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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 316 of 518 (810199)
05-25-2017 8:47 AM
Reply to: Message 314 by Percy
05-25-2017 7:29 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Percy writes:
Faith doesn't have a problem with more than 2 alleles. What she has a problem with is more than 2 alleles where the additional alleles do anything different than the original alleles. She claims that the new alleles must do the same things the old alleles did, i.e., have the same functions as the old alleles. She claims that the new alleles cannot have new functions.
Then research on the HLA-B gene alone proves her wrong. The variant alleles produce different proteins and definite differences in immune reactions.
Here's a paper that shows differences in producing immune reactions to a measles vaccine. Three HLA-B alleles are identified that perform particularly badly, and two that perform particularly well, with others in between.
Variance in HLA-B performance against measles.
quote:
Despite the success of the current measles vaccine in controlling disease in industrialized countries, the importance of vaccine failure has become increasingly apparent. Our objective was to determine if associations exist between seronegativity after measles vaccination and class I human leukocyte antigen (HLA) alleles. We undertook a cross-sectional observational study in Rochester, Minnesota, with 242 school-age children previously recruited from a communitywide seroprevalence study. We studied two groups of subjects: 72 were seronegative (EIA =<0.8 after a single dose of measles vaccine) and 170 were seropositive (enzyme immunoassy [EIA] =<1.0 after one dose). We used the resources of Mayo Clinic's tissue typing laboratory for serotyping class I HLA-A and HLA-B alleles via microlymphocytotoxicity assays. We found no statistically significant associations with class I HLA-A but did find associations with class I HLA-B, which includes alleles associated with seronegativity (B8, B13, and B44) and those associated with seropositivity (B7 and B51).

This message is a reply to:
 Message 314 by Percy, posted 05-25-2017 7:29 AM Percy has replied

Replies to this message:
 Message 321 by Percy, posted 05-26-2017 10:18 AM bluegenes has replied

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


Message 317 of 518 (810203)
05-25-2017 10:39 AM
Reply to: Message 314 by Percy
05-25-2017 7:29 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Percy writes:
What she has a problem with is more than 2 alleles where the additional alleles do anything different than the original alleles.
That was the context I was using. If Faith defines alleles by function then there are more than two alleles for that gene.

This message is a reply to:
 Message 314 by Percy, posted 05-25-2017 7:29 AM Percy has replied

Replies to this message:
 Message 322 by Percy, posted 05-26-2017 10:35 AM Taq has not replied

  
NoNukes
Inactive Member


Message 318 of 518 (810210)
05-25-2017 11:39 AM
Reply to: Message 315 by Percy
05-25-2017 7:46 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
I think more than just one gene must be at work, because the Wikipedia article on Blood Type says that "33 blood-group systems have been identified, including the ABO and Rh systems.
The ABO gene is a single gene with only three alleles. Perhaps this direct statement will clear up the confusion.
ABO blood group system - Wikipedia(gene)
quote:
he ABO gene resides on chromosome 9 at the band 9q34.2 and contains 7 exons.[4] This gene encodes three alleles: the A allele produces α1,3-N-acetylgalactosamine transferase (GTA); the B allele encodes α1,3-galactosaminyl transferase (GTB); and the O allele lacks both enzymatic activities because of the frameshift caused by a deletion of guanine-258 in the gene which corresponds to a region near the N-terminus of the protein.[7][8] This results in a frameshift mutation and translation of an almost entirely different protein that is unable to modify oligosaccharides which end in fucose linked to galactose.[9] Remarkably, the difference between the A and B glycosyltransferase enzymes is only four amino acids (Arg/Gly-176, Gly/Ser-235, Leu/Met-266, and Gly/Ala-268).[9][8] Other minor alleles have been found for this gene.[4]
Edited by NoNukes, : terminology correction.

