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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
Faith 
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Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 384 of 518 (810844)
06-02-2017 5:10 AM
Reply to: Message 381 by NoNukes
06-01-2017 10:57 PM


Re: Not trashed at all, in fact falling more clearly into place
The sequence with multiple genes that can occupy a single location
Do you mean "alleles" instead of genes? If genes what do you mean by "occupy a single location?" Do you mean a segment of the DNA that is one gene after another for a particular system perhaps? I really can't follow you here.
...is different from entirely different genes at multiple locations on a chromosome. What can be similar is the phenotype that results.
In this case you are talking about genes for the same system being separated on the DNA strand?
Again I'm not sure what you are talking about, and it becomes even more puzzling when you mention a comparison with the phenotype. Sorry, I'm completely lost.
Edited by Faith, : No reason given.

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


Message 385 of 518 (810845)
06-02-2017 6:01 AM
Reply to: Message 383 by bluegenes
06-02-2017 5:05 AM


Re: Multiple Alleles an Inefficient System
bg writes:
Actually, there is a multi-gene/multi-allele system in Class I, because HLA*A and HLA*C do similar things and also have multiple alleles.
I don't know what these terms mean so all I can do is get a vague idea that there are different genes in something called a Class I that do similar things and have multiple alleles without having any idea what the class designation means or the different A and C categories mean. I also am not in a position to know whether their doing similar things is normal or a degenerated situation due to the Fall.
The problem with a fixed system (two unchanging alleles per gene) is that the pathogens are many and varied, and they mutate all the time. If a lethal mutant develops a strain that bypasses both fixed, immutable alleles on HLA-B and everything else in the immune system, that's potential species extinction. But it's very hard for a pathogen to get all of us if there are many alleles around.
It's a very logical idea, I grant, but it's also rather a Just-So story that one would expect to be incompatible with the processes of the ToE. Mutations are usually described as occurring rarely in the first place, and certainly beneficial ones far more rarely, and beyond that you are expecting that some will occur that manage to match up against a specific evolving pathogen? The odds strike me as astronomical -- no, impossible.
I'm not sure how my fixed system would work in this case either though. Either there is already a gene for the situation with an allele for the situation or there isn't I guess.
HIV is a classic example of a new, well adapted strain of something lethal, and sure enough, a small percentage of the population are immune to it.
OK but how that immunity has come about remains a question for me. You apparently impute it to the statistically impossible arrival of the appropriate mutation(s)?
Making a guess at how the fixed system would work in this case I have to imagine a gene that is already capable of protecting against HIV for whatever reason, that has been compromised by way too many mutations so that it is no longer reliably protective, but some "small percentage of the population" still has that immunity. It's no more improbable to my mind than the extremely improbable arrival of an appropriate mutation your system requires.
On each gene, half the population would be homozygous.
Homozygosity in the immune system would certainly be a disadvantage, but hardly answerable by the expectation of a mutation coming along just in time that's exactly matched to a pathogen that has just come along. Is it possible that the immune system has some kind of built-in solution to homozygosity?
Do you mean the intelligent designer could just match the genes to all the parasites out there that he had also, presumably, designed?
I have to imagine an original system design that is efficient enough to protect against all threats, yes, but on the other hand what exists now is not the original system but the damaged remains of the system due to the Fall. I don't expect any kind of perfection at this point. Both the damage to the original system and the evolution of new pathogens can be the consequence of the Fall. Reconstructing the original situation might be impossible by this point.
But then the originally designed parasites mutate, and.....?
Unfortunately it's all part of the degeneration due to the Fall, and coping with it is a monumental project, which biology ought to be focused on rather than accepting it all as just how things work normally through the processes of evolution.
Variance is what has been selected for, and although the different genes could all be present in Adam and Eve, all the variant alleles can't be.
True, but there is still the question in my mind just how variant these alleles are anyway. I expect major redundancy and nothing truly novel, the main upshot of their occurrence being to undermine rather than further the original functions of the immune system even if some of them do fortunately protect against some diseases.
So, that gives us positive selection on new functional information within our YEC model.
I think that "new functional information" is wishful and not real -- the idea that all these extra alleles are not only needed but actually formed to deal with constantly changing pathogens is logical and pretty but statistically impossible, the Just-So story I mentioned earlier. There seems to be some hit or miss positive function left, that's the best that can be said of it. (I also don't see selection playing anywhere near the big role the ToE gives it.)
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 383 by bluegenes, posted 06-02-2017 5:05 AM bluegenes has replied

