating from one gene to all genes. Just because skin color may or may not be determined by two genes with two alleles each does not mean that other physical characteristics are governed the same way.

This message is a reply to:
 Message 120 by Faith, posted 05-12-2017 1:30 PM Faith has replied

Replies to this message:
 Message 122 by Faith, posted 05-12-2017 1:42 PM Taq has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 122 of 518 (808748)
05-12-2017 1:42 PM
Reply to: Message 121 by Taq
05-12-2017 1:35 PM


Re: Getting from the super genome to two alleles per gene
The main problem with this very narrow argument is that you are extrapolating from one gene to all genes. Just because skin color may or may not be determined by two genes with two alleles each does not mean that other physical characteristics are governed the same way.
Could be, but the vast majority of traits probably follow the simple Mendelian system.
I LOVE that it's so "narrow." Simplicity is beautiful.

This message is a reply to:
 Message 121 by Taq, posted 05-12-2017 1:35 PM Taq has replied

Replies to this message:
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PaulK
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Posts: 17822
Joined: 01-10-2003
Member Rating: 2.3


Message 123 of 518 (808749)
05-12-2017 1:44 PM
Reply to: Message 120 by Faith
05-12-2017 1:30 PM


Re: Getting from the super genome to two alleles per gene
It's a pretty trivial - in fact inevitable - result.
Gary Parker is just engaging in abstract theorising, trying to prop up the (daft) idea that the "races" of human beings come from Noah's three kids and their wives.
We don't need such superficial and intellectually empty theorising. But it seems that we do need - or at least have a good use for - far more than two alleles for some genes.

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 Message 120 by Faith, posted 05-12-2017 1:30 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 124 of 518 (808750)
05-12-2017 2:17 PM
Reply to: Message 66 by bluegenes
05-11-2017 11:14 AM


Re: The YEC model requires ...
I never answered this post, bluegenes, but that's largely because it's hard for me to get into your frame of reference. I was rereading the thread and see that in Message 74 you ask me to return to this post and think along these lines:
See if Message 66 makes it any clearer to you. Particularly, concentrate on the point that we would only have mutations (new alleles) on ~1% of our coding genes as individuals. The rest would be identical to the four in Adam and Eve. So, take a random gene and examine it on 100 people, and you'd expect the original 4 alleles + perhaps 1 individual with a new one on average.
So I think I understand that the list of numbers refers to allele/gene sequences possessed by the particular number of Cubans indicated?
You treat them all as beneficial alleles that each does something different to protect the immune system? You seem to be saying that these variations in the sequence must each do something specific in the immune system? But this appears to be an assumption simply from the fact of the many sequence differences rather than something you actually know about their function?
My contrary assumption would be, as usual, that all those difference in DNA sequences are probably mostly "neutral" mutations that don't change the original function of the allele. Is there evidence against this idea?
I don't really grasp what point you are trying to make about the numbers or percentages of these mutations within a population, except that it is based on assuming that they do something good for the population, which I'm doubting. So that where you see the numbers as indicating some percentage of good I see them as indicating some percentage of bad.
That's as far as I can get with this, and I'm responding now even though what you are saying remains unclear, because I felt I should respond with SOMETHING after all.
We inhabit two different frames of reference about these things. Mine is spelled out in more detail than usual in Message 120
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 66 by bluegenes, posted 05-11-2017 11:14 AM bluegenes has not replied

Replies to this message:
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 125 of 518 (808752)
05-12-2017 2:46 PM
Reply to: Message 122 by Faith
05-12-2017 1:42 PM


Re: Getting from the super genome to two alleles per gene
Faith writes:
Could be, but the vast majority of traits probably follow the simple Mendelian system.
Probably? Why?
I LOVE that it's so "narrow." Simplicity is beautiful.
I meant "narrow" as in focused on just one species. Also, biology isn't simple.

