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Author Topic:   Y.E.C. Model: Was there rapid evolution and speciation post flood?
bluegenes
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Posts: 3119
From: U.K.
Joined: 01-24-2007
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(2)
Message 271 of 425 (809490)
05-18-2017 2:33 PM
Reply to: Message 270 by Taq
05-18-2017 1:25 PM


Re: How to understand some but not all. Good grief
Taq writes:

Since they were able to show that more than two alleles for each gene bound different peptides, this demonstrates that are more than two alleles for these genes as defined by function.

Even better. In this paper, they're classifying HLA class 2 molecules by function into 7 "supertypes", so they're looking for similarities. Even those in the same supertype only average ~46% shared peptide binding function. It looks like the products of the variant HLA alleles are virtually all significantly different in function.

Functional classification of HLA Class 2 molecules.

quote:

We found that the repertoire overlaps between molecules within the same supertype averaged about 46%, ranging from a high of 60% for the DP2 supertype to a low of 23% for the main DQ supertype (Table 3 and Fig. 2a). Average repertoire overlaps for molecules in the main DR, DR4, DRB3, main DP, and DQ7 supertypes were 46%, 55%, 31, 56, and 54%, respectively.

This as a massive increase in functional information since Adam and Eve.


This message is a reply to:
 Message 270 by Taq, posted 05-18-2017 1:25 PM Taq has responded

Replies to this message:
 Message 277 by Taq, posted 05-19-2017 10:53 AM bluegenes has not yet responded

  
Percy
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Posts: 15646
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 272 of 425 (809574)
05-19-2017 9:09 AM
Reply to: Message 255 by bluegenes
05-18-2017 9:53 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
I'm still trying to decode this paragraph from the book:

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.

Just for reference, here's the diagram listing all the genes of the MHC complex:

Let's break that paragraph down. First it says, "every person will express at least three different antigen-presenting MHC class I molecules." If there are over a hundred class I MHC genes, why do people express only "three different antigen-presenting MHC class I molecules"? Shouldn't most people be expressing many, many different molecules, sometimes as many as 200, depending upon the degree of heterozygosity.

Then it says, "three (or sometimes four) MHC class II molecules." If there are around 60 class II MYC genes, why do people express only "three (or sometimes four)" MHC class II molecules. Shouldn't most people be expressing many, many different molecules, sometimes as many as 120, depending the degree of heterozygosity.

Then after giving these very precise numbers of "three (or sometimes four)" it continues on to contradict itself and say "the number of different MHC molecules expressed on the cells of most people is greater." So who knows what to think?

Now before you reply let me quote some of what you say about this paragraph:

bluegenes writes:

In fact, the number (of different foreign body detecting + presenting molecules) expressed in the cells of most people is greater because of the very large amount of different alleles (coding sequences) on most of these genes (meaning the two copies of each gene per. individual are very likely to be different =heterozygosity) and the fact that all alleles are codominant (the products of both are expressed - neither is recessive).

So you agree that it's more than "three (or sometimes four)", and the paragraph concludes by stating that it's more, but then why did they ever give figures like "three (or sometimes four)". And am I right in stating that it should be much, much more than this paragraph states or implies?

This quote from the book is an important piece of the information Faith is looking for:

quote:
Most polymorphic genes encode proteins that vary by only one or a few amino acids, whereas the different allelic variants of MHC proteins differ by up to 20 amino acids. The extensive polymorphism of the MHC proteins has almost certainly evolved to outflank the evasive strategies of pathogens.

So it is a fact that the MHC complex has over a couple hundred genes that taken together have thousands of different alleles that produce very different proteins. The question Faith has to address is how this happened in just six thousand years starting with a maximum of four alleles per gene in the population (I know Faith is claiming there were only two alleles per gene, but she's never supported this statement).

So, are you beginning to understand why I'm saying that the YECs need to include mutation and positive selection into their model?

Yes, I understand, but I'm looking for the data that proves this view. Faith now has to accept that the MHC complex has hundreds even thousands of unique alleles that produce unique proteins, but she still doesn't have the frequency data, and she doesn't understand why that data indicate that it would have taken much more than six thousand years.