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
I never considered a difference of opinion in politics, in religion, in philosophy, as cause for withdrawing from a friend. Thomas Jefferson
Seems to me if its clear that certain things that require ancient dates couldn't possibly be true, we are on our way to throwing out all those ancient dates on the basis of the actual evidence. -- Faith
Some of us are worried about just how much damage he will do in his last couple of weeks as president, to make it easier for the NY Times and Washington post to try to destroy Trump's presidency. -- marc9000

This message is a reply to:
 Message 315 by Percy, posted 05-25-2017 7:46 AM Percy has seen this message but not replied

  
NoNukes
Inactive Member


Message 319 of 518 (810214)
05-25-2017 12:17 PM
Reply to: Message 306 by Percy
05-24-2017 9:29 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
I can't pin it down in detail for rabbits, but skin/hair color in humans is governed by many genes, so the same must be true of other mammals.
I provided a reference for this before. Since the reference (khanacademy) was possibly not a persuasive one, I will provide a second one here:
Color Genetics: The C Series - Full Color, Chinchilla, Sable, Himalayan or Pointed White, & REW | The Nature Trail
quote:
Although there are five main color genes that determine the color of a rabbit’s fur, the c-series of genes is called the color gene. The color gene, which controls where and how much color will be expressed rather than which color will be expressed, is definitely one of the most difficult to understand. The first complication is that there are more variations of this gene than of most color genes. Another complication is that some genes are incompletely dominant over others. But in spite of its complications, genes at the C-locus is one of the most fascinating to work with.
So there are multiple genes that affect color, but among those genes, the functionality of the c gene and its affect on how the color is expressed is well known. So you have a point regarding the system for determining fur color, and yet we still have an example to discuss. Namely, a single gene controlling an easily visible phenotypic parameter with multiple alleles at a single location. Five alleles for that particular gene have been identified.
Given that, I don't really care whether or not Faith was serious about accepting the example. Again if I were arguing the other side, I would point out that there are no real limits to how many rabbits were specially created so there is not a hard limit of only four total alleles for a gene as there is for humans. Perhaps for the sake of this argument, human examples are best.
My argument for the ABO gene being a further example is similar. Even if ABO is not the complete picture for blood type, that gene does have a definite and functional expression on human phenotype and accordingly is a legitimate example of a gene with more than two alleles.
From wikipedia.
quote:
ABO blood types are also present in some other animals, for example rodents and apes, such as chimpanzees, bonobos, and gorillas
Edited by NoNukes, : fix quote tags
Edited by NoNukes, : No reason given.

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
I never considered a difference of opinion in politics, in religion, in philosophy, as cause for withdrawing from a friend. Thomas Jefferson
Seems to me if its clear that certain things that require ancient dates couldn't possibly be true, we are on our way to throwing out all those ancient dates on the basis of the actual evidence. -- Faith
Some of us are worried about just how much damage he will do in his last couple of weeks as president, to make it easier for the NY Times and Washington post to try to destroy Trump's presidency. -- marc9000

This message is a reply to:
 Message 306 by Percy, posted 05-24-2017 9:29 AM Percy has replied

Replies to this message:
 Message 324 by Percy, posted 05-26-2017 10:51 AM NoNukes has replied

  
NoNukes
Inactive Member


Message 320 of 518 (810233)
05-25-2017 11:00 PM
Reply to: Message 313 by Taq
05-24-2017 6:02 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
This is yet another example of a human gene with more than 2 alleles.
I understand that. My question is why we would not allow Adam and Eve to possess four alleles between them.
I understand from wikipedia that there are more, somewhat rare, alleles for ABO type, so that the number in question exceeds even the three. However, I don't have any information regarding functionality.

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
I never considered a difference of opinion in politics, in religion, in philosophy, as cause for withdrawing from a friend. Thomas Jefferson
Seems to me if its clear that certain things that require ancient dates couldn't possibly be true, we are on our way to throwing out all those ancient dates on the basis of the actual evidence. -- Faith
Some of us are worried about just how much damage he will do in his last couple of weeks as president, to make it easier for the NY Times and Washington post to try to destroy Trump's presidency. -- marc9000

