I have been following the back and forth for a few days.
I think you are too wrapped up in what you know. From what Faith replies it isn't clear that she even knows what allele means. At least, it doesn't instantly conjure up all that it does for you. You've jumped ahead much too fast.
Go waaaay slower and see if you can get a bit of this across.
One area of confusion that I think I see is that one group of you is talking about genes and their alleles and Faith jumps from that to talking about variations in the external animals that we see (phenotype).
To simplify lets try to stick to the genes for a moment.
As I understand Faith's argument (and, I think, the general YEC one) it says that with a few different variations of a gene (alleles) we can mix and match to get lots of different external looks -- like eye color.
So mutations and different alleles are not needed.
However, others aren't paying attention to that yet. The argument is ignoring eye color (for example) and just looking at the genes.
It has two parts: 1) It starts with the YEC assertion that a few thousand years ago there were only a handful of humans alive (after the flood). These few would have had at most something like 10 alleles for each gene in them.
2) Today we see many more alleles for some genes than that.
This means that: a) There have been mutations in the human genes. I think that is argued to not be true by some of the creationist community. Faith agrees ( I think ) that there are mutations.
b) The mutations are at least not deleterious since the individuals have been passing them on for 1,000's of years. This is what the definition of a neutral or beneficial mutations is. That is, can the individual with it successfully reproduce and pass it on.
So the remaining question is: Are the mutations neutral or beneficial?
If they are neutral they are, by definition, not selected for or against so they only spread through the population by random drift.
So the issue of whether there are any beneficial mutations can be settled by examining if there are any alleles other than the orginal handful that are spread more widely than drift can do in a few 1,000 years.
As I understand the discussion so far the answer to that is - yes.
Therefore the conclusion is that the human genome has acquired beneficial mutations since the flood or the flood was much longer ago than a few 1,000 years.
If there have been beneficial mutations then the original genome was not "perfect".
That is all that can be concluded from the discussion so far.
Also, as most board members are of European ancestry, many will have visible phenotype features that owe their existence to mutants of this gene.
Well, here's the ToE assumption stated outright: all characteristics are the result of mutations; all alleles were originally mutations. (how original genes and their alleles got created by mutations when there was no DNA for them to alter is a puzzle but anyway...)
No, not a ToE assumption. First: it is a requirment of your model. There weren't very many alleles to begin with and now there are more so there, by your model have to have been mutations.
Second: The ToE doesn't say what any "original" allele was. You do.
(and 3rd you are jumping way out there by suddenly talking about orgination of DNA which doesn't have anything to do with this discussion -- focus!).
There is no such thing as a "bona fide" allele. Each allele is just a different pattern of base pairs in the gene they are all equal at that level.
3) But to be bona fide alleles they have to do something different. Why isn't it even discussed whether they do or not? I mean it's common knowledge that most mutations don't, how come it's so easy to assume these do?
It is not an assumption and this thread has explained it already. In fact several times. The whole discussion about frequency is because of that.
I tried to summarize for you to make it simpler. Did you read that? That's in Message 130
The alleles that are the subject of this discussion are mutations, which I don't regard as alleles. And as the Mendel squares easily demonstrate, more than two alleles per gene are not needed for all the diversity we see in living things.
Then what are they? An allele is any pattern as part of the DNA of an organism marked out as a gene in the DNA. If it is changed by any means at all then it is a new allele. Why do you disagree with this?
Yes, according to the ToE, but we're trying to have a debate here, right? Or maybe not. I am anyway. So the views of both debaters really should be kept in mind don't you think? By the YEC model I'm trying to keep on the table there is definitely a bone fide allele. I reject the ToE idea that they are the result of mutations. I keep trying to keep this clearly stated too, so there shouldn't be a lot of confusion. If you just want to insist on the ToE there is no debate and so buhbye
Please define what a 'bona fide' allele is so we can tell it apart from others. We are not talking about the ToE model here, we are talking about your model. Since there were fewer (many fewer) alleles in your model around 4 to 6,000 years ago where did the additional ones come from?
Sorry, I missed it. All I've seen is assumptions and no evidence. They are called "alleles" rather than mutations, that's an assumption. As "alleles" they are said to have increased in frequency. I've said that isn't the case if they are just different sequences with the same function being counted separately, which would create a false increase in frequency.
If we are to discuss we'll have to have a common vocabulary. I don't see why we have to have a new word for something that is already defined. An allele is any different sequence whether it has a different result in the phenotype or not.
There has been, according to your model, an increase in these different sequences (whatever you want to call them). Are you now saying there aren't more sequences (alleles is the word to everyone else) than there were a few 1,000 years ago?
Because the claim is that these "alleles" code for a different protein and different function of the gene than the allele whose sequence they changed, but there is no evidence that they code for anything other than the original allele did (the one at that particular locus whose sequence they changed). A change in sequence that does not change the protein or function is just a neutral mutation. Calling it an allele confuses things.
For some of them that is the claim indeed. However, to keep this simple let's go one step at a time. We already have the terms you are looking for and you used it. A change of allele that does nothing can be called neutral and if it does something and is harmful it is deleterious and if it does something different and helps then it is beneficial. I think there is a word for a set of alleles that all produce the same protein but I don't know it. Neutral can do us for now don't you think?
If you don't want to use the word allele (which most of the world uses) what would you like to use ? "different sequence" That is ok too.
Its sequence codes for a different protein and different trait than other sequences for the same locus. If it only does what the others do it's a neutral mutation. If you are still stuck on calling it an allele please provide a term that allows for this crucial distinction I'm talking about.
Until someone supplies us with the official terms let us use "effectively different sequence". That is, one that has an external effect.
They aren't alleles according to what I say above, they are merely mutations, changes in the DNA sequence that do not code for a new protein or a new trait, and in my model there are lots of mutations occurring all the time, most of them neutral which is why I'm assuming that's what these are, or deleterious. Mutations ARE increasing. In my model they are not true alleles and they are not a good thing for the organism.
So while using different terms than the rest of the world uses you and I agree that there are different sequences in the DNA now. That is mutations are changing things and have been for 4 to 6 thousand years.
Whether they are a good thing or not when they are an "effectively different sequence" (different allele to the rest of the world isn't determined yet.
According to this thread there has been an increase in these different sequences and that seems to be treated as synonymous with a change in function of the gene. I wouldn't doubt the increase in changed sequences, which is an increase in mutations, which fits with the YEC model just fine. I disagree with their assumed beneficial change in function: I haven't seen it proved, I've only seen it assumed. A change in sequence happens all the time; it's called a mutation; mutations are KNOWN to be predominantly neutral. Why are these treated as functioning alleles instead.
An increase in different sequences (alleles) is something we agree on then. We don't have much choice since they are measured so this is a simple fact. That doesn't have anything with effectively different sequences being beneficial or not yet. So far we agree that they are just there.
A change in sequence happens all the time; it's called a mutation; mutations are KNOWN to be predominantly neutral. Why are these treated as functioning alleles instead.
Something we agree on then. What effect they might have we can look at next.