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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
Taq
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Posts: 8482
Joined: 03-06-2009
Member Rating: 5.2


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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Faith 
Suspended Member (Idle past 309 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 17 of 518 (808273)
05-09-2017 2:27 PM
Reply to: Message 10 by Percy
05-09-2017 10:45 AM


Re: Counting Alleles
Restating the problem, assume that around 6500 years ago there were originally only two people, Adam and Eve.
Since each gene of a person can have at most two alleles, then Adam could have contributed at most two alleles for each gene, and the same for Eve.

Well, if I'm getting what you are saying, I think it's really only one that each person would contribute to the next generation. We possess two alleles per gene (no matter how many there might be circulating in the population), one from father and one from mother (I got blue eyes from a combination of my parents' alleles: a b from my mother's Bb and a b from my father's bb; my sister got her brown eyes from our mother's B and of course our father's b).

Again, we all get a gene made up of two alleles from our parents, NO MATTER how many there might be in the whole human population.

Is this correct?

This means that the most number of alleles any gene could have for both Adam and Eve (the total human population in the beginning) and all their descendants is four, so the most number of alleles of any gene in the modern human population is also four.

If each person had their own two alleles different from others' yes, and I was thinking along those lines until just recently. But when I realized how the blue eyes/ brown eyes gene works I saw that the same two in each person works fine; it's standard for that particular gene. And then seeing that only two genes for skin color with two alleles each is all it takes to produce 16 different skin colors (abe; Well, sixteen combinations but the color shades are probably eight), the entire range of color from darkest through many shades in the mid range to lightest, it became clear that we don't NEED more than two alleles per gene to get a lot of diversity.

That's a different question from whether there ARE more alleles for some genes in the population, and bluegenes has given the example of blood type which is an interesting one. Also, Parker, who gives the skin color example, says he thinks there may be three genes involved in skin color -- not more than two alleles per gene though. But his calculation of 16 different shades is based on only two genes with two alleles each.

Since we know today through genetic analysis that some genes of the human population have more than four alleles true that there have been mutations in those genes, or that there were originally more than two people, or both that there have been mutations and there were originally more than two people.

Yes, and I'd been assuming that all those different alleles were proof of functioning mutations, but when it occurred to me they may not actually change anything in what the gene does I figured they aren't really functioning alleles but neutral mutations. Or most or some of them anyway. Bluegenes' example of blood types is all I know about so far of more than two alleles for a gene that actually change its function. (But some discussion is needed on this too since O and AB are sort of combinations of A and B(?)

Edited by Faith, : No reason given.


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Faith 
Suspended Member (Idle past 309 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 18 of 518 (808275)
05-09-2017 2:42 PM
Reply to: Message 12 by Taq
05-09-2017 11:16 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?

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

But again not needing it isn't the same as whether it exists or not. If it does I don't see how it would contribute to any different rate of speciation in any time period.

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?

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. He also suggested there may be three genes for skin color but his calculation was based on two.

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.

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

Edited by Faith, : No reason given.


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RAZD
Member (Idle past 270 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 19 of 518 (808276)
05-09-2017 2:54 PM
Reply to: Message 16 by Taq
05-09-2017 1:44 PM


Counting Alleles - note on junk DNA
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.

Note that some creationists, including Faith iirc, posit junk DNA as either a source of new alleles or as a repository to old ones no longer used.

To change from active DNA to junk DNA or vice versa would de facto take at least one mutation.

And of course you can take some one's allele DNA and make a copy of it from bits and pieces of junk DNA ... but that is not a test or validation of the concept: you could also do such rearrangements and end up with the DNA for an elephant.

Enjoy


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This message is a reply to:
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herebedragons
Member (Idle past 597 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 20 of 518 (808278)
05-09-2017 3:05 PM
Reply to: Message 18 by Faith
05-09-2017 2:42 PM


Re: Counting Alleles
different people give different percentages of how much junk DNA may be actually functional and so on.

