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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.6


Message 46 of 518 (808401)
05-10-2017 2:41 PM
Reply to: Message 43 by Faith
05-10-2017 2:05 PM


Re: Counting Alleles
Faith writes:
Tis indeed all abstract, but so is the ToE, so is the claim that mutations are the source of variation, and in that case not just abstract but pure wishful thinking.
Which of these is abstract or wishful thinking?
1. Mutations happen.
2. The difference in function between alleles is due a difference in DNA sequence.
3. The physical differences between species is due to DNA sequence differences in their genomes.

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 Message 43 by Faith, posted 05-10-2017 2:05 PM Faith has replied

Replies to this message:
 Message 47 by Faith, posted 05-10-2017 8:05 PM Taq has replied

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


Message 47 of 518 (808442)
05-10-2017 8:05 PM
Reply to: Message 46 by Taq
05-10-2017 2:41 PM


Re: Counting Alleles
Taq writes:
Faith writes:
Tis indeed all abstract, but so is the ToE, so is the claim that mutations are the source of variation, and in that case not just abstract but pure wishful thinking.
Which of these is abstract or wishful thinking?
These are not statements of the ToE.
1. Mutations happen.
All the time and it is not a good thing.
2. The difference in function between alleles is due a difference in DNA sequence.
Yes but misleading since evos attribute the differences to mutation which mostly creates no differences in function or undesirable differences.
3. The physical differences between species is due to DNA sequence differences in their genomes.
Another misleading definition and I'm not sure it's completely true as stated anyway. That is, the crucial differences may be in particular parts of the genome; that is, in particular sequences that are responsible for particular differences rather than in a mere summation of sequence differences.
Edited by Faith, : No reason given.

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 Message 46 by Taq, posted 05-10-2017 2:41 PM Taq has replied

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bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 48 of 518 (808462)
05-11-2017 1:13 AM
Reply to: Message 41 by Faith
05-10-2017 1:19 PM


The YEC model requires beneficial mutations and strong positive selection.
Faith writes:
Can. But only as an accident, a fluke, and so rarely as to be of no use to the organism. Besides which, again, this is far more an article of faith than it is a demonstrated reality. And meanwhile mutations are known to have produced thousands of genetic diseases, and in the best scenarios they simply don't change anything.
You're making a mistake in arguing strongly against beneficial mutations and positive selection, because your Y.E.C. model requires them. On the loci where we find multiple alleles, neutral evolution (drift) will not account for what we can observe.
Consider. There can only be a maximum of 4 original alleles per locus. But on some genes we easily find many in a small population sample. The rate of occurrence of new variants on any given gene, and the 300 generation timespan, mean that, although there could be many variations on a gene scattered throughout the population, all the new ones would be rare on drift alone.
However, with strong positive selection on the new variants, we might be able to move your model closer to the actual observed results, that many of the new variants are common (because far more than 4 alleles are common on many of these loci). It's necessary that new variants on the extremely polymorphous MHC genes were beneficial on arrival and faced positive selection if there were only 4 alleles at these loci 300 generations ago.
So, in order to get the best possible Y.E.C. model, the one that best fits the evidence, beneficial mutation and strong positive selection are necessary. Seriously.

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 Message 41 by Faith, posted 05-10-2017 1:19 PM Faith has replied

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 Message 49 by Faith, posted 05-11-2017 1:19 AM bluegenes has replied

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


Message 49 of 518 (808463)
05-11-2017 1:19 AM
Reply to: Message 48 by bluegenes
05-11-2017 1:13 AM


Re: The YEC model requires ...
I'm going with two alleles per gene
More than one gene for some traits
No beneficial mutations, they are all an interference
Strong selection isn't needed, nor drift, though either might occur; just migration + isolation
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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 Message 48 by bluegenes, posted 05-11-2017 1:13 AM bluegenes has replied

Replies to this message:
 Message 50 by bluegenes, posted 05-11-2017 1:28 AM Faith has replied
 Message 58 by Percy, posted 05-11-2017 7:43 AM Faith has replied
 Message 63 by Taq, posted 05-11-2017 10:48 AM Faith has not replied

  
bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 50 of 518 (808466)
05-11-2017 1:28 AM
Reply to: Message 49 by Faith
05-11-2017 1:19 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Faith writes:
I'm going with two alleles per gene
But that's demonstrably false. Or do you mean originally (Adam and Eve)?
Faith writes:
More than one gene for some traits
Certainly.
Faith writes:
No beneficial mutations, they are all an interference
Strong selection isn't needed, nor drift, just migration + isolation
Then why are so many alleles in the MHC common?
Edited by bluegenes, : redundancy removed

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 Message 49 by Faith, posted 05-11-2017 1:19 AM Faith has replied

