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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
bluegenes
Member (Idle past 1372 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 301 of 518 (810139)
05-24-2017 4:32 AM
Reply to: Message 291 by Percy
05-23-2017 9:40 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Percy writes:

Asking the same question I asked Taq, why do you say that the alleles bind to peptides, instead of that proteins produced by the alleles bind to the peptides?

Casual language, like saying General Custer's orders killed the Indians, rather than his soldiers, or their weapons. "Guns kill" says the anti-gun lobby. "Guns don't kill, people do" say the NRA. It's lucky people like you are around to remind us all that it's actually the bullets.

Percy writes:

I found the paper impenetrable.

What the papers show is that the proteins produced by the differing alleles are different, and that they function differently in relation to pathogens. As I pointed out in the post you're replying to, the HLA-B (one gene) alleles are well known to have very different effects in relation to different diseases. If you want, I can dig up specific numbered alleles (like, from memory, HLA-B27 and HlA-B57 being good against HIV (Aids), HLA B-53 against a lethal form of West African Malaria, HLA-B7 and B51 working well against measles and so on and on and on.....

Edited by bluegenes, : typo


This message is a reply to:
 Message 291 by Percy, posted 05-23-2017 9:40 AM Percy has responded

Replies to this message:
 Message 304 by Percy, posted 05-24-2017 8:32 AM bluegenes has not yet responded

  
Percy
Member
Posts: 20105
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 302 of 518 (810147)
05-24-2017 8:10 AM
Reply to: Message 297 by Taq
05-23-2017 2:51 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
Taq writes:

The next thing that Faith wants to know is how the connection is made between binding to different peptides and improving the performance of the immune system.

Although the HLA proteins were only tested against dengue virus, the same pattern carries over to other pathogens. Different alleles will bind differently to certain pathogens, changing the defenses you have against those pathogens. I believe bluegenes listed some of those examples in previous posts.

I think Faith would object that you've got computer simulations and laboratory experiments that show alleles binding to different peptides, but that that's not evidence that they have different functions. Where is the evidence that allele X binding to peptide Y of dengue fever has any different effect than allele X binding to peptide Z of dengue fever?

--Percy


This message is a reply to:
 Message 297 by Taq, posted 05-23-2017 2:51 PM Taq has responded

Replies to this message:
 Message 307 by Taq, posted 05-24-2017 10:38 AM Percy has responded

  
Percy
Member
Posts: 20105
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 303 of 518 (810148)
05-24-2017 8:27 AM
Reply to: Message 298 by NoNukes
05-24-2017 12:52 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
NoNukes writes:

For now, why isn't the blood type answer a sufficient example?

I don't know why Faith answered as she did in Message 299, but the sudden capitulation is inconsistent with the rest of her posts to this thread and I don't think she's saying what she believes.

I don't think either blood type or rabbit fur color proves multiple functional new alleles have come about, because multiple genes must be involved. The Wikipedia article on Blood Type says that "33 blood-group systems have been identified, including the ABO and Rh systems," which implies multiple genes at work. And I couldn't find anything about rabbit fur color earlier in the thread, but I assume it too is governed by multiple genes.

--Percy


This message is a reply to:
 Message 298 by NoNukes, posted 05-24-2017 12:52 AM NoNukes has responded

Replies to this message:
 Message 305 by Faith, posted 05-24-2017 9:15 AM Percy has responded
 Message 312 by NoNukes, posted 05-24-2017 5:52 PM Percy has responded

  
Percy
Member
Posts: 20105
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 304 of 518 (810149)
05-24-2017 8:32 AM
Reply to: Message 301 by bluegenes
05-24-2017 4:32 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
bluegenes writes:

As I pointed out in the post you're replying to, the HLA-B (one gene) alleles are well known to have very different effects in relation to different diseases.

I think this is what Faith is asking for, that it be shown that alleles binding to different peptides have "different effects in relation to different diseases."

--Percy


This message is a reply to:
 Message 301 by bluegenes, posted 05-24-2017 4:32 AM bluegenes has not yet responded

  
Faith 
Suspended Member (Idle past 339 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 305 of 518 (810153)
05-24-2017 9:15 AM
Reply to: Message 303 by Percy
05-24-2017 8:27 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
I don't know why Faith answered as she did in Message 299, but the sudden capitulation is inconsistent with the rest of her posts to this thread and I don't think she's saying what she believes.

I'm just tired of fighting it and trying to leave for a while. I can't answer the supposed evidences given so even though I might again try to answer them in the future, not right now. I need a break. Capitulating just means I can't prove my case and am giving up trying.

I don't think either blood type or rabbit fur color proves multiple functional new alleles have come about, because multiple genes must be involved. The Wikipedia article on Blood Type says that "33 blood-group systems have been identified, including the ABO and Rh systems," which implies multiple genes at work. And I couldn't find anything about rabbit fur color earlier in the thread, but I assume it too is governed by multiple genes.

