Molecular Population Genetics and Diversity through Mutation

Progress. This represents a yielding to an objection that has been raised in every single thread on this topic. In previous incarnations, the answer has been that folks don't understand. This time, something different... (emphasis added by me) Will we ever get such an explanation? Or will we see back tracking over this idea. Because the idea give up here is absolutely central to Faith's position.

The idea that the alleles were added a long time ago is NOT central to my position, it's one of various hypotheses I have about how polymorphous loci came about.I suspect you think I was giving up the idea that to get a breed means eliminating the alleles for other breeds? If so, and I'm sure it is so, it's just another example of your amazing knack for misreading me. My last line about mistakes in replication should have made it clear if nothing else.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

Where have I ever said it doesn't? I just think evo theory is wrong about what they actually are and do.

You complained before about the use of too much jargon, and it's true that scientists do sometimes use unnessecary jargon, as with any specialists. Some degree of jargon is useful though, as it allows people to express a clear and well-defined concept, whereas common everyday words may be interpreted slightly differently by different people.And I think that's part of what's causing this discussion to move nowhere, in that you're using slightly different definitions for certain bits of jargon that are causing us all to talk past you. As a case in point: 'Allele' just means different form of a gene. If a mutation occurs in a gene, then we have a new allele. If the new allele creates a less fit organism, then it's a deleterious allele. If it functions the same way as the old despite its different gene sequence, or if the differences have no effect on fitness, then the mutation was neutral. It's a new allele regardless, though, since it's a different form of a gene.---------------------------The 'tandem', in 'tandem repeat', just means 'in a row', which is the original meaning of tandem. The more common meaning of 'cooperating' I think comes from tandem bicycles, since the riders cooperate. But a tandem bicycle is called a tandem in the first place because the cyclists are sat in a row.

"Allele" implies USEFUL CODING FUNCTIONAL form of a gene, not "neutral" unfunctioning mutations or deleterious mutations. However, I can try to remember to put in some kind of qualifier since evo thinking is nutty enough to confuse the two.Yes I know what tandem means. But you have to know what is being repeated in the first place and I still say "repeat" should suffice without adding "tandem."Edited by Faith, : No reason given.

Actually, Faith, you don't get to redefine the English language on a whim.

The English language carries whole theories, you know, and I use it correctly to express the theory I hold. But I don't mean to confuse and where I think to do so I will add necessary qualifiers to please the holders of the utterly irrational Evo Theory.

Is it your theory that there are no deleterious alleles?

No, it doesn't, which is why I said we need to introduce some definitions Otherwise we're just going to misunderstand each other and get nowhere. Which is standard for most arguments on the internet but probably not what we should aim for.

So can we have confirmation that you now accept beneficial mutations?

Because you don't understand how the terminology works nor how scientists use terms to describe known phenomenon doesn't make it "nutty." That you trying to come up with new ways of interpreting how new species arise is fine, but using terminology in odd ways is very confusing.Allele refers to alternate forms of a gene at a given locus. We don't usually refer to genes with mutations in introns as different alleles; we would refer to them as different haplotypes. We also don't refer to different forms of a gene in different species as 'alleles'; we refer to them as homologous. But I haven't really wanted to introduce this terminology because it is somewhat confusing and this topic is already confusing enough. So I have been using a loose definition of allele to mean simply "a variant form of a gene" and including the concepts of haplotype and homology in the term.But, yes, 'allele' implies mutations or variations in coding regions and more specifically, in the gene product. But as to your assertion that it implies "useful coding functional" not "neutral unfunctioning mutations or deleterious mutations" is nonsense. In the old days an allele referred to the phenotypic effects of different genes, but we are in the molecular age now. We can detect different gene alleles regardless of their phenotypic effects.You complain that Dr. A is referring to phenotype while you are referring to genotype and then you insist that to be different alleles have to have "useful" phenotypic effects? So what is it, phenotype or genotype? If we are talking about genotype, then the resulting phenotype is not the issue. Well, the use of the word 'tandem' would be so as to distinguish 'tandem repeats' from other types of repeats such as 'interspersed repeats'. I know scientists have a bad habit of given things odd names, believe me, I have had to learn them. But as caffeine said, they are intended to express a clear and well-defined concept. Often one or two words can convey an entire concept. As I confessed to NosyNed, sometimes I don't even recognize these terms as "jargon." they are just the words that are used to convey a particular concept. If you want to have serious discussions about genetics, it would do you well to learn the terminology.HBD

I respectfully disagree. It is essential to your position, because you think all of the genetic diversity in, for example dogs, must have been present in wolves with mutations playing no role at all. You routinely argue, for example, that black moths existed all along.If you are going to give up on that idea, and still not allow mutations, you owe us some other mechanism you have yet to explain. Come up with that, and then I will agree with you that the idea you renounce is not so important.But I would bet on you simply going back on the idea regarding alleles. Maybe you'll just forget what you said here.

Cute. This is simply your way of having your cake and eating it as well. By defining allele in this way, you can deny that mutations create alleles rather than continuing to argue that evolution that evolution does not work despite the fact that mutations add diversity.I've recommended to you that you back off to that position at various times during the thread. Are you actually doing so? Shouldn't you let Genomics know how you define allele?

The thing is apparently you guys accept even disease-causing mutations as simply "alleles" then, right? I would like to be able to make a distinction between what the different "alleles" do, and actually most of the time I DO use a word like "healthy" to make the difference. Perhaps it doesn't convey anything to someone who doesn't make those distinctions.As we were discussing this it occurred to me that maybe these polymorphic genes aren't a natural or healthy thing either. You'd never point that out I guess. I didn't even expect my suspicion to be right. But amazingly, according to Wikipedia it is. Now that puts a whole different light on this subject and on this idea that I have to come up with a way to account for all those extra alleles. Well, I was assuming they were normal healthy variants and none of you said any different. So now it seems we can do just fine with the four normal healthy alleles in each pair on the ark.All this does is prove what I already knew, that mutations are bad for living things. Why you all go on treating them as normal variants is the puzzle.The only hint given in the Wikipedia article that they might have a normal function is the fact that genes for hair color are polymorphic. See, I just thought there were many genes that controlled hair color, and there may be.I'd been assuming some basic concord about all these things. Big mistake.Mutations "add diversity" eh? Yeah, diverse diseases for sure.Edited by Faith, : No reason given.

Correct. Like sickle cell anaemia."severe hereditary form of anaemia in which a mutated form of haemoglobin distorts the red blood cells into a crescent shape at low oxygen levels. It is commonest among those of African descent."And neutral mutations that do nothingAnd beneficial mutations that help organisms survive - like our moth.There's no plan - mutations just happen and occasionally they're good or bad or irrelevant. It's chance Faith, chance. That's the bit you don't like isn't it?