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 Message 51 by Faith, posted 05-11-2017 1:30 AM bluegenes has replied

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


Message 51 of 518 (808467)
05-11-2017 1:30 AM
Reply to: Message 50 by bluegenes
05-11-2017 1:28 AM


Re: The YEC model requires ...
You haven't shown that those alleles actually do anything. You think they do, but it's all an assumption from what you've said.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 50 by bluegenes, posted 05-11-2017 1:28 AM bluegenes has replied

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 Message 52 by bluegenes, posted 05-11-2017 1:47 AM Faith has replied

  
bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 52 of 518 (808470)
05-11-2017 1:47 AM
Reply to: Message 51 by Faith
05-11-2017 1:30 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Faith writes:
You haven't shown that those alleles actually do anything. You think they do, but it's all an assumption from what you've said.
We'd all be dead if they didn't!
But you're missing the point. They are there. The mutation rate and drift (including the effects of migration etc) will not give us the observed pattern.
Perhaps you mean to suggest that the variants don't have different functions? Did you look at the paper I linked to earlier?
Message 26
bluegenes writes:
To further illustrate what I was saying about extreme polymorphism in the immune system:
The major histocompatibility complex (MHC) and its functions. NCBI
quote:
Because of the polygeny of the MHC, every person will express at least three different antigen-presenting MHC class I molecules and three (or sometimes four) MHC class II molecules on his or her cells. In fact, the number of different MHC molecules expressed on the cells of most people is greater because of the extreme polymorphism of the MHC and the codominant expression of MHC gene products.
The term polymorphism comes from the Greek poly, meaning many, and morphe, meaning shape or structure. As used here, it means within-species variation at a gene locus, and thus in its protein product; the variant genes that can occupy the locus are termed alleles. There are more than 200 alleles of some human MHC class I and class II genes, each allele being present at a relatively high frequency in the population. So there is only a small chance that the corresponding MHC locus on both the homologous chromosomes of an individual will have the same allele; most individuals will be heterozygous at MHC loci. The particular combination of MHC alleles found on a single chromosome is known as an MHC haplotype. Expression of MHC alleles is codominant, with the protein products of both the alleles at a locus being expressed in the cell, and both gene products being able to present antigens to T cells. The extensive polymorphism at each locus thus has the potential to double the number of different MHC molecules expressed in an individual and thereby increases the diversity already available through polygeny
It is important that the alleles have slightly different products because it helps give variety to our immune system.
This same variety can be observed in other species of mammal. They do not appear to have been through a tight bottleneck in the last few thousand years. I coloured the sentence and bolded the last part because the fact that each allele is present at a high frequency in the population should mean something to anyone attempting to build a YEC model. The model needs to be compatible with this diversity.
You have to argue for positive selection, otherwise only the original Adam and Eve alleles would be common (only 4 common alleles, or 2 if you like).

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 Message 51 by Faith, posted 05-11-2017 1:30 AM Faith has replied

Replies to this message:
 Message 53 by Faith, posted 05-11-2017 2:00 AM bluegenes has replied
 Message 54 by Faith, posted 05-11-2017 2:09 AM bluegenes has replied

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


Message 53 of 518 (808471)
05-11-2017 2:00 AM
Reply to: Message 52 by bluegenes
05-11-2017 1:47 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
I did read that but since it is hard for me to read anything of any length I may have missed something. the question I have is whether there is really any difference among the alleles since "neutral" mutations don't change the function. So when function is described -- the codominant function of two alleles -- isn't it possible most or all of the alleles do the same thing?

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 Message 52 by bluegenes, posted 05-11-2017 1:47 AM bluegenes has replied

Replies to this message:
 Message 55 by bluegenes, posted 05-11-2017 2:22 AM Faith has not replied
 Message 64 by Taq, posted 05-11-2017 10:50 AM Faith has not replied

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


Message 54 of 518 (808472)
05-11-2017 2:09 AM
Reply to: Message 52 by bluegenes
05-11-2017 1:47 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
You have to argue for positive selection, otherwise only the original Adam and Eve alleles would be common (only 4 common alleles, or 2 if you like).
I don't think so. Just random recombination of Adam and Eve's two genes with two alleles per gene for skin color could produce in one generation all the different skin colors. There is no lack of diversity in this system. Diversity is all a matter of the many possible combinations of the two alleles per gene.
But my main argument is for a random selection anyway, the random favoring of certain alleles over others in the simple migration of a part of a population to another location where it has reproductive isolation. You get new gene frequencies that way, that bring out new phenotypes, others decreasing and even eventually disappearing from the new population. The original two alleles per gene now seems to me to be completely sufficient for all the diversity of life we see, including the formation of every species including some exotic or strange ones.
Edited by Faith, : No reason given.

