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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


(1)
Message 350 of 518 (810730)
06-01-2017 8:40 AM
Reply to: Message 348 by Faith
06-01-2017 3:38 AM


Re: falling into place
Faith writes:
If none of the original genes had an allele that protects against malaria I suppose the mutant would be beneficial but it seems unlikely it isn't protected by the original alleles, there being some 240 genes in the immune system complex, as Percy reports in Message 242. With that many genes of two alleles each every known disease should be covered, no extra alleles needed.
In that message I had misinterpreted this sentence from the book The major histocompatibility complex (MHC) and its functions.
quote:
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.
This is saying that some genes of the MHC genes have more than 200 alleles. The book also explains that the frequency of occurrence for many alleles in the population is high enough to indicate strong selection, which means they're beneficial. This evidence proves false your ideas of an original two alleles for each gene and of mutations not being beneficial.
...having malaria protection scattered throughout the population is too hit or miss,...
This is what is observed.
...and besides, whatever belongs to the original two-allele system possessed by all people is more available for selection than the mutant since who knows where that's going to pop up?
The observed alleles are of ancient mutations that have spread and become distributed throughout the population, not of new mutations that just "pop up". Their frequency indicates strong selection.
--Percy

This message is a reply to:
 Message 348 by Faith, posted 06-01-2017 3:38 AM Faith has replied

Replies to this message:
 Message 351 by jar, posted 06-01-2017 8:54 AM Percy has seen this message but not replied
 Message 353 by Faith, posted 06-01-2017 11:25 AM Percy has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 386 of 518 (810850)
06-02-2017 7:58 AM
Reply to: Message 353 by Faith
06-01-2017 11:25 AM


Re: falling into place
Faith writes:
As for "popping up," that doesn't have to imply the mutation is new, just that because the alleles are scattered throughout the population any particular allele would be relatively rare and its location not predictable.
But they are not relatively rare - the alleles have a high frequency. That indicates strong selection. Alleles without strong selection are, as you called it, "relatively rare."
Evolution decrees that the high frequency means strong selection based on beneficial function. I continue to believe this is illusory and that it's really an overall destructive pattern in the immune system brought about by mutations, which as always are destructive mistakes even when they don't immediately cause disease.
That makes no sense. Mutations that are destructive and deleterious would have a low frequency in the population.
The fact that there are thousands of known genetic diseases in human beings is evidence that something is seriously misunderstood about the nature of mutations.
The alleles associated with genetic diseases have a low frequency in the population, just as expected. Those that bring both benefits and deficits, such as sickle cell, have a higher frequency. Those that bring only benefits have a higher frequency yet.
As I've been recognizing in the last few posts, there can't be any advantage to multiple alleles for a gene because they scatter the protective effects in the population,...
This is the herd effect. The frequency of the alleles is high enough to provide a beneficial level of protection to the population as a whole. And of course there's still the protection to the individuals.
--Percy

This message is a reply to:
 Message 353 by Faith, posted 06-01-2017 11:25 AM Faith has replied

Replies to this message:
 Message 389 by Faith, posted 06-02-2017 8:33 AM Percy has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


(1)
Message 387 of 518 (810851)
06-02-2017 8:11 AM
Reply to: Message 354 by Faith
06-01-2017 11:36 AM


Re: falling into place
Faith writes:
Yes, it is interesting that evolution allows for all that sloppiness so that it can't be easily used as evidence against it.
"Evolution" is just the term we apply to what we observe in nature. You can't argue that evolution must be wrong because so much sloppiness wouldn't work, because that is exactly what we observe working.
Probability alone suggests such inefficiency couldn't produce a single living cell let alone the complex living systems that exist, but aficionados will not be persuaded against their dear theory.
Now you're talking about the origin of life, not evolution.
I wonder how much more extinction and death it might take for the establishment to stop to consider maybe they are calling a disease process normal.
Mutations are both a blessing and a curse. They are what sustains variety and drives change, but they also cause disease and death.
--Percy

This message is a reply to:
 Message 354 by Faith, posted 06-01-2017 11:36 AM Faith has replied

Replies to this message:
 Message 392 by Faith, posted 06-02-2017 8:56 AM Percy has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 388 of 518 (810852)
06-02-2017 8:26 AM
Reply to: Message 357 by Faith
06-01-2017 11:55 AM