--Percy


This message is a reply to:
 Message 255 by bluegenes, posted 05-18-2017 9:53 AM bluegenes has responded

Replies to this message:
 Message 275 by bluegenes, posted 05-19-2017 9:59 AM Percy has responded

    
Percy
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Posts: 15646
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 273 of 425 (809576)
05-19-2017 9:14 AM
Reply to: Message 256 by jar
05-18-2017 10:00 AM


Re: On Adam & Eve?
jar writes:

If the Bible story was true and Eve really was cloned from Adam's rib bone would "Adam and Eve: maximum possible 4" be correct or "Adam and Eve: maximum possible 2"?

God would have had to change the X chromosome to a Y, so we know he made at least some genetic changes when he made Eve. It doesn't seem possible to know from just the Bible what specific genetic changes God made, so that seems to argue that the possibility of a maximum of 4 alleles per gene has to be considered, not ruled off the table.

--Percy


This message is a reply to:
 Message 256 by jar, posted 05-18-2017 10:00 AM jar has not yet responded

    
Percy
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Posts: 15646
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 274 of 425 (809578)
05-19-2017 9:28 AM
Reply to: Message 260 by Faith
05-18-2017 11:38 AM


Re: On Adam & Eve?
Faith writes:

they don't look identical to me:

The two strands are mirror images of each other. A always pairs with T, and C always pairs with G. When DNA replicates by splitting the two strands, that's how identical copies form.

AbE: I see this question has already been answered in better detail - apologies.

One question I've sometimes wondered about, and maybe someone here has an answer, is how geneticists decide which half of the paired DNA strands to list. For example, if they provide this short DNA sequence:

AGTTCCAGT...

They could just as easily have provided the sequence of the other strand:

TCAAGGTCA...

Which to choose?

--Percy

Edited by Percy, : AbE.


This message is a reply to:
 Message 260 by Faith, posted 05-18-2017 11:38 AM Faith has not yet responded

Replies to this message:
 Message 276 by Taq, posted 05-19-2017 10:43 AM Percy has acknowledged this reply
 Message 278 by herebedragons, posted 05-19-2017 11:06 AM Percy has acknowledged this reply

    
bluegenes
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Posts: 3119
From: U.K.
Joined: 01-24-2007
Member Rating: 3.2


Message 275 of 425 (809580)
05-19-2017 9:59 AM
Reply to: Message 272 by Percy
05-19-2017 9:09 AM


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

Let's break that paragraph down. First it says, "every person will express at least three different antigen-presenting MHC class I molecules." If there are over a hundred class I MHC genes, why do people express only "three different antigen-presenting MHC class I molecules"? Shouldn't most people be expressing many, many different molecules, sometimes as many as 200, depending upon the degree of heterozygosity.

No. Only three of the class 1 genes are "antigen presenting" genes, and 3 (sometimes 4) in class 2, hence the 6 or 7 antigen presenting molecules. These are the famously polymorphic genes with multiple codominant alleles, hence the likelihood of most people expressing a lot more, up to double, the number of molecules.

Forget the rest of the genes! They do other things, known and unknown, and are not particularly polymorphic, and if not, can all be present in Adam and Eve.


This message is a reply to:
 Message 272 by Percy, posted 05-19-2017 9:09 AM Percy has responded

Replies to this message:
 Message 279 by Percy, posted 05-19-2017 4:50 PM bluegenes has responded

  
Taq
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Posts: 6843
Joined: 03-06-2009
Member Rating: 3.9


Message 276 of 425 (809585)
05-19-2017 10:43 AM
Reply to: Message 274 by Percy
05-19-2017 9:28 AM


Re: On Adam & Eve?
Percy writes:

One question I've sometimes wondered about, and maybe someone here has an answer, is how geneticists decide which half of the paired DNA strands to list. For example, if they provide this short DNA sequence:

AGTTCCAGT...

They could just as easily have provided the sequence of the other strand:

TCAAGGTCA...

Which to choose?