This message is a reply to:
 Message 313 by Taq, posted 05-24-2017 6:02 PM Taq has not replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 321 of 518 (810260)
05-26-2017 10:18 AM
Reply to: Message 316 by bluegenes
05-25-2017 8:47 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
bluegenes writes:
Here's a paper that shows differences in producing immune reactions to a measles vaccine. Three HLA-B alleles are identified that perform particularly badly, and two that perform particularly well, with others in between.
Variance in HLA-B performance against measles.
quote:
...
We found no statistically significant associations with class I HLA-A but did find associations with class I HLA-B, which includes alleles associated with seronegativity (B8, B13, and B44) and those associated with seropositivity (B7 and B51).
So let me combine this with other data from the Wikipedia article on the HLA-B gene. In most cases the designation (e.g., B7) represents multiple alleles that are grouped together because of their similar function. I didn't include the broad antigens from the table at Wikipedia because I didn't understand their relationship to the antigens listed on the same line.
B5Measles seropositivity
B7Measles seropositivity
B8Measles seronegativity
B13Measles seronegativity
B27HIV protection
Autoimmunity
Psoriasis
Ankylosing spondylitis
Inflammatory bowel disease
Reactive arthritis
B35HIV susceptibility
B37Immune system
B41Immune system
B42Immune system
B44Measles seronegativity
B46Rice farming association
B47Adrenal 21-hydroxylase deficiency
B48Immune system
B51Measles seropositivity
Behet's disease
B52Ulcerative colitis
Takayasu's arteritis
B53Immune system
B59Immune system
B67Immune system
B73Immune system
B78Immune system
B81Immune system
B*82Immune system
B*83Immune system
What this table tells us is that we know very little about which HLA-B alleles protect against which pathogens. For most of them all that is known is that they're associated with the immune system, or that they're associated with disease, which is consistent with Faith's assertion that mutations are only harmful.
--Percy

This message is a reply to:
 Message 316 by bluegenes, posted 05-25-2017 8:47 AM bluegenes has replied

Replies to this message:
 Message 323 by Taq, posted 05-26-2017 10:50 AM Percy has replied
 Message 328 by bluegenes, posted 05-27-2017 9:39 AM Percy has replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 322 of 518 (810262)
05-26-2017 10:35 AM
Reply to: Message 317 by Taq
05-25-2017 10:39 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Taq writes:
That was the context I was using. If Faith defines alleles by function then there are more than two alleles for that gene.
I know Faith claims an original 2 alleles, so the three beta-hemoglobin alleles just force her to concede that there were an original 4 alleles maximum. Just for completeness, here are those three beta-hemoglobin alleles plus another couple I found at the Wikipedia article on HBB
HbANormal
HbSSickle cell trait
HbCSickle cell trait
Malaria resistance
HbE
HBB Absence
β-thalassemia (life threatening disease)
The Wikipedia article says there are "numerous HBB variants", but I couldn't find more than 4 different functions, and you need more than 4 alleles with different functions.
--Percy

This message is a reply to:
 Message 317 by Taq, posted 05-25-2017 10:39 AM Taq has not replied

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


Message 323 of 518 (810264)
05-26-2017 10:50 AM
Reply to: Message 321 by Percy
05-26-2017 10:18 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Percy writes:
What this table tells us is that we know very little about which HLA-B alleles protect against which pathogens.
You can add influenza to the list:
"To study whether individual HLA class I alleles are used preferentially or equally in human virus-specific CTL responses, the contribution of individual HLA-A and -B alleles to the human influenza virus-specific CTL response was investigated. To this end, PBMC were obtained from three groups of HLA-A and -B identical blood donors and stimulated with influenza virus. In the virus-specific CD8(+) T cell population, the proportion of IFN-gamma- and TNF-alpha-producing cells, restricted by individual HLA-A and -B alleles, was determined using virus-infected C1R cells expressing a single HLA-A or -B allele for restimulation of these cells. In HLA-B*2705- and HLA-B*3501-positive individuals, these alleles were preferentially used in the influenza A virus-specific CTL response, while the contribution of HLA-B*0801 and HLA-A*0101 was minor in these donors."
Preferential HLA usage in the influenza virus-specific CTL response - PubMed

This message is a reply to:
 Message 321 by Percy, posted 05-26-2017 10:18 AM Percy has replied

