Molecular Population Genetics and Diversity through Mutation

I did not call isolation "alone" the primary thing, but the fact they were populations that began with small numbers. We know that about the lizards. It's the starting from small numbers that causes the new gene frequencies that are the basis for the changes in the population, which when recombined down the generations in isolation are the reason for the new phenotype. There is no way to rule out natural selection for the lizard population because nobody knows their history on the island; for the same reason there is no way to rule it IN either, although just because it's an article of the Evo Faith it is considered to be one of the factors. There is no need for it, their own gene frequencies alone would make the changes. I just didn't mention their history. They are considered to be an "ancient" breed whose history is not known for sure although it is thought they were originally a cross between a wolfhound and the English mastiff. That would make their genetic diversity higher than either of those breeds. They have many of the genetic disorders common to highly bred dogs, however, such as hip dysplasia. But you're right, because they are a cross they aren't the best choice to illustrate my argument. But reality is messy and there may not be a perfect choice. There are certainly plenty of purebred dogs with all the signs of genetic reduction even if their history isn't a perfect reflection of the pattern I describe. They ARE based on small numbers in reproductive isolation, that's what a breed IS, and especially since standards were set in the 19th century to define the perfect or most desired physical characteristics of each breed. This led to mating strategies to emphasize those characteristics that certainly reduced genetic diversity and brought about many genetic diseases.Edited by Faith, : No reason given.

Depends on the severity of the selection, and in any case they will be decreased as the fitter are selected.

I just heard a talk about how Islam is going to run Europe and the UK within a decade and how all your leaders keep denying it, same as most of you all here. This reminds me of that. Wishfulness reigns. Couldn't resist the comparison.

Thank you for that totally illogical and meaningless point.

As you said there’s plenty to ponder in your post, but there are a few things I can answer right away because you are refuting a straw man rather than my argument: You really need to quote me because you get things just wrong enough that I don’t recognize them. I’ve agreed many times that multiple alleles need an explanation, some kind of mutation, so I’m certainly not saying that can’t happen.Also, as long as there is any genetic diversity in a breed you can get changes. What I’ve said is that after you have an established breed you don’t WANT any more changes because they mess up the breed. As I say above, I’ve MANY times acknowledged that there must be some mechanism that increases alleles per locus, even some form of mutation. So you’ve refuted nothing on this point. No, what I’ve said is that there is a TREND to genetic REDUCTION down any evolving line, and dogs in particular seem to have so much genetic diversity they might never reach the point of depletion. You've said these breeds are "fixed" but without giving specific information about their level of genetic diversity, homozygosity etc. Perhaps you think that's explained somewhere in this post, so perhaps I'll figure it out if so, but my impression is that you haven't effectivelydiscounted continuing genetic diversity.Also, one idea I’ve been pondering and mentioned a few times is that when it comes to intensification of traits this can be the result of strong repetition of the same genotype generation after generation. I think I even read about this somewhere at some time or other. I brought this up in relation to the big-headed lizards and Darwin’s pigeons with exaggerated breasts: neither of those characteristics is in the original population, but seem to be the result of many generations of strong selection of the same genotype. This would not require mutation, and could even occur at fixed loci.Also, I do still have to cope with your tendency to use jargon: I think I know what "tandem repeats" means but it's jargon and would be a lot clearer in descriptive English.So I hope to be back soon with some responses to the rest of your post.Edited by Faith, : No reason given.

I don't think it "occurs," I think it "occurred." I don't think of this as an ongoing thing like the mutations that are mostly useless. I think the addition of alleles at a single locus has to be a special thing that's different. It's a guess because I can't think of another explanation for polymorphous loci, but I haven't changed my view in general. There may be another explanation, however. But these would be ACCURATE mutations, not like the destructive bunch we're always talking about.ALSO, I wish you'd get it straight: I've never said that mutations would not increase genetic diversity. Sheesh, WHAT I'VE SAID IS THAT

• If they make ordinary alleles they'll be reduced in the selective processes of forming a new breed or species anyway, and the result of those processes is always going to be reduced genetic diversity no matter what the source of the diversity in the first place;
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• If they get added after the species is formed they'll wreck the species or breed

Edited by Faith, : No reason given.