This message is a reply to:
 Message 122 by Faith, posted 05-12-2017 1:42 PM Faith has not replied

Replies to this message:
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 126 of 518 (808753)
05-12-2017 2:49 PM
Reply to: Message 124 by Faith
05-12-2017 2:17 PM


Re: The YEC model requires ...
Faith writes:
My contrary assumption would be, as usual, that all those difference in DNA sequences are probably mostly "neutral" mutations that don't change the original function of the allele. Is there evidence against this idea?
Is there evidence FOR this idea?
I don't really grasp what point you are trying to make about the numbers or percentages of these mutations within a population, except that it is based on assuming that they do something good for the population, which I'm doubting. So that where you see the numbers as indicating some percentage of good I see them as indicating some percentage of bad.
From all indications you seem to accept natural selection, so we can proceed from there.
If these alleles were detrimental or less beneficial than other alleles then we wouldn't find them in about the same abundance. This is because less beneficial or detrimental alleles would be selected against.

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 Message 124 by Faith, posted 05-12-2017 2:17 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 127 of 518 (808754)
05-12-2017 2:53 PM


The model in more detail
Here's the Mendel square for skin color from Gary Parker again, showing the range of colors from darkest to lightest based only on two genes of two alleles each:
/
/
If you look up skin color online you'll find some cosmetics sites that show a much greater range of colors, which makes sense considering that there are more than two genes for skin color.
You'll also find the usual assumption that the colors evolved, which of course I'm arguing against. What evolves, meaning microevolves of course, is separate populations characterized by a particular skin color or range of colors, but these are not new creations based on mutations, they are merely selected and isolated shades from the great range of possibilities originally built into the human genome.
Adam and Eve had the genes to produce every skin color there is. Depending on how many children they had they could have produced the entire range in one generation, but certainly produced quite a large range of them in any case. The rest would have appeared in subsequent generations.
What makes a skin color or any other trait characteristic of a population or race is some form of selection of the color or few colors, and the selection as I've been arguing is in most cases random, a matter of migration of individuals that possess a particular portion of the gene pool ending up as an isolated population in some new place, where they develop a characteristic skin color through generations of inbreeding. That's all it takes for there to be hundreds of different populatios with different characteristics. It's all in the original genome, brought to visible expression by random seleciton and reproductive isolation.
I'm stating a basic principle here. I know that reality is a lot messier, that populations split and merge and cross in various ways, produce hybrids and all kinds of variations down the generations, but it's all based on the original set of possibilities from the combinations you can get from the original genome. This is true for human beings and it's also true for sexually reproducing animals.
And each new race or population develops its characteristic traits by LOSING all the genetic material for other traits, many of which become characteristic of other populations. The original genome for each Kind had tremendous genetic diversity that in various combinations produced all the separate populations or "species" of all Kinds, but each new species has its characteristic phenotypes as a result of losing the genetic material for all the others.
Evolution defeats Evolution.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

Replies to this message:
 Message 128 by Taq, posted 05-12-2017 3:02 PM Faith has replied
 Message 135 by bluegenes, posted 05-13-2017 6:51 AM Faith has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 128 of 518 (808756)
05-12-2017 3:02 PM
Reply to: Message 127 by Faith
05-12-2017 2:53 PM


Re: The model in more detail
Faith writes:
Here's the Mendel square for skin color from Gary Parker again, showing the range of colors from darkest to lightest based only on two genes of two alleles each:
We already know that Parker's model is not correct. The Wiki page lists at least 7 genes involved in skin color:
Human skin color - Wikipedia

This message is a reply to:
 Message 127 by Faith, posted 05-12-2017 2:53 PM Faith has replied

Replies to this message:
 Message 129 by Faith, posted 05-12-2017 3:08 PM Taq has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 129 of 518 (808757)
05-12-2017 3:08 PM
Reply to: Message 128 by Taq
05-12-2017 3:02 PM


Re: The model in more detail
Taq writes:
Faith writes:
Here's the Mendel square for skin color from Gary Parker again, showing the range of colors from darkest to lightest based only on two genes of two alleles each:
We already know that Parker's model is not correct. The Wiki page lists at least 7 genes involved in skin color:
Parker himself (in 1982) said there was at least one more gene for skin color than his chart shows and you should have noticed by now that I've allowed for many more than that. The point of this chart is to demonstrate that from a mere two genes with two alleles each the variations are enormous even in only one generation. That alone should make the case for the production of all the diversity of living things from the original genome for each Kind. But if you add many other genes for each trait you simply increase that enormous variation. Beyond my ability to create the appropriate Mendel square.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 128 by Taq, posted 05-12-2017 3:02 PM Taq has replied

Replies to this message:
 Message 131 by Taq, posted 05-12-2017 3:15 PM Faith has replied