Replies to this message:
 Message 325 by Percy, posted 05-26-2017 11:14 AM Taq has not replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 324 of 518 (810265)
05-26-2017 10:51 AM
Reply to: Message 319 by NoNukes
05-25-2017 12:17 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
NoNukes writes:
So there are multiple genes that affect color, but among those genes, the functionality of the c gene and its affect on how the color is expressed is well known. So you have a point regarding the system for determining fur color, and yet we still have an example to discuss. Namely, a single gene controlling an easily visible phenotypic parameter with multiple alleles at a single location. Five alleles for that particular gene have been identified.
Can we get a list of those alleles and their functions?
Again if I were arguing the other side, I would point out that there are no real limits to how many rabbits were specially created so there is not a hard limit of only four total alleles for a gene as there is for humans. Perhaps for the sake of this argument, human examples are best.
There's still the ark bottleneck. There could be at most four original alleles for unclean animals and 28 for clean.
But I agree, human examples are best.
My argument for the ABO gene being a further example is similar. Even if ABO is not the complete picture for blood type, that gene does have a definite and functional expression on human phenotype and accordingly is a legitimate example of a gene with more than two alleles.
Faith should give up on her insistence that there were an original two alleles. She has no basis for the claim, and it just makes her position unnecessarily more insensible.
--Percy

This message is a reply to:
 Message 319 by NoNukes, posted 05-25-2017 12:17 PM NoNukes has replied

Replies to this message:
 Message 326 by NoNukes, posted 05-26-2017 11:16 AM Percy has replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 325 of 518 (810270)
05-26-2017 11:14 AM
Reply to: Message 323 by Taq
05-26-2017 10:50 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
This is a reissue of the table of HLA-B allele groups based on information provided by Taq:
B5Measles seropositivity
B7Measles seropositivity
B8Measles seronegativity
B13Measles seronegativity
B27HIV protection
Autoimmunity
Psoriasis
Ankylosing spondylitis
Inflammatory bowel disease
Reactive arthritis
B35HIV susceptibility
B37Immune system
B41Immune system
B42Immune system
B44Measles seronegativity
B46Rice farming association
B47Adrenal 21-hydroxylase deficiency
B48Immune system
B51Measles seropositivity
Behet's disease
B52Ulcerative colitis
Takayasu's arteritis
B53Immune system
B59Immune system
B67Immune system
B73Immune system
B78Immune system
B81Immune system
B*82Immune system
B*83Immune system
B*2705Influenza
B*3501Influenza
--Percy

This message is a reply to:
 Message 323 by Taq, posted 05-26-2017 10:50 AM Taq has not replied

  
NoNukes
Inactive Member


Message 326 of 518 (810271)
05-26-2017 11:16 AM
Reply to: Message 324 by Percy
05-26-2017 10:51 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Can we get a list of those alleles and their functions?
It was in the reference, but perhaps pulling that out is not a high priority given what we agreed on with respect to animals.
There's still the ark bottleneck. There could be at most four original alleles for unclean animals and 28 for clean.
There is also the matter of how kind is defined. It is not the same thing as species. Too much trouble to establish an upper limit for rabbit alleles if we can find human examples.
Faith should give up on her insistence that there were an original two alleles. She has no basis for the claim, and it just makes her position unnecessarily more insensible.
There is some basis. Eve was formed completely from material taken from Adam.
Edited by NoNukes, : No reason given.

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
I never considered a difference of opinion in politics, in religion, in philosophy, as cause for withdrawing from a friend. Thomas Jefferson
Seems to me if its clear that certain things that require ancient dates couldn't possibly be true, we are on our way to throwing out all those ancient dates on the basis of the actual evidence. -- Faith
Some of us are worried about just how much damage he will do in his last couple of weeks as president, to make it easier for the NY Times and Washington post to try to destroy Trump's presidency. -- marc9000

This message is a reply to:
 Message 324 by Percy, posted 05-26-2017 10:51 AM Percy has replied

Replies to this message:
 Message 327 by Percy, posted 05-27-2017 7:35 AM NoNukes has replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 327 of 518 (810287)
05-27-2017 7:35 AM
Reply to: Message 326 by NoNukes
05-26-2017 11:16 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
NoNukes writes:
There is some basis. Eve was formed completely from material taken from Adam.
But wouldn't God have had to change the alleles for Eve's genes, else Eve would have just been a clone of Adam? At a minimum he would have had to change the Y chromosome to an X. In creating the Eve's new X chromosome he wouldn't have just been changing alleles, he would have been creating entire new genes that don't exist on the Y chromosome. Given that we know God must have made genetic changes while creating Eve, I don't think any claims can be made as to its extent and that it must be allowed that an original gene could have had a maximum of four alleles.
--Percy
Edited by Percy, : Fix mixup between X and Y.