I'm already sorry I answered any of your post because here we are into a discussion and I haven't even had a chance to think through that post of yours. So now I have another one to answer -- although I already answered some of it. I guess I shouldn't do that. This I answered above. I think of them as part of the Creation design for variety within a Kind. However, maybe mutations isn't the right word since I object to the whole idea of accidental replication as doing anything good. Not after a breed is formed. But I haven't been able to get to that paper yet anyway. Yes, I think of the extra alleles having already been added a long time ago. Yes I guess I'm going to have to give up that idea. Some explanation is needed but not accidental replication events. They can't because you can't get a breed unless they're at ;east reduced, and eventually eliminated. So maybe I'll eventually read it. Oh but it did exist in the original pair. Yes, I get your point except that isn't how I think of it. I don't think of those extra alleles as novel, I think of them as possibilities belonged to other genes and somehow got transferred when those genes died, all those genes in junk DNA for instance. I don't know what the mechanism for their getting attached to new loci is but it's more along those lines than what you are thinking. Sorry I have not thought all that through and am misleading you. I know there has to be some mechanism for the polymorphous loci because it invoilves a large number of individuals. But mutations are predominantly accidents that are of no use to the organism so I can't think of that as the solution, it has to be some other kind of "mutation." Of course now that I think of it I don't know how many of those extra alleles are really alleles either, do I? Do you? I mean as opposed to "neutral" or "deleterious" mutations. True. But now you are raising all kinds of questions. Most of the diversity mutations bring about is unhealthy or useless. If the alleles at polymorphous loci are really functional alleles they have to be something other than mutations as usual.And again, when a breed or species forms those that compete with the traits of the breed get reduced so you end up with less genetic diversity in any case. I have no idea how it does it. It just seems to get more intense from generation to generation. Darwin's pigeon breasts didn't just show up in one generation, they increased as he kept selecting for them. I think it possible that's how the big heads of the Pod Mrcaru lizards showed up too. Do you have another explanation? Well, "repeats" of WHAT is a question. And what does "tandem" add to the picture? Repeats of some of the four bases then. Why "tandem?" Doesn't "repeat" say all that needs to be said? I agree that the "some kind of mutation" is confusing. But I've always accepted the existence of polymorphous loci and take it into account in the scenario about reducing genetic diversity. l How they occurred in the first place is the question, but I'm not accepting standard mutations since most of them do nothing good.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

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.

"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.

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.

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.

Wonderful. No difference between disease and health, no difference between healthy genetic diversity needed by the genetically impoverished seals and some kind of useless mutational diversity. This is science? HE WAS REFERRING TO PHENOTYPIC DIVERSITY WHICH MAKES HASH OUT OF MY ARGUMENT WHICH IS ALL ABOUT GENETIC DIVERSITY. If you can't grasp that much and obviously you can't just as he can't this discussion is hopeless. How do I keep trying to convince myself it's not when it so clearly is?All the more hopeless since I found out that polymorphic genes seem to be predominantly disease-causers and none of you bothered to mention that fact, just carrying on as if I somehow have to account for all those extra "alleles" that weren't on the ark. The deception in this discussion is worse than even I imagined. It's appalling, it's disgusting. There's far more needed than adjusting terminology. Which I can't do anyway because the terminology is skewed toward the in-sanity I'm trying to avoid. Why you can't see it is the puzzle.Edited by Faith, : No reason given.

Yeah sickle cell anemia exchange for malaria. Wonderful. The occasional fluke like the moths and the pocket mice, which is still not easy to explain despite the insistence here, doesn't save mutations from the opprobrium they deserve.And "neutral" mutations are killers of normal alleles. At least they set the stage for their complete killing when another mutation comes along. There is nothing benign about "neutral" mutations.Edited by Faith, : No reason given.

I may yet come back and answer the rest of your post as originally planned, but for now I kind of got the wind knocked out of me. All the straw man misrepresentations of my argument after all this time are really disappointing. Then there was that Wikipedia article that pretty much defined polymorphic genes as disease-causers. Being so surprised by that is my own fault of course because I shouldn't have been assuming they were normal variants. Trusting you guys in a sense, not realizing that you don't distinguish between disease-causing alleles and normal variants. I should have realized it, it's been said before here, I guess I just couldn't believe it because it's too irrational -- wow, I guess I learned THAT lesson.In fact as I think about it now ALL mutations of alleles create polymorphic genes. That's what the mutations DO to alleles. Sort of flabbergasting that I hadn't put all that together before. That really is true. There is no point in taking mutations seriously at all knowing how very very few of them ever do anything beneficial. I don't know why it took that Wikipedia article to drive that home to me since it's what I've thought all along, but for some reason it clinched it. Nothing like an abrupt disillusionment to shake a person up.But as I said I do still want to try to consider the arguments for mutation, yours and Genomicus' at least, though nothing could be less interesting at the moment. Edited by Faith, : No reason given.Edited by Faith, : No reason given.