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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
Taq
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Posts: 8469
Joined: 03-06-2009
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Message 5 of 518 (808157)
05-08-2017 3:53 PM
Reply to: Message 4 by Davidjay
05-08-2017 11:32 AM


Davidjay writes:

Wow, a new thread, promoted instanteously, and very loosely worded, with no proofs of any statement declared by the Original poster.
Amazing, I must learn that methodology.... in proposing and getting accepted.

One suggestion would be to address the information in the opening post instead of trying to change the subject of every thread to numerology. Another would be to address the arguments made by other people instead of twisting their words to mean the opposite of what they actually said. Once you show that you can stay on topic and debate honestly, then your threads will be promoted more quickly.


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Taq
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Posts: 8469
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Member Rating: 6.0


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Message 7 of 518 (808159)
05-08-2017 4:22 PM


Counting Alleles
Just so we are all on the same page . . .

By my count, if the entire human race is descended from Noah's sons and their wives then we could have a maximum of:

1. Four alleles shared between the three sons, assuming that the four possible allleles (two paternal and two maternal) are found in at least one son.

2. Six alleles between the three wives (i.e. two each).

That makes for a total of 10 possible alleles for each gene. Do any YEC's want to argue against this count?

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


Replies to this message:
 Message 8 by Faith, posted 05-09-2017 8:55 AM Taq has responded

  
Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


Message 12 of 518 (808243)
05-09-2017 11:16 AM
Reply to: Message 8 by Faith
05-09-2017 8:55 AM


Re: Counting Alleles
Faith writes:

I don't know where the notion came from, but isn't it true that genes have two and only two alleles?

More to the point, if there are hundreds or even thousands of alleles for a single gene, would this require rapid evolution starting with the survivors of the ark, or as Percy states, starting with the two people who founded the human species?

What hit me recently is that genes have the two alleles, so that all those other alleles must be mutations that don't affect the function, the protein product or the phenotypic outcome.

Why couldn't there be more than two alleles, and why couldn't they all differ in function?

From the example of the skin color range it's clear that some traits are governed by more than one gene, each gene having two forms or alleles.

How did you determine that all skin color related genes only have two alleles?

I've many times suggested that "junk DNA" is a record of formerly functioning genes that have lost their function due to the Fall, most of it probably through destructive mutations. I still think this very likely but since it is now being claimed that it isn't junk and actually has a function I guess I have to wait and see what is concluded about that.

90% of the human genome is still considered junk when junk DNA is defined as DNA sequence which has no significant impact on fitness. We can determine it is junk because of the rate at which it accumulates mutations. Pseudogenes make up a small proportion of junk DNA.


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


Message 16 of 518 (808268)
05-09-2017 1:44 PM
Reply to: Message 14 by Faith
05-09-2017 1:15 PM


Re: Counting Alleles
Faith writes:

Sounds like you didn't read my whole post since I deal with that claim about genes having more than two alleles, so it needs to be answered.

You claimed that there are only two functional alleles for each gene, but never cited any evidence to back that up. It still needs to be dealt with.

As I said in my post, after giving the Bb example of a typical gene with two alleles, I suspect all those extra alleles people talk about are the result of mutations that don't change the function of the gene.

We need more than suspicion.


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


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Message 22 of 518 (808281)
05-09-2017 3:24 PM
Reply to: Message 18 by Faith
05-09-2017 2:42 PM


Re: Counting Alleles
Faith writes:

The skin color example I've given implies that there is so much variation built into two genes made up of two alleles each that we don't need greater numbers of alleles to get the entire range of diversity in humans and animals that we see today.

Where is the reference demonstrating that all human skin color is determined by two genes with two alleles each?

Three or four genes for the same trait with two alleles each would give enormous diversity.

Again, where is the evidence that all diversity is governed by two alleles at each gene locus?

Gary Parker showed it in a chart in "What is Creation Science?" -- the 16 different shades that result from only two genes with two alleles each.

What scientific papers is this based on?

Some people equate pseudogenes with junk DNA; different people give different percentages of how much junk DNA may be actually functional and so on.

That's because pseudogenes are junk DNA. There is also junk DNA that isn't pseudogenes. The different calculations on the amount of junk DNA are due to how people detect neutral drift in the genome, but those calculations are all returning numbers between 90 and 95% junk DNA. There is simply no rational reason to think that a majority of the human genome is functional, or that it has been functional at any recent point in history.

Edited by Taq, : No reason given.


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


Message 24 of 518 (808287)
05-09-2017 3:56 PM
Reply to: Message 23 by bluegenes
05-09-2017 3:40 PM


Re: Counting Alleles: 4 bunny alleles, many phenotypes
bluegenes writes:

Many of our immune system variant alleles will certainly have varying effects, because that's how they function - to combat many different foreign invaders.

A good example is HLA-DRB1 which has hundreds to thousands of known alleles.


