A New Run at the End of Evolution by Genetic Processes Argument

I'd like to try to answer this briefly if I can, hoping not to lose the sense of it, rather than taking it point by point. Maybe I'll have to do a second mop-up post to cover all the issues.You are right that I've overemphasized selective breeding as the main method, and that cross breeding is just as common and that there are lots of byways involved in any breeding program. (At least with dogs. I think maybe with cattle and horses there may be more selective breeding, but that's a guess. The Pod Mrcaru lizards and the Jutland cattle remain good examples I think. Selection not of individuals but of small numbers from larger populations.)However, it remains true that I have been speaking only of selective breeding as the cause of reduced genetic diversity. Yes you remind me that you did agree with this basic idea. I don't know how it got from there back to the usual messy debate, but maybe more from others who didn't agree with you than from your own posts.This idea originally came from the Wikipedia page on Speciation where the isolation of a portion of a population is presented as the only path to Speciation. Many versions of it are given ("allopatric" etc) but still it's the same basic process of forming a daughter population on the way to Speciation. Loss of genetic diversity through that process is what I've been emphasizing although I don't think it's even mentioned on that page, as it normally isn't in any discussion of these things.Speciation itself isn't my focus, but the way they depict getting to it certainly must require a reduction in genetic diversity, and that's what I took hold of. I've tried to be careful to differentiate it from all the other ways populations behave, from healthy stasis or stability to keeping up gene flow between them, to forming hybrid zones, even rejoining an earlier population, because all that ADDS genetic diversity and is in the opposite direction from Speciation. Again, speciation isn't my focus but is one logical outcome I'd expect from the formation of daughter populations and the necessary reduction of genetic diversity from one to another. They don't depict more than one population split on that page but I extended the idea to ring species where I think the processes are even clearer. Again making clear that the retention of gene flow and hybrid zones and all that are working in the opposite direction from what I'm trying to keep in mind.Since you've agreed that genetic diversity is reduced by selection, then the question that is left is whether the additive processes such as cross breeding, hybridization etc., lead to speciation, or to evolution in a certain sense at all, any sense that could foster evolution from species to species which is what this is ultimately all about. I've been claiming they don't and I believe they don't but I'm going to have to try to make the case better eventually, if not in this post. It's hard to believe I've been that totalistic about it since I'm certainly aware of cross breeding, and of migration and other additive genetic processes in nature. Selection IS my focus, but breeding is only one way of trying to make the point that selection reduces genetic diversity. Your charts have made it clear that selection isn't the dominant method I thought it was, but you are also wrong to claim that a mixture of cross breeding and selection could show that reduced genetic diversity doesn't occur as I've been claiming. It CAN'T occur if you include additive processes and I do think I've been very clear about that. No. Not for establishing genetic relationships. Some of the earliest breeds to be registered had been in existence hundreds of years; even some of the later ones for that matter. As I found out when I read up on the ones you had chosen there is NO genetic relationship between them that could say anything about genetic diversity. The only remotely related group is the retrievers: Sharing a common ancestor would only be a fair response to my argument if the derivation was purely selective and without any cross breeding. But that is not the case. In what I read there is no mention of cross breeding in the development of the Labrador, implying that it was a direct descendant of the St. John's water dog. That could mean pure selection or it could involve cross breeding with other water dogs, but not with other breeds. For my point to be made requires only selection. The Golden retriever was a mix of the St. John's with that particular retriever in England. You cannot compare that genetically with the Labrador because they are not in the same path of descent despite having a common ancestor. They are cousins at best. Even if they had both been selectively developed directly from the St. John's without outbreeding of any kind, although they should have genetic diversity reduced from the St. John's, there would be no necessary relation between them as to genetic diversity. But it says nothing about my argument about genetic diversity.In your Message 178 where you first present the charts, it is at least very clear that the various breeds have fewer alleles than the total of all the breeds, which may be merely obvious, but it does demonstrate that when you split off a portion of the population you reduce the genetic diversity, which is after all the main thing I've been saying. So the overall number was 1780 and the breeds varied between 400 and 800. THIS should be broken down and studied among other things, if it's possible from those charts to find any actual genetic lines of descent that could be pursued for the purpose. The number of alleles is what we need to be looking for, but only where you know the line of descent and it's all selective. Even with cross breeding the numbers in that study show an obvious reduction from the parent population, whatever it was in each case.And yes, of course it should mirror the level of heterozygosity. So far so good for my argument. There is no need to do that once I've presented the data from Wikipedia on each breed (in Message 194) showing the utter lack of genetic relatedness. If a Wikipedia article written presumably by people familiar with that particular breed doesn't have the exact genetic history, how can we be sure that phylogenetic chart has it all right? And again, any cross breeding undoes any claim to falsify loss of genetic diversity from any particular lineage. What I demonstrated is that there is no way to tell anything about genetic diversity from the given genetic information, but that your claim that you've falsified my argument is totally misbegotten. You can't have proved any such thing from the available information. Well, but you've already conceded that selection reduces genetic diversity so what would be the point? What's left to sort out is what all this has to do with the ToE.As for demonstrating the trend to reduced genetic diversity what is needed is a series of populations that are known to have been derived one from another in a series WITHOUT any gene flow between them, no hybrid zones etc. I've figured it might be possible to do this with known ring species, but not if it's not known whether or not a given population in the ring was formed in complete reproductive isolation or not. That's where my idea of a laboratory experiment came in, where you take some kind of small animal, say maybe twenty individuals, and let them breed freely, then take out a number of individuals from the resultant population into another cage or area and let them also breed freely and keep doing that as long as you are getting new phenomes. When you aren't I would assume you've reached genetic depletion. You could make more splits than these but you'd have to keep very careful track of each population, each individual, DNA counts and so on. One thing that is particularly interesting from the study you posted is that clearly it IS possible to estimate allele counts, heterozygosity etc. But since you've conceded that this process should lead to reduced genetic diversity I guess we don't need to do this study for you anyway. Maybe it would be helpful for the diehard believers that mutation will always come along and increase genetic diversity. Yes, of course, which I've said half a billion times myself in one way or another, but nevertheless the point I'm making is ONLY about selection, and what I've been claiming is that that is the only direction of evolution that really IS evolution, that could conceivably lead from species to species. HOWEVER, it IS messy and I DO have to figure out how to say more clearly why the additive processes couldn't. I know they couldn't but that's not very convincing. Take your time. I need to take my time too.Edited by Faith, : No reason given.Edited by Faith, : add message reference