Re: Not trashed at all, in fact falling more clearly into place
Faith writes:
2) We have examples of thriving multiple alleles genes.
Diseases may thrive just as well.
Diseases cannot thrive if they affect the afflicted organism's ability to thrive and reproduce. This prevents a disease allele from achieving a high frequency in the population.
It seems clear to me that the insistence on its normality and health is based only on belief in the ToE,...
It's based upon observation. Mutation (copying errors) take place in almost every reproductive event.
It obviously exists for pete's sake, I haven't said it doesn't or can't, but yes I am trying to discredit what I see as a gigantic illusion that imputes helpfulness and normality to something that will eventually have to show itself to be inevitably destructive.
Except that it's obviously not "inevitably destructive". Most DNA doesn't do anything, and most mutations occur in those DNA regions. Those mutations that occur in active regions can have a beneficial, neutral or deleterious effect. They will be selected for or against based on their position on the spectrum from very beneficial to very deleterious.
First, those examples aren't quite as clear as you are claiming, they are in fact a pretty motley collection of hits and misses.
They were pretty clear, and they disproved your assertion that there were an original two alleles per gene, and that mutations can't be beneficial.
When I saw, only a few posts ago, that multiple alleles means scattered effects, that clinched it for me.
The alleles are distributed at different frequencies amongst the individuals of the population, but the important overall effect is for the population as a whole, which is very beneficial.
--Percy

This message is a reply to:
 Message 357 by Faith, posted 06-01-2017 11:55 AM Faith has not replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


(1)
Message 391 of 518 (810855)
06-02-2017 8:46 AM
Reply to: Message 366 by Faith
06-01-2017 2:07 PM


Re: Not trashed at all, in fact falling more clearly into place
Faith writes:
The MHC system has 240 genes, eye color and skin color have half a dozen or more genes.
But some genes of the MHC system have more than 200 alleles at frequencies too high to have occurred with an original two alleles per gene a mere 6000 years ago.
An extra allele in most cases, based on what we know about mutations, is either going to produce the same protein as the original or it's going to do something destructive.
Or it's going to produce something beneficial.
If it does do something different it will nevertheless be something that is done by some gene in the system;...there is no need for anything new, and the likelihood of getting something truly new and functional is about zero.
This bare assertion is obviously false. Even your own argument that a new allele could be deleterious argues against this, since a deleterious allele that is lethal couldn't already exist in the organism.
--Percy

This message is a reply to:
 Message 366 by Faith, posted 06-01-2017 2:07 PM Faith has not replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 394 of 518 (810860)
06-02-2017 9:36 AM
Reply to: Message 389 by Faith
06-02-2017 8:33 AM


Re: falling into place
Faith writes:
If there are many alleles per gene any given allele, even if "relatively" high frequency, is going to be relatively rare in the population as a whole because of sharing the field with so many others.
It isn't said what high frequency means in numbers or percentages either. In some contexts 5% could be high frequency.
Bluegenes would have to confirm, but I'd guess that anything above a percent or so is a relatively high frequency in the population. Here is Bluegene's list of the HLA-A (Human Leukocyte Antigen) allele frequencies from Cuban's with a dengue 2 virus infection history from Message 66:
HLAGene Frequency (%)
A*0222.7
A*3010.6
A*249.5
A*688.0
A*037.0
A*296.5
A*235.5
A*015.5
A*314.5
A*743.5
A*333.0
A*322.5
A*342.0
A*362.0
A*251.5
A*261.5
A*661.5
A*111.0
A*801.0
At the known human mutation rate there has not been enough time since Adam and Eve for all these alleles to arise, let alone spread through the population.
Also, as I argued way back on the thread, the frequency would be an illusion if the alleles are neutral mutations that produce the same phenotype as the allele they displaced, since they will simply be passed on without impediment. Selection in this case can't be a factor.
It is known that they bind to different antigens.
...meaning that the whole collection of mutant alleles is not a good thing for the function of the immune system because it scatters the protective effects in the population.
The meaning is the opposite, that the distribution of "protective" alleles throughout the population is a good thing. It provides protection of at least some individuals from a wide variety of threats so that the population has a lessened chance of being wiped out, and there's the benefit of herd immunity when the proportion of the population that is protected is high.
It is assumed under the ToE that the mutant alleles do something new and useful;
No, it is not assumed. As described several times now for the HLA genes, the alleles bind to different antigens.
My point was about mutations in general -- there is an enormous number of genetic diseases they've brought about that persist in the population...
Genetic disorders can only persist in the population if they don't prevent reproduction, and as the Wikipedia article on Genetic Disorders tells us:
quote:
Most genetic disorders are quite rare and affect one person in every several thousands or millions.
In other words, unlike the frequencies in Bluegenes table which were at least 1%, most genetic disorders have low frequencies that range from roughly between 0.00002% and 0.02%.
And some of this is demonstrable I'm sure; but a lot of it is just an article of faith based on the ToE and not a known reality.
It is all demonstrable. What we know about evolution is based upon observation of nature.
Is this demonstrable in relation to these mutant alleles or just a wishful statement in any given case?
Herd immunity is well understood. The protection to the entire herd is a function of the proportion of individuals in a population with immunity or some level of protection. As the Wikipedia article on Herd Immunity tells us:
quote:
The greater the proportion of individuals in a community who are immune, the smaller the probability that those who are not immune will come into contact with an infectious individual.
When the proportion with protective alleles is too small to provide herd immunity then at least some individuals are protected and the population survives with fewer individuals, but now with a very high frequency for the protective alleles.
But as I keep saying, if the original immune system had all the beneficial alleles that are now out there in the form of mutants, it would have had a much more reliable and concentrated protective effect because possessed by all individuals.
This is true. Were it so then disease immunity would be much more effective. Unfortunately, it isn't what we observe.
However, if the herd effect does apply I'll take that into account.
I'd take it into account only for protective alleles with a very high frequency.
--Percy