This message is a reply to:
 Message 326 by NoNukes, posted 05-26-2017 11:16 AM NoNukes has replied

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 Message 331 by NoNukes, posted 05-27-2017 6:09 PM Percy has seen this message but not replied

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


Message 328 of 518 (810289)
05-27-2017 9:39 AM
Reply to: Message 321 by Percy
05-26-2017 10:18 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Percy writes:
What this table tells us is that we know very little about which HLA-B alleles protect against which pathogens. For most of them all that is known is that they're associated with the immune system, or that they're associated with disease, which is consistent with Faith's assertion that mutations are only harmful.
With enough research involving enough strains of enough pathogens, all could eventually be associated with disease, because none can cover all the ground of our many and ever varying parasites.
You can add B63, B57, and B58 as having a positive effect against HIV; B44, B52,B62,B76, andB77 as having a positive effect against Dengue fever; B53 having a positive effect against Malaria; and B35, which you've got down as being bad news for those infected by HIV, is good news against infection with Prurigo Hebra (a skin disease).
Ultimately, with enough knowledge, we should find good and bad news for them all.
Variety is selected for, and individual alleles face positive selection every time something they're particularly effective against sweeps a local population (B53 is at high levels of frequency in malarial areas of West Africa, for example).

This message is a reply to:
 Message 321 by Percy, posted 05-26-2017 10:18 AM Percy has replied

Replies to this message:
 Message 329 by Percy, posted 05-27-2017 11:46 AM bluegenes has replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 329 of 518 (810291)
05-27-2017 11:46 AM
Reply to: Message 328 by bluegenes
05-27-2017 9:39 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Okay, reissuing the table again:
B5Measles seropositivity
B7Measles seropositivity
B8Measles seronegativity
B13Measles seronegativity
B27HIV protection
Autoimmunity
Psoriasis
Ankylosing spondylitis
Inflammatory bowel disease
Reactive arthritis
B35HIV susceptibility
Prurigo Hebra protection
B37Immune system
B41Immune system
B42Immune system
B44Measles seronegativity
Dengue fever protection
B46Rice farming association
B47Adrenal 21-hydroxylase deficiency
B48Immune system
B51Measles seropositivity
Behet's disease
B52Ulcerative colitis
Takayasu's arteritis
Dengue fever protection
B53Malaria protection
B57HIV protection
B58HIV protection
B59Immune system
B62Dengue fever protection
B63HIV protection
B67Immune system
B73Immune system
B76Dengue fever protection
B77Dengue fever protection
B78Immune system
B81Immune system
B*82Immune system
B*83Immune system
B*2705Influenza
B*3501Influenza
This is already more than four alleles with positive effects.
--Percy

This message is a reply to:
 Message 328 by bluegenes, posted 05-27-2017 9:39 AM bluegenes has replied

Replies to this message:
 Message 330 by bluegenes, posted 05-27-2017 12:19 PM Percy has seen this message but not replied

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


Message 330 of 518 (810293)
05-27-2017 12:19 PM
Reply to: Message 329 by Percy
05-27-2017 11:46 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Percy writes:
This is already more than four alleles with positive effects.
We could find plenty more, and your own pair of HLA-B alleles could have saved your life many times without us knowing. We tend to identify alleles that perform poorly against certain diseases because we're looking at the genes of the sick, not the healthy. But failing on one disease doesn't mean a negative mutant. The alleles failing at measles could have saved those kids' ancestors from smallpox for all we know.
When an allele is very successful, like B53 against West African malaria, the success can actually cause problems. More and more people could become homozygous on the B gene, therefore decreasing their range of immunity against other things. Also, if a mutant strain of malaria arrived that could avoid recognition by B53, there could be big problems, and that new strain would become dominant.
But variety means there could always be rarer alleles present that could cope with the new strain, so variety makes the species strong.

This message is a reply to:
 Message 329 by Percy, posted 05-27-2017 11:46 AM Percy has seen this message but not replied

  
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