The post about rabbits is Message 23 where bluegenes clearly says the varieties of fur color are from different alleles for one gene. Says it, doesn't prove it, so if you can pin it down to multiple genes more power to you.


This message is a reply to:
 Message 303 by Percy, posted 05-24-2017 8:27 AM Percy has responded

Replies to this message:
 Message 306 by Percy, posted 05-24-2017 9:29 AM Faith has not yet responded

  
Percy
Member
Posts: 20105
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


(1)
Message 306 of 518 (810154)
05-24-2017 9:29 AM
Reply to: Message 305 by Faith
05-24-2017 9:15 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Faith writes:

The post about rabbits is Message 23...

Ah, "bunnies", not "rabbits" - thanks for the reference.

...where bluegenes clearly says the varieties of fur color are from different alleles for one gene. Says it, doesn't prove it, so if you can pin it down to multiple genes more power to you.

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.

--Percy


This message is a reply to:
 Message 305 by Faith, posted 05-24-2017 9:15 AM Faith has not yet responded

Replies to this message:
 Message 319 by NoNukes, posted 05-25-2017 12:17 PM Percy has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 307 of 518 (810158)
05-24-2017 10:38 AM
Reply to: Message 302 by Percy
05-24-2017 8:10 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Percy writes:

I think Faith would object that you've got computer simulations and laboratory experiments that show alleles binding to different peptides, but that that's not evidence that they have different functions.

A change in binding specificity is a change in function by every definition used in biology.


This message is a reply to:
 Message 302 by Percy, posted 05-24-2017 8:10 AM Percy has responded

Replies to this message:
 Message 308 by Percy, posted 05-24-2017 10:53 AM Taq has responded

  
Percy
Member
Posts: 20105
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 308 of 518 (810161)
05-24-2017 10:53 AM
Reply to: Message 307 by Taq
05-24-2017 10:38 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Taq writes:

A change in binding specificity is a change in function by every definition used in biology.

Faith is looking at outcome to determine change in function. If allele A binds to peptide X and dengue fever goes away, and if allele B binds to peptide Y and dengue fever goes away, that isn't a difference in function.

--Percy


This message is a reply to:
 Message 307 by Taq, posted 05-24-2017 10:38 AM Taq has responded

Replies to this message:
 Message 309 by Taq, posted 05-24-2017 11:25 AM Percy has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 309 of 518 (810163)
05-24-2017 11:25 AM
Reply to: Message 308 by Percy
05-24-2017 10:53 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Faith writes:

Faith is looking at outcome to determine change in function. If allele A binds to peptide X and dengue fever goes away, and if allele B binds to peptide Y and dengue fever goes away, that isn't a difference in function.

Function is not a synonym for outcome. What these alleles demonstrate is that different functions can produce the same outcome.

More to your point, bluegenes already referenced how different alleles do result in different outcomes. For example, different alleles are more effective at fighting off malaria or HIV.


This message is a reply to:
 Message 308 by Percy, posted 05-24-2017 10:53 AM Percy has responded

Replies to this message:
 Message 310 by Percy, posted 05-24-2017 1:04 PM Taq has responded

  
Percy
Member
Posts: 20105
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 310 of 518 (810165)
05-24-2017 1:04 PM
Reply to: Message 309 by Taq
05-24-2017 11:25 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Taq writes:

Function is not a synonym for outcome. What these alleles demonstrate is that different functions can produce the same outcome.

Faith will have to confirm, but I think for her the outcome she can observe is what is key. Different chemical pathways to the same outcome is a difference without a distinction for her.

More to your point, bluegenes already referenced how different alleles do result in different outcomes. For example, different alleles are more effective at fighting off malaria or HIV.

Let me recount the rough details on this one. The HLA-B53 allele fights malaria, and another HLA-B allele fights another form of malaria, and other HLA-B alleles are effective against HIV. Other HLA-B alleles fight other diseases, such as dengue fever. So the HLA-B gene is an example of different alleles producing different outcomes.

While researching this I came across the Wikipedia article on the History and Naming of Human Leukocyte Antigens, while includes a great deal of information about the HLA-A gene. This gene is of key significance in organ transplants. The types of HLA-A alleles must be matched as closely as possible or the organ will be rejected. Organ rejection is a substantial outcome.

--Percy


This message is a reply to:
 Message 309 by Taq, posted 05-24-2017 11:25 AM Taq has responded

Replies to this message:
 Message 311 by Taq, posted 05-24-2017 2:23 PM Percy has acknowledged this reply

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 311 of 518 (810168)
05-24-2017 2:23 PM
Reply to: Message 310 by Percy
05-24-2017 1:04 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
Percy writes:

Faith will have to confirm, but I think for her the outcome she can observe is what is key. Different chemical pathways to the same outcome is a difference without a distinction for her.