The standard nomenclature is to label them the (+) and (-) strands. In prokaryotes with their circular chromosome, the + strand is determined by the strand containing the origin of replication which is the place at which replication of the genome begins. I'm not sure what the convention for choosing the positive strands in eukaryotes is, but I would guess that it is somewhat more arbitrary than that found in prokaryotes.

The other standard nomenclature is to always list DNA sequences in the 5' to 3' direction. Let's say we have this double strand of DNA:


5'--ATTAGGCCA--3'
3'--TAATCCGGT--5'

For the lower strand you would list the sequence as TGGCCTAAT, which is the reverse of the double strand.

As you would probably guess, some genes are found on the + strand and some on the - strand. If you are dealing with a gene then the convention is to give the sequence of the open reading frame in the 5' to 3' direction no matter what strand it is found on. Most databases will list which strand the gene is found on.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 274 by Percy, posted 05-19-2017 9:28 AM Percy has acknowledged this reply

  
Taq
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Posts: 6843
Joined: 03-06-2009
Member Rating: 3.9


Message 277 of 425 (809587)
05-19-2017 10:53 AM
Reply to: Message 271 by bluegenes
05-18-2017 2:33 PM


Re: How to understand some but not all. Good grief
bluegenes writes:

This as a massive increase in functional information since Adam and Eve.

Just from what we know about tissue transplantation we already knew that there was a wide range of function in these alleles. The reason that finding donors is difficult is because the binding specificities of the HLA proteins has to match or be very close, and there are hundreds of alleles out there with different binding specificities.

If, as Faith hypothesizes, there are only two alleles per HLA protein then it should be quite easy to find perfect matches, but that just doesn't happen with any regularity.


This message is a reply to:
 Message 271 by bluegenes, posted 05-18-2017 2:33 PM bluegenes has not yet responded

  
herebedragons
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Posts: 1334
From: Michigan
Joined: 11-22-2009
Member Rating: 6.4


Message 278 of 425 (809591)
05-19-2017 11:06 AM
Reply to: Message 274 by Percy
05-19-2017 9:28 AM


Re: On Adam & Eve?
One question I've sometimes wondered about, and maybe someone here has an answer, is how geneticists decide which half of the paired DNA strands to list.

For Sanger sequencing, the region of interest is amplified using PCR. A forward and reverse primer is used that bind opposite strands at the extents of the target region as in the image below.

After amplification, the PCR products are cleaned and all small nucleotides and primers are removed. Then half of the purified product is put in a well with forward primer and the other half is put into a well with reverse primer. These are processed so that the resulting sequence reads are complimentary which are then aligned using software. The software automatically detects that the strands are complimentary and converts one of them. A consensus sequence is generated from the aligned sequences and this is what is reported.

I'm not sure if this is convention per se, but typically the strand that is amplified by the forward primer is the strand that gets reported. When designing primer pairs, typically you try to located the forward primer at the front of the gene so that the resulting sequence will end up in the same orientation as the direction the gene is transcribed.

NexGen sequencing does not use primers to initiate sequencing and relies much more on software to assemble the individual sequences (100 - 150 bp) but the convention would be the same: to report a gene sequence so that the reported sequence is in the same orientation as the gene is transcribed.

Occasionally you will find a sequence reported in the opposite direction, but software will usually identify it and it can be converted to match the rest of the sequences you are working with.

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 274 by Percy, posted 05-19-2017 9:28 AM Percy has acknowledged this reply

  
Percy
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Posts: 15646
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 279 of 425 (809623)
05-19-2017 4:50 PM
Reply to: Message 275 by bluegenes
05-19-2017 9:59 AM


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

No.

I guess I must have misunderstood what an "antigen presenting molecule" is. I was assuming from context that it was a synonym for a protein coded for by one of the MHC genes. Now that I know that is wrong, let me try again. Looking this up at Wikipedia I found "antigen presenting cell," but not "antigen presenting molecule." Wikipedia says that an "antigen presenting cell" is one that...well, never mind, this is getting complicated, and I'm not even sure I'm on the right track. Can you boil this down for me?