It also depends on how one defines "function." Is a spacer between gene copies "functional?" Are sections of DNA that fold into secondary structures (that may or may not have an influence on expression) "functional?" etc, etc.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


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herebedragons
Member (Idle past 597 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 21 of 518 (808280)
05-09-2017 3:07 PM
Reply to: Message 19 by RAZD
05-09-2017 2:54 PM


Re: Counting Alleles - note on junk DNA
Note that some creationists, including Faith iirc, posit junk DNA as either a source of new alleles or as a repository to old ones no longer used.

Faith has stated that, at least some "junk DNA" is dead genes, genes that have been inactivated by mutations. I doubt she would consider that a source of new genes.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 19 by RAZD, posted 05-09-2017 2:54 PM RAZD has acknowledged this reply

  
Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 5.2


(1)
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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bluegenes
Member (Idle past 1342 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 23 of 518 (808283)
05-09-2017 3:40 PM
Reply to: Message 17 by Faith
05-09-2017 2:27 PM


Counting Alleles: 4 bunny alleles, many phenotypes
Faith writes:

Bluegenes' example of blood types is all I know about so far of more than two alleles for a gene that actually change its function. (But some discussion is needed on this too since O and AB are sort of combinations of A and B(?)

A bit late for Easter, but here's some cute bunnies. They have four alleles on a gene that deals with colouring, and a lot of phenotypes can be produced from them.

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

There's a problem inherent with the model of building up the variation from a recent 4,500 yr old bottleneck.

And I haven't even got around to the Y Chromosome diversity yet!

Would you say that your views are fairly close to those of the Answers in Genesis guy who I quoted earlier in the thread?


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Replies to this message:
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Taq
Member
Posts: 8482
Joined: 03-06-2009
Member Rating: 5.2


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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bluegenes
Member (Idle past 1342 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 25 of 518 (808289)
05-09-2017 4:21 PM
Reply to: Message 24 by Taq
05-09-2017 3:56 PM


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

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.

The interesting thing is, on most genes, as individuals, we shouldn't be varying from Adam and Eve's original 4, especially with the Noah bottleneck, because 300 generations of mutations shouldn't give a hit on an average sized gene per. person. So, if it's very easy to find a lot more than 4 alleles in a small sample of the population, our YEC model looks to be in trouble.

Quelle surprise


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bluegenes
Member (Idle past 1342 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 26 of 518 (808294)
05-09-2017 6:55 PM
Reply to: Message 17 by Faith
05-09-2017 2:27 PM


Immune system variation
To further illustrate what I was saying about extreme polymorphism in the immune system:

The major histocompatibility complex (MHC) and its functions. NCBI

quote:

Because of the polygeny of the MHC, every person will express at least three different antigen-presenting MHC class I molecules and three (or sometimes four) MHC class II molecules on his or her cells. In fact, the number of different MHC molecules expressed on the cells of most people is greater because of the extreme polymorphism of the MHC and the codominant expression of MHC gene products.

The term polymorphism comes from the Greek poly, meaning many, and morphe, meaning shape or structure. As used here, it means within-species variation at a gene locus, and thus in its protein product; the variant genes that can occupy the locus are termed alleles. 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. So there is only a small chance that the corresponding MHC locus on both the homologous chromosomes of an individual will have the same allele; most individuals will be heterozygous at MHC loci. The particular combination of MHC alleles found on a single chromosome is known as an MHC haplotype. Expression of MHC alleles is codominant, with the protein products of both the alleles at a locus being expressed in the cell, and both gene products being able to present antigens to T cells. The extensive polymorphism at each locus thus has the potential to double the number of different MHC molecules expressed in an individual and thereby increases the diversity already available through polygeny


It is important that the alleles have slightly different products because it helps give variety to our immune system.

This same variety can be observed in other species of mammal. They do not appear to have been through a tight bottleneck in the last few thousand years. I coloured the sentence and bolded the last part because the fact that each allele is present at a high frequency in the population should mean something to anyone attempting to build a YEC model. The model needs to be compatible with this diversity.