This message is a reply to:
 Message 389 by Faith, posted 06-02-2017 8:33 AM Faith has replied

Replies to this message:
 Message 399 by NoNukes, posted 06-02-2017 1:21 PM Percy has seen this message but not replied
 Message 402 by Faith, posted 06-02-2017 5:38 PM Percy has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


(2)
Message 395 of 518 (810861)
06-02-2017 9:49 AM
Reply to: Message 392 by Faith
06-02-2017 8:56 AM


Re: falling into place
Faith writes:
Not really, it is a theory that is imposed on nature so consistently that you think you are observing it.
All the facts we've provided to you in this thread reflect what has been observed.
But if you are just looking at those facts you may miss the larger picture that they are displacing what was once a far more efficient immune system.
There is no evidence of this in our genome. And as has been pointed out to you several times, there has been insufficient time since Adam and Eve for all the alleles we observe to arise and persist at the frequencies we observe.
Because of the Fall, which only a creationist is going to see unfortunately, the fact that things continue to function at all is a great blessing,...
The creationist doesn't see it, he only believes it. There is no real-world evidence of a Fall, and the ad hoc nature of the way our genes work is just what one would expect from chance and selection.
OK. How about "such inefficiency can't reliably protect against any given disease."
Except that it does work reliably enough (in the absence of antibiotics and vaccines) to keep the human race alive, which is all evolution attempts to achieve.
I may agree in the case of the immune system that they are better than some other things they are known to do since at least some of them offer some protection against disease.
They exist in the population at too high a frequency to do little or nothing. Strong selection is at work.
Variety and change are both built into the original DNA, in those two-allele genes of multiple-gene systems; it's very efficient when not garbled up by mutations.
It isn't possible for what we observe in our genome today to have arisen and distributed throughout the population in a mere 6000 years from an original two alleles per gene.
--Percy

This message is a reply to:
 Message 392 by Faith, posted 06-02-2017 8:56 AM Faith has replied

Replies to this message:
 Message 401 by Faith, posted 06-02-2017 5:35 PM Percy has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 403 of 518 (810934)
06-03-2017 8:21 AM
Reply to: Message 401 by Faith
06-02-2017 5:35 PM


Re: falling into place
Faith writes:
Not if the immune system is one of those regions that is particularly vulnerable to mutations,...
There is no evidence that the genes driving the immune system are "particularly vulnerable to mutations".
...which the enormous number of them suggests is the case although someone here denied this somewhere on the thread;...
The large number of different alleles at a high frequency is an indication of selection pressures.
...and if the great majority of them are neutral,...
They are not neutral. They bind to different antigens.
--Percy

This message is a reply to:
 Message 401 by Faith, posted 06-02-2017 5:35 PM Faith has not replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 404 of 518 (810935)
06-03-2017 8:34 AM
Reply to: Message 402 by Faith
06-02-2017 5:38 PM