Only three of the class 1 genes are "antigen presenting" genes, and 3 (sometimes 4) in class 2, hence the 6 or 7 antigen presenting molecules.

If only 3 class I genes are involved, and only 3 (sometimes 4) class II genes, then now I'm confused why Taq gave me a diagram and an Excel list of all the MHC genes.

But anyway, if we're only talking about 6 or 7 genes then it would be helpful to know the names of the genes, the number of alleles for each one in the population, and how we know that the alleles produce unique proteins.

These are the famously polymorphic genes with multiple codominant alleles, hence the likelihood of most people expressing a lot more, up to double, the number of molecules.

Okay, that gives us as many as 14 "antigen presenting molecules" for a single individual.

--Percy


This message is a reply to:
 Message 275 by bluegenes, posted 05-19-2017 9:59 AM bluegenes has responded

Replies to this message:
 Message 280 by Taq, posted 05-19-2017 4:56 PM Percy has responded
 Message 287 by bluegenes, posted 05-22-2017 5:04 PM Percy has responded

    
Taq
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Posts: 6843
Joined: 03-06-2009
Member Rating: 3.9


Message 280 of 425 (809624)
05-19-2017 4:56 PM
Reply to: Message 279 by Percy
05-19-2017 4:50 PM


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

If only 3 class I genes are involved, and only 3 (sometimes 4) class II genes, then now I'm confused why Taq gave me a diagram and an Excel list of all the MHC genes.

The MHC complex includes antigen presenting proteins and other proteins. It isn't exclusive to antigen presenting proteins.

It's a bit like getting an inventory of everything in the Louvre. There are going to be paintings and statues on the list, but there are also going to be mops and buckets on the list.


This message is a reply to:
 Message 279 by Percy, posted 05-19-2017 4:50 PM Percy has responded

Replies to this message:
 Message 281 by Percy, posted 05-19-2017 5:15 PM Taq has responded

  
Percy
Member
Posts: 15646
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 281 of 425 (809626)
05-19-2017 5:15 PM
Reply to: Message 280 by Taq
05-19-2017 4:56 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
Before replying I want to first thank everyone trying to explain this to me, even if I didn't reply to each message.

Taq writes:

The MHC complex includes antigen presenting proteins and other proteins. It isn't exclusive to antigen presenting proteins.

We're arguing to Faith that there are more alleles that produce functionally different proteins with significant frequencies in the population than could have arisen since Adam and Eve, and I've been inquiring about the data that proves this point, but if I've gone off track in one area maybe I've gone off track in others, too. Am I right about the point we're trying to make to Faith? If so, has the data I'm looking for been presented? If so, could someone point me to it?

--Percy


This message is a reply to:
 Message 280 by Taq, posted 05-19-2017 4:56 PM Taq has responded

Replies to this message:
 Message 282 by NoNukes, posted 05-19-2017 7:43 PM Percy has responded
 Message 285 by Taq, posted 05-22-2017 11:48 AM Percy has responded

    
NoNukes
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Posts: 9748
From: Central NC USA
Joined: 08-13-2010
Member Rating: 3.1


Message 282 of 425 (809632)
05-19-2017 7:43 PM
Reply to: Message 281 by Percy
05-19-2017 5:15 PM


Re: The YEC model requires beneficial mutations and strong positive selection.
We're arguing to Faith that there are more alleles that produce functionally different proteins with significant frequencies in the population than could have arisen since Adam and Eve

I think the answer is more simple that that. The argument is that more alleles exist than either the pair of Adam and Eve, or the collection of folks on the ark actually could have possessed.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

I never considered a difference of opinion in politics, in religion, in philosophy, as cause for withdrawing from a friend. Thomas Jefferson

Seems to me if its clear that certain things that require ancient dates couldn't possibly be true, we are on our way to throwing out all those ancient dates on the basis of the actual evidence. -- Faith

Some of us are worried about just how much damage he will do in his last couple of weeks as president, to make it easier for the NY Times and Washington post to try to destroy Trump's presidency. -- marc9000


This message is a reply to:
 Message 281 by Percy, posted 05-19-2017 5:15 PM Percy has responded

Replies to this message:
 Message 283 by Percy, posted 05-20-2017 8:13 AM NoNukes has responded

    
Percy
Member
Posts: 15646
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(1)
Message 283 of 425 (809665)
05-20-2017 8:13 AM
Reply to: Message 282 by NoNukes
05-19-2017 7:43 PM


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

I think the answer is more simple that that. The argument is that more alleles exist than either the pair of Adam and Eve, or the collection of folks on the ark actually could have possessed.