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


Message 389 of 518 (810853)
06-02-2017 8:33 AM
Reply to: Message 386 by Percy
06-02-2017 7:58 AM


Re: falling into place
Percy writes:
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."
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.
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.
Percy writes:
Faith writes:
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.
But I said "even when they don't immediately cause disease" which means they aren't destructive and deleterious in themselves, they may even be beneficial in that they protect against some form of disease, though redundantly perhaps; what I said is that they are an "overall destructive pattern" in the immune system, 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. Certainly if the allele is a neutral mutation which merely produces the same protection as the original, and it is now just one of many mutant alleles scattered in the population, the original no longer has the scope and influence it had originally when everybody possessed it. It is assumed under the ToE that the mutant alleles do something new and useful; this I'm doubting.
Percy writes:
Faith writes:
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.
My point was about mutations in general -- there is an enormous number of genetic diseases they've brought about that persist in the population even if selected out in certain contexts, and what's to stop new ones from continuing to show up and remain? Clearly selection is far from a guarantee of riddance.
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.
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.
Percy writes:
Faith writes:
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.
Is this demonstrable in relation to these mutant alleles or just a wishful statement in any given case?
Percy writes:
And of course there's still the protection to the individuals.
Who are that limited segment of the population to possess the particular mutant allele. 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.
However, if the herd effect does apply I'll take that into account. Perhaps it is the answer to the problem of homozygosity that bluegenes brought up earlier.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 386 by Percy, posted 06-02-2017 7:58 AM Percy has replied

Replies to this message:
 Message 394 by Percy, posted 06-02-2017 9:36 AM Faith has replied
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 392 of 518 (810856)
06-02-2017 8:56 AM
Reply to: Message 387 by Percy
06-02-2017 8:11 AM


Re: falling into place
Percy writes:
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.
Not really, it is a theory that is imposed on nature so consistently that you think you are observing it.
Percy writes:
You can't argue that evolution must be wrong because so much sloppiness wouldn't work, because that is exactly what we observe working.
Yes as I said to jar I know because it is accepted as normal by the ToE it can't be used as evidence against it. Even if I can't argue it here I can still think it and I do. The sloppiness that seems to work in nature, like all those mutant alleles that are really a confused mess of different functions, manage to work sort-of, I agree; some of them in the immune system manage to protect against disease when they encounter it. 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. 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, but those who see the ToE as expressing the normal way things operate will completely miss the big picture of overall degeneration and take a highly compromised and broken functioning for the best possible.
Percy writes:
Faith writes:
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.
OK. How about "such inefficiency can't reliably protect against any given disease."
Percy writes:
Faith writes:
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.
That would be a very good statement of exactly what I mean by the effects of the Fall, except that I strongly dispute the idea that they sustain variety and drive change. Strongly dispute it. 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. But overall the idea that they do anything so positive as sustain variety and drive change is that article of faith based on the ToE again. 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.

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 Message 387 by Percy, posted 06-02-2017 8:11 AM Percy has replied

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


Message 400 of 518 (810885)
06-02-2017 4:26 PM
Reply to: Message 390 by herebedragons
06-02-2017 8:42 AM