Re: falling into place
Here is the table of alleles I presented in Message 321 that comes from the Wikipedia article on the HLA-B gene. The different alleles are distinguished from one another because they bind to different antigens:
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
And here's a list of HLA-A genes from Bluegenes for HLA allele frequencies from Cuban's with a dengue 2 virus infection history that I previously presented in Message 394:
HLAGene Frequency (%)
A*0222.7
A*3010.6
A*249.5
A*688.0
A*037.0
A*296.5
A*235.5
A*015.5
A*314.5
A*743.5
A*333.0
A*322.5
A*342.0
A*362.0
A*251.5
A*261.5
A*661.5
A*111.0
A*801.0
--Percy

This message is a reply to:
 Message 402 by Faith, posted 06-02-2017 5:38 PM Faith has not replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 410 of 518 (811021)
06-04-2017 8:41 AM
Reply to: Message 406 by Faith
06-03-2017 3:46 PM


Re: YEC requires selection on mutants
Faith writes:
I see mutations as mistakes.
Of course they're mistakes. As NoNukes said, they're copying errors. The most common adjective for "mutation" is "random", as in random mutation.
Haven't seen any evidence that all these alleles do anything new,...
Yes you have. You've been presented the examples of blood type, rabbit fur color, and the human immune system. All of these have alleles with new functions beyond the original two. In the case of the human immune system there are hundreds of alleles with new functions that couldn't have arisen in the number and frequencies that we observe in the short time available since Adam and Eve, not at currently observed mutation rates.
Time since Adam and Eve is irrelevant since things started over with the Flood and that's where counting alleles would have to begin I suppose.
The time since Adam and Eve is all that is relevant, since that is when you claim to know how many alleles there were.
All that's needed to create all the known diversity since the Ark is two alleles per gene shared by all individuals.
This is a new claim. When you say "two alleles per gene shared by all individuals" are you saying there were still only two alleles per each gene in the human population, just as with Adam and Eve? Or are you trying to say that each individual contributed two unique alleles per gene to the human population?
If there are too many mutations to have occurred in the last 4500 years since the Ark, what can I do but assume that for some reason they occurred a lot faster than usual since then, at least in the immune system which appears to be unusual for its great number.
A far higher mutation rate is required by your scenario, and there's no evidence of this higher rate. The large number of alleles in the human immune system also require a long period of strong selection in order to appear at their high frequencies in the population. There hasn't been near enough time since Adam and Eve for that to happen.
You don't need selection to increase the number of a certain allele in the population if it does the same thing as the original alleles or SOME original allele somewhere in the original system. Anything that actually functions is going to be passed on no matter what because there's no reason for it not to be.
In the human immune system we know the alleles perform different functions because the MHC molecules they produce bind to different antigens.
--Percy

This message is a reply to:
 Message 406 by Faith, posted 06-03-2017 3:46 PM Faith has replied

Replies to this message:
 Message 411 by Faith, posted 06-04-2017 1:22 PM Percy has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


(1)
Message 418 of 518 (811245)
06-06-2017 8:51 AM
Reply to: Message 411 by Faith
06-04-2017 1:22 PM


Re: YEC requires selection on mutants
Faith writes:
I was talking in the context of the immune system, and since I don't recall anything about what the originals do there's no way of knowing if the changes do anything new.
...
Again, the original function needs to be known and I don't recall that being identified. If it was I missed it. Please repeat it or link to it.
...
Different from each other, yes, but unknown if different from the original alleles.
The original function of the original alleles doesn't need to be known. We know that the original two alleles bound to at most two different antigens. And we know that today there are hundreds of alleles that bind to hundreds of different antigens. Therefore the different alleles of the modern human immune system have different functions, and many more functions, than the original two.
A far higher mutation rate is required by your scenario, and there's no evidence of this higher rate.
What evidence could there possibly be?
We've sequenced ancient DNA and there is no evidence for your higher mutation rate, for example, Oldest-known human genome sequenced:
quote:
A 45,000-year-old leg bone from Siberia has yielded the oldest genome sequence for Homo sapiens on record revealing a mysterious population that may once have spanned northern Asia. The DNA sequence from a male hunter-gatherer also offers tantalizing clues about modern humans’ journey from Africa to Europe, Asia and beyond, as well as their sexual encounters with Neanderthals.
They sequenced this ancient human DNA to such a level of detail that they could detect Neanderthal DNA, and yet there is no evidence of the large differences with modern human DNA that would have indicated a high mutation rate sometime between then and now.
--Percy

This message is a reply to:
 Message 411 by Faith, posted 06-04-2017 1:22 PM Faith has replied

Replies to this message:
 Message 419 by Faith, posted 06-07-2017 10:47 AM Percy has seen this message but not replied

  
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