My understanding is that Faith accepts this argument. She believes that Adam and Eve together contributed at most two alleles for each gene, and that any gene today that has more than two alleles has experienced mutations, but she believes the alleles neutral, performing the same functions as the original two alleles.

Efforts have been to persuade Faith of two things:

  • That the frequency of the alleles indicates strong selection and therefore different function. Faith rejects this argument, arguing that if the alleles did the same thing as existing alleles then they would also have strong selection.

  • That there has not been enough time since Adam and Eve to create the distribution of alleles we observe in the human population.

I'm seeking the evidence that proves these two points. It may have been presented already, but not in a form I understand.

This might have been mentioned already, but this was new to me: the MHC complex and the HLA complex are the same thing.

--Percy


This message is a reply to:
 Message 282 by NoNukes, posted 05-19-2017 7:43 PM NoNukes has responded

Replies to this message:
 Message 284 by Faith, posted 05-20-2017 3:19 PM Percy has responded
 Message 298 by NoNukes, posted 05-24-2017 12:52 AM Percy has responded

    
Faith
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Posts: 25609
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.0


Message 284 of 425 (809733)
05-20-2017 3:19 PM
Reply to: Message 283 by Percy
05-20-2017 8:13 AM


Re: The YEC model requires beneficial mutations and strong positive selection.
Efforts have been to persuade Faith of two things:

That the frequency of the alleles indicates strong selection and therefore different function. Faith rejects this argument, arguing that if the alleles did the same thing as existing alleles then they would also have strong selection.

That there has not been enough time since Adam and Eve to create the distribution of alleles we observe in the human population.

My answer to this, for the record, has been that if they are neutral mutations/alleles there is no limit on how many there would be in a given time frame. I'd also add at this point that the fact that there are so many is evidence in itself that they are neutral mutations according to the YEC framework.

I'm seeking the evidence that proves these two points. It may have been presented already, but not in a form I understand.

It should be pretty clear by now that there isn't any.


This message is a reply to:
 Message 283 by Percy, posted 05-20-2017 8:13 AM Percy has responded

Replies to this message:
 Message 286 by Taq, posted 05-22-2017 11:50 AM Faith has not yet responded
 Message 292 by Percy, posted 05-23-2017 9:50 AM Faith has responded

    
Taq
Member
Posts: 6843
Joined: 03-06-2009
Member Rating: 3.9


(1)
Message 285 of 425 (809957)
05-22-2017 11:48 AM
Reply to: Message 281 by Percy
05-19-2017 5:15 PM


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

Am I right about the point we're trying to make to Faith? If so, has the data I'm looking for been presented? If so, could someone point me to it?

I presented a paper in post 270 that discusses many different alleles (i.e. much greater than 2) for HLA-A and HLA-B that have different function. Jar [edit: bluegenes] and I also discuss the paper in posts 271 and 277.

What they did was chop up proteins from the dengue virus and determine which of these chopped up proteins, called peptides, bound to which allele for both HLA-A and HLA-B. What they found is that different peptides bound to different alleles. No two alleles bound the same peptides.

HLA-A and HLA-B are antigen presenting proteins, so when they bind different viral peptides it indicates that they differ in function. Each gene has more than two functions spread out over many alleles which directly contradicts Faith's claims.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 281 by Percy, posted 05-19-2017 5:15 PM Percy has responded

Replies to this message:
 Message 288 by bluegenes, posted 05-22-2017 5:12 PM Taq has responded
 Message 290 by Percy, posted 05-23-2017 9:15 AM Taq has responded

  
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