  
NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


(2)
Message 130 of 518 (808758)
05-12-2017 3:08 PM
Reply to: Message 125 by Taq
05-12-2017 2:46 PM


From Someone Less Knowlegable
I'm going to have a shot at simplifying things.
One area of confusion that I think I see is that one group of you is talking about genes and their alleles and Faith jumps from that to talking about variations in the external animals that we see (phenotype).
To simplify lets try to stick to the genes for a moment.
As I understand Faith's argument (and, I think, the general YEC one) it says that with a few different variations of a gene (alleles) we can mix and match to get lots of different external looks -- like eye color.
So mutations and different alleles are not needed.
However, others aren't paying attention to that yet. The argument is ignoring eye color (for example) and just looking at the genes.
It has two parts:
1) It starts with the YEC assertion that a few thousand years ago there were only a handful of humans alive (after the flood). These few would have had at most something like 10 alleles for each gene in them.
2) Today we see many more alleles for some genes than that.
This means that:
a) There have been mutations in the human genes. I think that is argued to not be true by some of the creationist community. Faith agrees ( I think ) that there are mutations.
b) The mutations are at least not deleterious since the individuals have been passing them on for 1,000's of years. This is what the definition of a neutral or beneficial mutations is. That is, can the individual with it successfully reproduce and pass it on.
So the remaining question is:
Are the mutations neutral or beneficial?
If they are neutral they are, by definition, not selected for or against so they only spread through the population by random drift.
So the issue of whether there are any beneficial mutations can be settled by examining if there are any alleles other than the orginal handful that are spread more widely than drift can do in a few 1,000 years.
As I understand the discussion so far the answer to that is - yes.
Therefore the conclusion is that the human genome has acquired beneficial mutations since the flood or the flood was much longer ago than a few 1,000 years.
If there have been beneficial mutations then the original genome was not "perfect".
That is all that can be concluded from the discussion so far.
How far off am I?
Edited by NosyNed, : No reason given.
Edited by NosyNed, : typos fixed

This message is a reply to:
 Message 125 by Taq, posted 05-12-2017 2:46 PM Taq has not replied

Replies to this message:
 Message 134 by bluegenes, posted 05-13-2017 2:49 AM NosyNed has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 131 of 518 (808759)
05-12-2017 3:15 PM
Reply to: Message 129 by Faith
05-12-2017 3:08 PM


Re: The model in more detail
Faith writes:
Parker himself (in 1982) said there was at least one more gene for skin color than his chart shows and you should have noticed by now that I've allowed for many more than that. The point of this chart is to demonstrate that even from a mere two genes with two alleles each the variations are enormous even in only one generation. That alone should make the case for the production of all the diversity of living things from the original genome for each Kind.
Again, you can't extrapolate from one gene to the entire genome.

This message is a reply to:
 Message 129 by Faith, posted 05-12-2017 3:08 PM Faith has replied

Replies to this message:
 Message 161 by Faith, posted 05-14-2017 7:54 AM Taq has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 132 of 518 (808761)
05-12-2017 3:32 PM


Multiple Alleles of OCA2 Produce a Wide Variety of Human Eye Colors
Ran across this paper:
A Three–Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation - PMC
It lists multiple alleles for the OCA2 gene, and those alleles are not equal in function. Different combinations of alleles produces different eye colors. This is an example of more than 2 alleles for the same gene.

Replies to this message:
 Message 159 by Faith, posted 05-14-2017 7:46 AM Taq has replied
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bluegenes
Member (Idle past 2476 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 133 of 518 (808779)
05-13-2017 2:00 AM
Reply to: Message 108 by Faith
05-11-2017 4:26 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
Faith writes:
They can be functional simply by not doing anything different than the original allele did, which is what "neutral" mutations do.
Yes, but they (new human immune system alleles) wouldn't be present in the proportions that they are after 300 generations on neutral evolution alone. Only positive selection on new variants would give that effect.
That's why I'm saying that, to get a plausible 6,500yr YEC model, we have to accept positive selection on many of those extra HLA alleles.
It will be the same for other animals after the Ark bottleneck, particularly those species (or kinds) that only had two members present. When we look at them now, lots of variants in the MHC will be present at proportions that are too high for neutral evolution (drift) to account for, as they could only have a maximum of 4 after the flood.
So, we have to put positive selection on MHC mutant alleles as part of any plausible YEC model.
If, like the folk at Answers in Genesis, you see "kind" at somewhere around the level of family, you will need positive selection during post flood speciation and niche filling as well, even if you argue that the genes/alleles were all present on the original Ark pair genomes.