I'm sorry, I'm trying to be accurate. I'm afraid of letting a statement stand that is only partially accurate that can later cause problems. OK, that's clear but the other phrasing wasn't. Seems so, yes. Um, this isn't my argument, it's merely an observation on which I base my argument. The thing is, it seems clear that you can have a very homogeneous population as far as general appearance goes, that nevertheless has high genetic diversity. They can't be "cookie cutter" homogeneous but nevertheless the overall appearance is remarkably homogeneous. I think of huge herd populations mainly. A million wildebeests look just about identical to each other, and yet there's every reason to think they have enough genetic diversity so that if a small number of them became reproductively isolated and formed a new subspecies they would look very different after a few generations. In fact there could be enough genetic diversity to form many such daughter populations out of the same larger population and each would end up differing from both the parent population and the other populations. All due to their different gene frequencies and their reduced genetic diversity from the original population. The thing I find hardest to explain is how there could be such apparent homogeneity with so much genetic diversity but it seems to be the case. Agree or disagree? OK, yes. Yes. Accurate representations of things I've said, but all these points aren't my argument, they are observations that contribute to my argument. Undergirding as it were. Support. Or context. Sorry if this seems a nitpick but to me it's not. The argument is that these processes require reduced genetic diversity.

HBD's Message 210 was fairly long, so there's no way anyone can be sure what "this" is. Please either use the quoting facility or describe the point you're addressing. From the Wikipedia page on speciation:

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There are four geographic modes of speciation in nature, based on the extent to which speciating populations are isolated from one another: allopatric, peripatric, parapatric, and sympatric.

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Allopatric speciation is when a population "splits into two geographically isolated populations."At the other end of the spectrum, sympatric speciation is when species evolve from "a single ancestral species all occupying the same geographic location."In other words, the Wikipedia page on speciation does *not* say that "isolation of a portion of a population is...the only path to speciation," at least not if you by "isolation" you mean geographic isolation. It says there can be a wide range in the degree of geographic isolation, from completely separate and isolated all the way to located in the exact same place.

By "this" I meant HBD's post as a whole. The illustrations of the four different modes show the separation of a portion of a population. All four of them. I NEVER mean only geographic isolation, I ALWAYS mean reproductive isolation.Edited by Faith, : No reason given.