Re: Multiple Alleles an Inefficient System
I have not been following this discussion super close because I just have not had time to. But I want to see if I understand your scenario and can put it into a clear narrative.
God created Adam and Eve with all the necessary genes and alleles to allow their immune system to fight off any pathogen that may attempt to invade their bodies. But because of the fall, mutations began to be introduced into an otherwise perfectly functioning system. As pathogens mutated they began to overcome the human immune system (through loss of information, of course) and they were then able to cause disease. As the human immune system began to mutate, the distribution of alleles became diluted and so a smaller and smaller proportion of people had a fully functioning immune system. Occasionally, a mutation in an immune system component would allow it to defend against a newer form of a pathogen, but this is an extremely rare exception.
Is this a good summary?
I hadn't thought it through in such detail, and I'm really only now trying to work out what I think the original created systems were, but to respond piece by piece to your statement:
God created Adam and Eve with all the necessary genes and alleles to allow their immune system to fight off any pathogen that may attempt to invade their bodies.
Yes.
But because of the fall, mutations began to be introduced into an otherwise perfectly functioning system.
And pathogens mutated. I'm not sure which came first, maybe more or less a simultaneous occurrence. Mutating pathogens could already be a problem if the system wasn't originally designed to deal with them, but I don't have a clear idea of whether it could or not.
As pathogens mutated they began to overcome the human immune system (through loss of information, of course) and they were then able to cause disease.
I don't see how loss of information comes into this. That's the result of evolution, the creation of new phenotypes by the loss of alleles. Mutated pathogens along with mutations to the immune system seem to me to both contribute to the loss of disease protection.
As the human immune system began to mutate, the distribution of alleles became diluted and so a smaller and smaller proportion of people had a fully functioning immune system.
More like: The mutations alter the original alleles, which were two per gene, and most of these would be neutral, not changing the phenotype or the action against a particular disease, and as these mutations accumulated, especially if there were many for a single gene, their effects would become scattered in the population making for a hit or miss system of protection against a particular disease. I suppose this implies that a smaller proportion of people would have a fully functioning immune system but I hadn't thought of it quite that way. It would depend partly on how many of the mutant alleles continue to do what the originals did. And since I'm doubtful that the mutant alleles would do anything truly novel I'm not sure I think they could really deal with new pathogens anyway. It could be that ability was already in the original system, however, and is now scattered through the population as other alleles proliferate at the same gene.
Occasionally, a mutation in an immune system component would allow it to defend against a newer form of a pathogen, but this is an extremely rare exception.
Well, but if there are many neutral mutations, meaning alleles that don't change the phenotype, they would continue to defend against diseases, whatever diseases the original protected against. For something truly new I would suppose it to be an extremely rare occurrence, yes.
I wasn't aiming to try to reconstruct the immune system but those are my guesses. I originally wanted to resolve the issue of Adam and Eve needing extra alleles and came to the conclusion that they didn't and also didn't even need the maximum possible four, just two per gene. That was a big discovery for me. That would mean that instead of the maximum possible on the Ark, which would have to have involved mutations at some earlier point, each gene in each individual would have had two alleles, but also greater heterozygosity than we have today, that being enough to create all the diversity that followed.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 390 by herebedragons, posted 06-02-2017 8:42 AM herebedragons has not replied

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


Message 401 of 518 (810887)
06-02-2017 5:35 PM
Reply to: Message 395 by Percy
06-02-2017 9:49 AM


Re: falling into place
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.
Not if the immune system is one of those regions that is particularly vulnerable to mutations, which the enormous number of them suggests is the case although someone here denied this somewhere on the thread; and if the great majority of them are neutral, not changing the phenotype, which means they would have high frequency without selection.

This message is a reply to:
 Message 395 by Percy, posted 06-02-2017 9:49 AM Percy has replied

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


Message 402 of 518 (810888)
06-02-2017 5:38 PM
Reply to: Message 394 by Percy
06-02-2017 9:36 AM


Re: falling into place
It is known that they bind to different antigens.
How many?
Which?

This message is a reply to:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 406 of 518 (810983)
06-03-2017 3:46 PM
Reply to: Message 405 by bluegenes
06-03-2017 9:43 AM


Re: YEC requires selection on mutants
I don't know if I'm tired, burning out on this topic, unable to make sense of the technical language or what, but I can't get anything out of what you are saying.
I see mutations as mistakes. Great if sometimes they don't destroy something. Haven't seen any evidence that all these alleles do anything new, so I assume they just do whatever the original alleles did for any given gene.
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. How could we know if any of the indiviudals on the Ark had mutant alleles anyway? All that's needed to create all the known diversity since the Ark is two alleles per gene shared by all individuals.
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.
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.
But I think I'm burned out on this topic.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 405 by bluegenes, posted 06-03-2017 9:43 AM bluegenes has replied

Replies to this message:
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 Message 410 by Percy, posted 06-04-2017 8:41 AM Faith has replied
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 408 of 518 (810999)
06-04-2017 12:01 AM
Reply to: Message 407 by NoNukes
06-03-2017 11:54 PM


Re: YEC requires selection on mutants
You seem to have missed the point given by bluegenes and others that selection is what causes the proliferation of a mutant allele, that is, causes its "relatively high frequency" in a population.
So what original gene provides protection against malaria so that there is no need for a mutation? Again you seem to be describing some kind of purposeful action when you know that mutations are errors/mistakes. That thinking is not logical.
I don't know. I don't know if anybody knows. All that's being discussed on this thread is the mutant alleles. The only "purposeful action" here is whatever the original allele did. All the immune system genes have specific functions directed against specific diseases. If a mutant allele does nothing more than produce the same phenotype there is no need for it, it would be better that there be no mutants since all they do is scatter the effects.