This message is a reply to:
 Message 108 by Faith, posted 05-11-2017 4:26 PM Faith has replied

Replies to this message:
 Message 145 by Faith, posted 05-13-2017 1:34 PM bluegenes has replied

  
bluegenes
Member (Idle past 2476 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 134 of 518 (808780)
05-13-2017 2:49 AM
Reply to: Message 130 by NosyNed
05-12-2017 3:08 PM


Re: From Someone Less Knowlegable
NosyNed writes:
So the remaining question is:
Are the mutations neutral or beneficial?
If they are neutral they are, by definition, not selected for or against so they only spread through the population by random drift.
So the issue of whether there are any beneficial mutations can be settled by examining if there are any alleles other than the original handful that are spread more widely than drift can do in a few 1,000 years.
As I understand the discussion so far the answer to that is - yes.
Therefore the conclusion is that the human genome has acquired beneficial mutations since the flood or the flood was much longer ago than a few 1,000 years.
That's pretty much it, but not just the flood, Adam and Eve as well.
NNed writes:
If there have been beneficial mutations then the original genome was not "perfect".
Well, there's a twist to that so far as the HLA alleles are concerned. Adam and Eve, like everyone else, would have had two copies at each locus, and if they had two different complimentary variants on each HLA gene, then they are as perfect as possible.
From then on, it's downhill at first, because with only 4 possible alleles, it's a one in three chance of someone having two of the same alleles on any given locus which, for these codominant alleles, is usually a disadvantage, because variety in immune system weaponry is the spice of life.
That's where new functional mutants can help, because every added one decreases the chances of a matching pair. So, it is not that the new alleles are more perfect than the original. Variety itself is facing positive selection, so the YECs needn't necessarily have a theological objection to this.

This message is a reply to:
 Message 130 by NosyNed, posted 05-12-2017 3:08 PM NosyNed has not replied

Replies to this message:
 Message 136 by jar, posted 05-13-2017 7:03 AM bluegenes has replied

  
bluegenes
Member (Idle past 2476 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 135 of 518 (808782)
05-13-2017 6:51 AM
Reply to: Message 127 by Faith
05-12-2017 2:53 PM


Re: The model in more detail
Faith writes:
Adam and Eve had the genes to produce every skin color there is. Depending on how many children they had they could have produced the entire range in one generation, but certainly produced quite a large range of them in any case. The rest would have appeared in subsequent generations.
And 80 generations later, all the original diversity was still present in Noah's sons and their wives?
Faith writes:
What makes a skin color or any other trait characteristic of a population or race is some form of selection of the color or few colors, and the selection as I've been arguing is in most cases random, a matter of migration of individuals that possess a particular portion of the gene pool ending up as an isolated population in some new place, where they develop a characteristic skin color through generations of inbreeding. That's all it takes for there to be hundreds of different populatios with different characteristics. It's all in the original genome, brought to visible expression by random seleciton and reproductive isolation.
By "random selection" do you mean drift (neutral evolution-no selection involved)?
Faith writes:
And each new race or population develops its characteristic traits by LOSING all the genetic material for other traits, many of which become characteristic of other populations. The original genome for each Kind had tremendous genetic diversity that in various combinations produced all the separate populations or "species" of all Kinds, but each new species has its characteristic phenotypes as a result of losing the genetic material for all the others.
So the ancestral bear kind on the Ark would have contained all the genes/alleles necessary to make a polar bear and a panda?
Even if so, surely natural selection on these would be necessary to produce things like the Arctic adaptations of the Polar?
Research on 59 Alpine Chamois found 19 alleles on one locus, and this level of polymorphism is turning out to be widespread, so I think you have to bring mutation and positive selection into your model, because mutation + drift from an Ark bottleneck doesn't fit what we see.
Evolution defeats Evolution.
We shall see!
I think YECs need to become super-selectionists in order to fit the genetics and the niche adaptations within kinds.

This message is a reply to:
 Message 127 by Faith, posted 05-12-2017 2:53 PM Faith has not replied

  
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