Thanks for a good reply that should help to move things forward. This is a confusing point. What the charts showed was what DOES occur; "additive process" plus "selective processes" tended to INCREASE diversity. I am not trying to show that selection CANNOT reduce diversity, I already agreed that it can (although I have previously shown ways that selection can INCREASE diversity as well). But what we observe happening in both breeding populations and natural populations over time is a TENDENCY to increase genetic diversity - because there is always "additive processes" at work. The chart shows that the general trend in dog breeds has been an increase in genetic diversity (as measured by heterozygosity). This is based on the assumption that the parent population (ancestral wolf) had all 1780 alleles, this is not necessarily the case. In fact, this study only looked at 100 markers so, in the original ark population of 2 individuals there could only be 400 alleles maximum at those markers (2 alleles per loci x 100 loci x 2 individuals). So... where did the additional 980 alleles come from?? The phylogenetic chart was built as an representation of the relationship between the genes, so it specifically addresses the genetic relationships. No, it's not certain that it is 100% accurate, but it does give significant insight into the genetic history of dog breeds. We have come a long way in developing statistical models that give us high confidence in the phylogenetic hypotheses we develop from studies like this. I don't get why you equate stability of a phenotype with depletion of genetic diversity... Hardy-Weinberg. Allele frequency will come to equilibrium rather quickly, although in a small population drift will may a significant role. However, drift won't make the entire population homozygous. And the dog breeding example shows that evolution also works through "additive processes" as well (cross breeding to create new breeds). Natural evolutionary processes can also involve hybridization and stabilizing selection (that increases or maintains diversity). So we should understand how ALL processes work, not just one particular piece that seems to support your position.HBD

Please explain how you can get reproductive isolation without geographic isolation.I am pretty convinced that there are no true examples of sympatric speciation. Cases where species have diverged in the same geographical area are actually cases of "micro-alleopatric" speciation where populations are kept separated within the same habitat (niche partitioning is a good example).We have talked about this before, the important issue is reduction in gene flow. Sympatric has the greatest POTENTIAL for gene flow but for some reason, gene flow does not occur at a high enough rate to offset the tendency of the two populations to diverge genetically.What factors would significantly reduce gene flow?HBD

I've understood it can be purely random, such as in the case of genetic drift. Or it could be sexual selection. Or it could be some kind of natural selection but I'm not sure how that would work.But I don't care about these specifics myself. The only thing that matters IS reproductive isolation, however that occurs. and if physical geographic isolation is the only way -- certainly it's the most certain way in any case -- that's fine with me. It's the principle of isolation that counts to keep the lines of descent clear.Edited by Faith, : No reason given.

But that is perfectly nonsensical, since, as I showed, there is no line of genetic descent there at all to show what is the cause of the increase in a particular case. If they aren't even related by descent, then differences in genetic diversity are meaningless. That's impossible as we've been using the term here, so I have to ask you to repeat that supposed proof that selection can increase ... not just "diversity" please, but genetic diversity... This might be the case with additive processes being always at work, but that chart is absolutely no evidence for it, being based not on lines of descent but the artificial event of registration. But again all I'm talking about is SELECTION, not addition.And if necessary I'll just take it back to the situation of daughter populations splitting from parent populations, where the concept may be clearest. Which is just plain weird since there is no way to determine the genetic relationship, if any, between any of them. That's not how I read it. I thought they were comparing the total number of alleles in the combined breeds with the number in each separate breed. There would be overlap of many of the alleles, so it isn't a straight addition. I really don't know what this means. I provisionally accept the accuracy of the numbers of alleles given, although I don't know how they arrived at them. This is too confusing for me to figure out. For starters I didn't think they were talking about the supposed original wolf population. Beyond that I don't know if the dogs on the ark all looked like wolves or what they looked like. And I also don't know how you get back to the ark with any of this information anyway. Even the oldest breeds can't be traced anywhere near that far back. Maybe, maybe not, how would you know? I haven't spent much time tracing the lineages depicted there but I don't have any reason to pay much attention to it after reading up on the individual breeds you claimed were related to each other in such a way as to falsify my argument, which turned out not to be the case. Well I can't just take your word for these things you know, not being an insider myself and finding so much to object to in the usual presentations of evolutionary theory that are so taken for granted, that I know shouldn't be. ABE: I didn't get what you meant here though I wrote the following paragraph not getting what you meant and I'll leave it as is anyway. Now I guess you are saying why wait for the phenome to emerge anyway? I suppose I should have said when you aren't getting any new PHENOTYPES AT ALL, that's when genetic depletion has been reached. The phenome isn't going to change in that case anyway. The next paragraph may be completely obsolete now, not sure. /ABE.Oh you mean where I'm describing how the phenome develops from some generations of recombination so that it forms a fairly homogeneous appearance? It took me a bit to figure out this must be what you meant. If so I don't particularly "equate" these things, it's just that I think this is what happens when you have an actual new subspecies, and it should be the best representative of the processes I'm talking about. There should be a reduction in genetic diversity in the daughter population from the original at any stage in its working through to that point of homogeneity or "stability" though, it's just that's where you get the clearest portrait of the formation of a subspecies, when it actually LOOKS like a subspecies. Such as with the Pod Mrcaru lizards. They ALL had the big heads and digestive system changes after thirty years of inbreeding in reproductive isolation. All the Galapagos turtles looked alike, all the big-beaked finches looked alike, etc etc etc. I just want the diversity to be measured at the point where we actually have a new phenome, new subspecies, and that also to be the point where a new random set of individuals are sent off to start their own isolated population. Not sure what your point is here.The rest of your post gets closer to the main issues so I'm going to leave that for the next post.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