This message is a reply to:
 Message 407 by NoNukes, posted 06-03-2017 11:54 PM NoNukes has replied

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


Message 411 of 518 (811042)
06-04-2017 1:22 PM
Reply to: Message 410 by Percy
06-04-2017 8:41 AM


Re: YEC requires selection on mutants
Percy writes:
Faith writes:
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. ;
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.
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.
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.
And obviously I have to assume that the mutation rate was faster in the past.
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?
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.
If all the alleles do is what original alleles did there wouldn't be any selection. The function doesn't have to be the same as the original gene, just the same as any of the original alleles in the system, which is possible if the coding sequences are similar.
Percy writes:
Faith writes:
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.
Different from each other, yes, but unknown if different from the original alleles.
However, I'll concede the point anyway since I can't prove anything for my side, all I can do is guess about it. So the point has been made that there are more alleles than could have arisen in the time since Adam and Eve. I'm still going with two alleles per gene at the Creation so I'll still be trying to prove it.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 410 by Percy, posted 06-04-2017 8:41 AM Percy has replied

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


Message 413 of 518 (811049)
06-04-2017 2:18 PM
Reply to: Message 412 by NoNukes
06-04-2017 1:56 PM


Re: YEC requires selection on mutants
NN writes:
For example, if the original pattern was recessive, while the new mutant is dominant, then disease immunity of the overall population can be increased.
Just as a matter of fact, all the genes in the immune system are codominant.
NN writes:
Faith writes:
I'm still going with two alleles per gene at the Creation so I'll still be trying to prove it.
Why not four? How many alleles per gene for humans after the Flood? Isn't that just as rigorous a test?
It's possible there were mutant alleles on the Ark, but otherwise I'd expect them to have all the same genes with two alleles each just like Adam and Eve.
Why only two? Because it's elegant and it's sufficient to produce all the known diversity. Keep in mind there are usually multiple genes for each trait in this system, perhaps always. Multiple alleles are not needed and as I've argued are far less efficient. It's possible the immune system is an exception, but I doubt it.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 412 by NoNukes, posted 06-04-2017 1:56 PM NoNukes has replied

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


Message 415 of 518 (811078)
06-04-2017 8:02 PM
Reply to: Message 414 by NoNukes
06-04-2017 3:21 PM


Re: YEC requires selection on mutants
NN writes:
Let me phrase the question in the terms framed by the title of this thread. There were eight folks on the ark of which three were sons of Noah and his wife. Even including mutant alleles, would there be enough mutant alleles to account for what we see today. That means more alleles to start with, but less time to grow to what we see today.
I've conceded this point for now because there is no way to know and all I can do is suppose that the rate of mutation was much greater than the rate assumed to be standard. I don't think any time was needed to "grow," if the mutants for the most part do just what the originals did. The nondeleterious ones would spread in the population from generation to generation without any aid from selective pressures. But again that's the best I can do for now and I'm happy enough to concede the point -- for now.
NN writes:
Faith writes:
Why only two? Because it's elegant and it's sufficient to produce all the known diversity.
Whether or not two is enough, it has been demonstrated that two alleles alone did not produce the observed diversity in say, blood type as one example. But it is your proposal and not mine. You are welcome to it.
Well, it has NOT been demonstrated that two is not sufficient to produce the vast majority of diversity we see, not even in relation to the immune system since the originals have not been defined. The O blood type is apparently a mutation that lost some of the functions of the A and B types but not the basic function of a blood type as far as I know, but even though it makes it universally usable it seems to be an inferior version and that can't be a good thing. And I don't think albinism is a good thing so the rabbit fur example is at least compromised in its supposed beneficiality.
But I really would rather not have to keep putting my guesses forward here.

This message is a reply to:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 419 of 518 (811347)
06-07-2017 10:47 AM
Reply to: Message 418 by Percy
06-06-2017 8:51 AM


Re: YEC requires selection on mutants
I have to concede on this argument though of course I will be looking for ways to reopen it in the future. At the moment I'm not in a position to argue it.
But I will make one point: if all those mutant alleles really contribute to protection against many diseases it's rather odd that we seem (to me anyway) to have a lot more immune deficiency diseases than ever before. I note mention of them here and there, but I also have personal experience of it: A friend of mine suddenly acquired one a few years ago and was dead within six months of his first symptoms, a rare muscle-wasting immune deficiency disease that hit him out of the blue in the midst of what had seemed like a condition of robust health.

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