The problem is that Faith's views are not relevant to how biology actually works. You can't start with two HLA-B alleles and produce all of the observed functional diversity of HLA-B proteins. If you do start with two HLA-B alleles, then you need lots of mutations to produce the functional diversity for the HLA-B gene.

Let me recount the rough details on this one. The HLA-B53 allele fights malaria, and another HLA-B allele fights another form of malaria, and other HLA-B alleles are effective against HIV. Other HLA-B alleles fight other diseases, such as dengue fever. So the HLA-B gene is an example of different alleles producing different outcomes.

That meshes with what I have read on the subject. It really isn't that surprising given how different HLA alleles bind to different peptides derived from human pathogens. This will almost necessarily result in different outcomes for different pathogens. If there are situations where there is strong natural selection, such as in the case of pathogens linked to high mortality rates (e.g. HIV, malaria), we can see selection for specific HLA alleles in those populations.


This message is a reply to:
 Message 310 by Percy, posted 05-24-2017 1:04 PM Percy has acknowledged this reply

  
NoNukes
Inactive Member


Message 312 of 518 (810172)
05-24-2017 5:52 PM
Reply to: Message 303 by Percy
05-24-2017 8:27 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
don't think either blood type or rabbit fur color proves multiple functional new alleles have come about, because multiple genes must be involved.

For a lot of traits, yes. But for blood type, and the particular rabbit gene in question, no. Human blood type, in particular, is determined by a single gene with three alleles. Period.

The real question for blood type is why three is sufficient. Four would be required.

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 303 by Percy, posted 05-24-2017 8:27 AM Percy has responded

Replies to this message:
 Message 313 by Taq, posted 05-24-2017 6:02 PM NoNukes has responded
 Message 315 by Percy, posted 05-25-2017 7:46 AM NoNukes has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 313 of 518 (810174)
05-24-2017 6:02 PM
Reply to: Message 312 by NoNukes
05-24-2017 5:52 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
NoNukes writes:

The real question for blood type is why three is sufficient. Four would be required.

For human beta-hemoglobin there are at least 3 alleles with different functions. There is HbA, HbS, and HbC. The A allele is the most common. The S allele is the sickle cell trait which confers resistance to malaria while also causing problems with your red blood cells. The C allele also confers resistance to malaria but it does not have the same deleterious side effects compared to the S allele.

This is yet another example of a human gene with more than 2 alleles.


This message is a reply to:
 Message 312 by NoNukes, posted 05-24-2017 5:52 PM NoNukes has responded

Replies to this message:
 Message 314 by Percy, posted 05-25-2017 7:29 AM Taq has responded
 Message 320 by NoNukes, posted 05-25-2017 11:00 PM Taq has not yet responded

  
Percy
Member
Posts: 20105
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 314 of 518 (810195)
05-25-2017 7:29 AM
Reply to: Message 313 by Taq
05-24-2017 6:02 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
Taq writes:

This is yet another example of a human gene with more than 2 alleles.

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.

--Percy


This message is a reply to:
 Message 313 by Taq, posted 05-24-2017 6:02 PM Taq has responded

Replies to this message:
 Message 316 by bluegenes, posted 05-25-2017 8:47 AM Percy has responded
 Message 317 by Taq, posted 05-25-2017 10:39 AM Percy has responded

  
Percy
Member
Posts: 20105
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 315 of 518 (810196)
05-25-2017 7:46 AM
Reply to: Message 312 by NoNukes
05-24-2017 5:52 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
NoNukes writes:

don't think either blood type or rabbit fur color proves multiple functional new alleles have come about, because multiple genes must be involved.

For a lot of traits, yes. But for blood type, and the particular rabbit gene in question, no. Human blood type, in particular, is determined by a single gene with three alleles. Period.

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 and Rh systems are just the most important classifications of blood type because of their impact on transfusions - there are others. From Wikipedia:

quote:
33 blood-group systems have been identified, including the ABO and Rh systems. Thus, in addition to the ABO antigens and Rh antigens, many other antigens are expressed on the RBC surface membrane. For example, an individual can be AB, D positive, and at the same time M and N positive (MNS system), K positive (Kell system), Lea or Leb negative (Lewis system), and so on, being positive or negative for each blood group system antigen. Many of the blood group systems were named after the patients in whom the corresponding antibodies were initially encountered.

According to Wikipedia, the Kell antigen system, "is the next most common immune red cell antibody after those in the ABO and Rh system."

These other blood group systems are governed by other genes and have their own alleles.

--Percy


This message is a reply to:
 Message 312 by NoNukes, posted 05-24-2017 5:52 PM NoNukes has responded

Replies to this message:
 Message 318 by NoNukes, posted 05-25-2017 11:39 AM Percy has acknowledged this reply

  
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