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


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Message 38 of 518 (808355)
05-10-2017 11:04 AM
Reply to: Message 28 by Faith
05-09-2017 10:47 PM


Re: Counting Alleles
Faith writes:

The problem has always been how to explain all the variation we see without a lot of alleles in the population, and if there are all those alleles, as there are in some cases, where did they come from since Adam and Eve could have had a maximum of four.

Your first hurdle would be the fact that for many genes there are more than four alleles for a given gene. If your model requires just four alleles then it is a non-starter since it is falsified by reality.

And that made me start thinking down the line of how the extra alleles have to be mutations, most of which probably don't change what the gene does.

The fact that single base sequence differences are responsible for the functional differences between alleles is a serious problem for your model.

You have argued that genetic diversity can only go in one direction, from high diversity to low diversity. In your model we could start with many skin colors, and then through natural selection end up with a single allele for a single skin color which is a loss in genetic diversity.

However, if all it takes is a difference at one base in a specific gene then it is a certainty that a mutation will produce an individual with a different skin color in that population. There is nothing to stop this from occurring. Therefore, natural selection can reduce genetic diversity, but mutations are always increasing genetic diversity.

Well, you are one of the guys who studies genetics, and apparently what all the extra alleles do is not known by you either.

Then how can you say that there are only two functional alleles per gene?


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


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Message 40 of 518 (808381)
05-10-2017 12:31 PM
Reply to: Message 39 by Faith
05-10-2017 12:17 PM


Re: Counting Alleles
To be clear, the conclusion I've come to is that just TWO alleles per gene is all it takes to produce all the diversity we see, not four, especially where there is more than one gene per trait, and even more especially where there were a lot more living genes, that are now junk DNA.

That would be a hypothesis, not a conclusion.

I was trying to account for all those extra alleles until I realized they aren't needed for diversity.

What evidence led you to that realization?

What combination of human alleles will produce a cat, or a chimp?

As I do keep arguing, the way genetic diversity is lost is by isolation of a group from the rest of the population. This produces new phenotypes -- this is in fact what evolution really is, the production of new phenotypes through the loss of genetic diversity, that's why "evolution defeats evolution." You'll get a new race by this process, new races of animals, new varieties of plants, but in every case by losing genetic diversity. Natural selection does this, as does domestic/artificial selection, but the most common way it happens in the wild is probably migration and geographic isolation of a new population.

That doesn't change the fact that mutations can produce new phenotypes.

OK, but how often does this happen? Mutations are accidents of replication, right?

Each person is born with 50 mutations. With a 3 billion base haploid genome and 3 possible changes at each base that is 9 billion possible substitution mutations. 9 billion mutations divided by 50 is 180 million. So it takes 180 million births to get every possible substitution mutation in the human genome. If the mutation involves a mutation at the 3rd base in a codon and there is 3rd base wobble then it would take even fewer mutations to produce the same mutation in the protein sequence. With the current human population, this mutation should be occurring nearly every year.

And if you do get such a beneficial change, say you get a different skin color in the population OK, but it won't be a novel skin color. Seems to me the best that could happen is that a formerly lost allele would be accidentally reproduced by mutation and bring back a lost skin color.

That would still be an increase in genetic diversity due to mutation.

But even with the known proliferation of mutations how often is even one beneficial mutation demonstrable?

They are demonstrated every time we compare the genomes of two different species. The mutations that are beneficial to humans are among those that separate us from chimps.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


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 Message 39 by Faith, posted 05-10-2017 12:17 PM Faith has responded

Replies to this message:
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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


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Message 45 of 518 (808400)
05-10-2017 2:38 PM
Reply to: Message 41 by Faith
05-10-2017 1:19 PM


Re: Counting Alleles
Faith writes:

Fine, but it's a new hypothesis for me, a new conclusion in relation to my former position.

A conclusion would require a testable hypothesis and supporting evidence, neither of which you have at the moment. It seems that you have the beginnings of a hypothesis. Now you just need to figure out how to test it and how it could be falsified.

The evidence is all in the reasoning. The fact that you can get two different eye colors from one gene with two alleles, and eight different skin colors from two genes with two alleles each.

That doesn't compute. Just because skin color may need only two alleles does not mean that other characteristics don't need more. You can't take one example and claim it is true for the rest of the genome.

And greater heterozygosity (genes with two different alleles) in former times along with a larger number of functioning genes (before they died and became "junk DNA") would produce a LOT of variation down the generations from there.

How did you determine that the hundreds of thousands of human pseudogenes were functional in the recent past? What evidence, if found, would falsify your hypothesis that human pseudogenes were active just a few thousand years ago?

Three genes for eye color, three for skin color, three for any other traits you want to name, in all their many possible combinations, would produce an enormous range of variation, new races/varieties/species too.

This is what led me to this question:

"What combination of human alleles will produce a cat, or a chimp?"

If a combination of human alleles can not produce a cat or a chimp, then how do we have cats and chimps? You seem to be saying that a human could give birth to a cat simply by a combination of human alleles already found in the mother and father.

If that isn't the case, then why are cats different from humans? If human alleles are not capable of producing the biodiversity we see, then what is producing it?