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 Message 52 by bluegenes, posted 05-11-2017 1:47 AM bluegenes has replied

Replies to this message:
 Message 56 by bluegenes, posted 05-11-2017 2:40 AM Faith has replied

  
bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 55 of 518 (808473)
05-11-2017 2:22 AM
Reply to: Message 53 by Faith
05-11-2017 2:00 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Faith writes:
I did read that but since it is hard for me to read anything of any length I may have missed something. the question I have is whether there is really any difference among the alleles since "neutral" mutations don't change the function. So when function is described -- the codominant function of two alleles -- isn't it possible most or all of the alleles do the same thing?
Again, you seem to be missing the point. If the changes are neutral, then new variants wouldn't be common after 300 generations, so you should want the common ones not to be neutral in order to fit a YEC model. The view expressed in the paper, that variation is useful, is better for your model than "neutral".

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 Message 53 by Faith, posted 05-11-2017 2:00 AM Faith has not replied

  
bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 56 of 518 (808475)
05-11-2017 2:40 AM
Reply to: Message 54 by Faith
05-11-2017 2:09 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Faith writes:
I don't think so. Just random recombination of Adam and Eve's two genes with two alleles per gene for skin color could produce in one generation all the different skin colors. There is no lack of diversity in this system. Diversity is all a matter of the many possible combinations of the two alleles per gene.
Again, the extreme variation at certain loci is there, whether or not 2 alleles would perform the function.
Faith writes:
But my main argument is for a random selection anyway, the random favoring of certain alleles over others in the simple migration of a part of a population to another location where it has reproductive isolation. You get new gene frequencies that way, that bring out new phenotypes, others decreasing and even eventually disappearing from the new population. The original two alleles per gene now seems to me to be completely sufficient for all the diversity of life we see, including the formation of every species including some exotic or strange ones.
Then how have many, many "new" alleles in the MHC become common in 300 generations? Mutation and drift certainly won't give that result. Almost all the mutants would be very rare.
The only thing that might (possibly) explain this is strong selection. Apart from that we would need humans and other mammals to have been around for far longer than 300 generations..........
So, which is it?
Edited by bluegenes, : missing s

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 Message 54 by Faith, posted 05-11-2017 2:09 AM Faith has replied

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Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 57 of 518 (808484)
05-11-2017 7:13 AM


Number of Genes for Eye Color and Skin Color
It is worth mentioning again that eye color is determined by at least 6 genes, and skin color by at least 10.
--Percy

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Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 58 of 518 (808487)
05-11-2017 7:43 AM
Reply to: Message 49 by Faith
05-11-2017 1:19 AM


Re: The YEC model requires ...
Faith writes:
I'm going with two alleles per gene
If by this you mean only two alleles per gene in the original human population, in your scenario this is demonstrably false. Both Adam and Eve could have contributed two unique alleles per gene for a total of four. Even though you believe you only need two alleles per gene, you actually have a potential maximum of four.
This is better for your scenario because now people have to demonstrate at least five alleles for a gene before they can claim any arose through mutation, and then they still have to show they produced new function.
--Percy
Edited by Percy, : Correct misstated sentence.

This message is a reply to:
 Message 49 by Faith, posted 05-11-2017 1:19 AM Faith has replied

Replies to this message:
 Message 60 by bluegenes, posted 05-11-2017 8:01 AM Percy has replied
 Message 67 by Faith, posted 05-11-2017 1:13 PM Percy has replied

  
bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 59 of 518 (808488)
05-11-2017 7:49 AM
Reply to: Message 57 by Percy
05-11-2017 7:13 AM


Re: Number of Genes for Eye Color and Skin Color
Percy writes:
It is worth mentioning again that eye color is determined by at least 6 genes, and skin color by at least 10.
And it's also worth mentioning that the human MC1R gene (one of the above) has more than 30 known alleles. Adam and Eve? Maximum 4.
Also, as most board members are of European ancestry, many will have visible phenotype features that owe their existence to mutants of this gene.

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bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 60 of 518 (808491)
05-11-2017 8:01 AM
Reply to: Message 58 by Percy
05-11-2017 7:43 AM


Re: The YEC model requires ...
Percy writes:
This is better for your scenario because now people have to demonstrate at least five alleles for a gene before they can claim any arose through mutation, and then they still have to show they produced new function.
In the MHC, there are plenty of examples of more than five in small samples, like 100 individuals. There can be more than five at a 5% rate or more in the sample. That's impossible from Adam and Eve in 300 generations by drift alone. It requires positive selection of novelty, and it is Faith (although she doesn't realise it) who needs new function and positive selection for her model.

This message is a reply to:
 Message 58 by Percy, posted 05-11-2017 7:43 AM Percy has replied

Replies to this message:
 Message 61 by Percy, posted 05-11-2017 8:27 AM bluegenes has replied

  
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