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Faith 
Suspended Member (Idle past 309 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 27 of 518 (808301)
05-09-2017 10:28 PM
Reply to: Message 15 by bluegenes
05-09-2017 1:33 PM


Re: Counting Alleles
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. Have you evidence of 100 different phenotypes from those 100 alleles in immune systems?

How about a mere four? If you can't show actual phenotypic differences between those four then the best explanation is that two of them are normal built-in alleles that do specific identifiable things like produce blue eyes or brown eyes, and the others don't do anything different, making them "neutral" mutations.

Human blood types come to mind. That's actually three alleles producing four phenotypes and six genotypes. And I'm pretty sure that there will be lots differences in phenotype in the immune system, as it depends on these variations.

The blood types is an interesting example, it needs some thinking about.

About all the alleles in the immune system it COULD be that all or most of them don't actually produce differences in phenotypes; maybe some do, but at the moment this isn't known, right?

Meanwhile it's becoming clearer to me that a great deal of variability is possible from two alleles per gene, especially where a trait has more than one gene.

More to the point, what makes you think humans can have all these variants, regardless of function, when there were a maximum of four 300 generations ago? Are you proposing a super high and probably lethal mutation rate? '

I do think they have to be mutations, most of them "neutral" and that the original was two alleles per gene and that is enough for a great deal of variability. But this is an idea I'm still trying on for size.

Edited by Faith, : No reason given.


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Faith 
Suspended Member (Idle past 309 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 28 of 518 (808302)
05-09-2017 10:47 PM
Reply to: Message 16 by Taq
05-09-2017 1:44 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.

Well, this is a thread for creationist ideas and I gave my thinking on how I arrived at this conclusion, which is new for me. 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. I don't remember what got me started rethinking this but I realized there's a lot of variability without a lot of extra alleles. 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.

It's all hypothetical at the moment, but it's based on seeing that there's a lot of variability available for instance in the example of a great range of shades of skin color from two genes with two alleles each. there are sixteen possible combinations that produce I think eight different shades from very dark to very light. Add one more gene with two alleles and I suppose you'd get more subtle variations added to the mix. A lot of variation, however, without a lot of alleles.

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.

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

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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Faith 
Suspended Member (Idle past 309 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 29 of 518 (808303)
05-09-2017 11:05 PM
Reply to: Message 23 by bluegenes
05-09-2017 3:40 PM


Re: Counting Alleles: 4 bunny alleles, many phenotypes
There's a problem inherent with the model of building up the variation from a recent 4,500 yr old bottleneck.

Not if you assume much greater genetic diversity among those on the Ark, especially much higher heterozygosity for more genes than we see today. More genes too. This is where I keep coming back to the idea that junk DNA is dead genes that used to be functional and contributed greatly to the greater genetic diversity, from which all the different species we see could easily have evolved since the Ark. Bottlenecks can be life-threatening now but that's because of the overall decrease in genetic diversity due to generations of microevolution from population to population; but the bottleneck of the Flood would merely have reduced the percentage of heterozygosity, but there would still have been quite enough for all the variation we see now.

Would you say that your views are fairly close to those of the Answers in Genesis guy who I quoted earlier in the thread?

Maybe so but it's hard for me to tell because he goes about his reasoning rather differently. He talks about "chromosomes" instead of genes for instance, which keeps throwing me. I suspect in the end we are on the same page but it's hard to tell.


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Faith 
Suspended Member (Idle past 309 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 30 of 518 (808305)
05-09-2017 11:09 PM
Reply to: Message 24 by Taq
05-09-2017 3:56 PM


Re: Counting Alleles: 4 bunny alleles, many phenotypes
A good example is HLA-DRB1 which has hundreds to thousands of known alleles.

Please clarify. I've been assuming these huge numbers of alleles refer to that many individuals each possessing one or two of them. So if you say hundreds to thousands you are talking about individuals, right? Or am I getting this wrong?


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