Can. But only as an accident, a fluke, and so rarely as to be of no use to the organism. Besides which, again, this is far more an article of faith than it is a demonstrated reality. And meanwhile mutations are known to have produced thousands of genetic diseases, and in the best scenarios they simply don't change anything.

If the alleles are currently of use to humans, then why wouldn't they be of use when they are produced by mutations?

Also, mutations aren't an article of faith. We can watch them happen. They are a fact. Why in the world would you claim that mutations don't happen?

You say all that as if it were a good thing. I can't see mutations as a good thing at all. Mostly neutral, secondly deleterious and very very rarely as a fluke maybe beneficial, usually in a way that piggybacks on something else like the sickle cell trade-off. I think all those mutations are bad for us, disease processes that over time will accumulate into actual diseases.

If the human genome can't be changed without causing disease, then how can other species survive with all of these differences? When we compare chimps and humans we find 40 million mutations separating them. How are chimps able to survive, disease free, with so many mutations?

Yes, but what are the odds you'll even get that? Mutations are accidents, the beneficial effects have to be rare flukes.

Winning the lottery is also a fluke of luck, yet it happens all of the time.

But this is only an assumption based on your acceptance of the ToE, it has not been demonstrated. You assume mutations are the explanation for the differences, you haven't proved it at all, it's just that the theory tells you this is how it happens. It's all theory, no evidence.

If the DNA sequence differences are not responsible for the physical differences between species, then what is?


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


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


Re: Counting Alleles
Faith writes:

Tis indeed all abstract, but so is the ToE, so is the claim that mutations are the source of variation, and in that case not just abstract but pure wishful thinking.

Which of these is abstract or wishful thinking?

1. Mutations happen.
2. The difference in function between alleles is due a difference in DNA sequence.
3. The physical differences between species is due to DNA sequence differences in their genomes.


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


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Message 62 of 518 (808511)
05-11-2017 10:44 AM
Reply to: Message 47 by Faith
05-10-2017 8:05 PM


Re: Counting Alleles
Faith writes:

These are not statements of the ToE.

That's a flat out lie. Those are all statements from the theory of evolution.

All the time and it is not a good thing.

That is an empty assertion with zero evidence to back it.

Yes but misleading since evos attribute the differences to mutation which mostly creates no differences in function or undesirable differences.

If differences in DNA sequence do not create differences in function, then how in the world do you explain why species look different from each other? How do you explain why alleles function differently from each other?

You aren't making any sense at all.

Another misleading definition and I'm not sure it's completely true as stated anyway. That is, the crucial differences may be in particular parts of the genome; that is, in particular sequences that are responsible for particular differences rather than in a mere summation of sequence differences.

Why aren't the differences between species due to the summation of differences in their genomes? Where in the world do you think the physical differences between species comes from?


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


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Message 63 of 518 (808513)
05-11-2017 10:48 AM
Reply to: Message 49 by Faith
05-11-2017 1:19 AM


Re: The YEC model requires ...
Faith writes:

I'm going with two alleles per gene

For the HLA-DRB1 gene there are thousands of alleles in the human population. Your model is falsified.

No beneficial mutations, they are all an interference

Chimps have 40 million mutations compared to the human genome and they do just fine. Your model is falsified once again.

If the human genome can't be changed at all without causing "interference" then humans should be the only species in existence. Obviously, they aren't. Your model is falsified.

Strong selection isn't needed, nor drift, though either might occur; just migration + isolation

Strong selection exists and occurs. Since your model can't incorporate reality, it is falsified.


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


Message 64 of 518 (808516)
05-11-2017 10:50 AM
Reply to: Message 53 by Faith
05-11-2017 2:00 AM


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

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

If the DNA sequence of the human genome can't be changed to produce new function then humans should be the only species on Earth. That is what your model predicts.

If changes in DNA sequence can lead to new function and new species, then mutations can produce new functions and new species.


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


Message 65 of 518 (808518)
05-11-2017 10:53 AM
Reply to: Message 61 by Percy
05-11-2017 8:27 AM


Re: The YEC model requires ...
Percy writes:

I agree, but I think more argument and clarification is needed for your position. Why is a (restating) "5% rate of occurrence or more in the sample for at least five MHC alleles" impossible in 300 generations by drift alone?

Another question would be why all other genes don't have the same variation.


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Taq
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Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


Message 71 of 518 (808576)
05-11-2017 1:53 PM
Reply to: Message 70 by Faith
05-11-2017 1:35 PM


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

In my model mutations are an accident, a disease process fundamentally, even if mot of the time they manage to avoid changing a functioning allele, meaning they have the same function as the allele they replace; or, rarely, even manage to create a new sequence that really does do something beneficially different (I have my doubts about this but that discussion would be far down the road for me).

This would mean that humans can be the only species in existence because the only possible function is that found in the human genome. Since this isn't true, your model is falsified.

I don't expect anything good to come of mutations, though, at best noninterference with the function of the allele they change.

Then you wouldn't expect other species to have a genome that differs from humans. Since they do differ, your model is falsified.


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