I will just take a minute to explain what genetic markers are and what they mean.A genetic or molecular marker is a section of DNA at a known location on a chromosome that is associated with a particular gene or region. Primers are used to bind the end of the fragment so that polymerase can copy the strand. A forward and reverse primer are used which generates a fragment of a specific length based on the sequences between them. Ideally the primers are located in a highly conserved region (such as an exon) and the amplified region is a highly variable region (such as an intron). Below is an example of such a marker - the so called ITS1 marker. The left and right facing arrows show the position and directionality of the primers. They are located in the 18S and 5.8S ribosomal subunits, which are highly conserved - meaning that almost all fungal ribosomal RNA genes will have this sequence (it will probably amplify other kingdoms as well, but I am not sure to what extent). The sequence that lies between those two conserved regions - identified as ITS-1 is highly variable, meaning it varies greatly among different species and even among isolates of the same species, because it is an intron (clipped out during ribosome assembly). It is used to identify isolates to species. I am only talking hypothetically here. I thought it was agreed that dogs were breed from wolves and there would have been a pair of wolf/dogs on the ark. It doesn't matter that we can trace any particular breed that far back, but the implication is that all dog breeds came from a single ancestral breeding pair. If that is the case, then the number of alleles in the original pair at these markers could not have been more than 400 total number of alleles - that would have been maximum heterozygosity. Remember, we don't care what they "looked like," we are looking at the pattern of genetic inheritance and the number of alleles present.Perhaps you have a different idea of what dogs were on the ark? AIG "scientifically" determined that the level of "kind" for dogs is at the family Candiae

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Canidae (Dog kind)
There are 13 genera and 35 species of canids (Wilson and Reeder 2005). There is considerable hybrid data, including a cross between a coyote and a red fox. This has led to the suggestion that fewer genera should be recognized because these animals are quite closely related (Van Gelder 1977). A number of creationist studies have been done, including a couple which examine diversity within the family (baraminology studies summarized in Lightner 2009; Pendragon 2011; previous baraminology studies summarized in Wood 2006). The strong cognitum and extensive hybrid data suggest the kind is likely at the level of the family.

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Mammalian Ark KindsSo it is not unreasonable for me to speculate that all dog breeds derived from a single "dog kind" pair on the ark since that is what creation scientists believe, and if that is true, total number of alleles has INCREASED 350% since then. Hmmm....Another conundrum...HBD

I don't think you are aware when you are using technical language. I have NO idea what anything you said means. I don't know what a "primer" is but you go on as if I do. I have no idea why a strip of fungal DNA should give any information about anything other than fungi. Sorry. your attempt at explanation just doesn't explain anything.As for wolves, I thought the study was merely talking about the sum total of alleles in the registered dogs they studied, not the whole dog population. In any case I have no idea what you mean about 400 alleles on the ark or how you get that from the DNA markers.This is a completely incomprehensible post to me.

dna primerIt is an EXAMPLE of a marker. The markers used in the study use the same principle, just target different regions of the genome. However, you may be surprised to know that you also have ribosomal RNA genes just like fungi. In fact, human 5.8S rRNA is 75% similar to a yeast 5.8S rRNA. So if the only information you have is a piece of 5.8S rRNA, you could correctly identify if that fragment was from a yeast, a human, a dog, a chimp, etc. What's the difference? Wouldn't you expect the entire population to have MORE total alleles? Your position is that the founding population had MORE alleles than the total number of alleles in all daughter populations - or at best, if no alleles have been lost they would have the same number of alleles. No new alleles can be created - according to you. There is 1780 alleles or MORE in the entire population. Each individual can only have a maximum of 2 alleles at each marker - you know this right? There are 100 markers that they sequenced and counted the number of different alleles. An individual that is heterozygous at every marker they studied would have a sum total of 200 alleles at those markers (100 loci markers x 2 alleles per loci). Two individuals that did not share any alleles in common would have a sum total of 400 alleles (200 alleles/individual x 2 individuals). Come on Faith. You have been studying this topic for over 10 years and have no concept of the BASICS??? I really thought you were trying. Or... are you simply feigning ignorance to avoid having to deal with the implications?**** The original pair of "dog kind" animals on the ark could NOT have had 1780 alleles at these 100 loci. That would be 17.8 alleles per loci. Where did all the extra alleles come from??? Mutations perhaps???HBDEdited by herebedragons, : No reason given.

You can drop the accusations, they are tiresome, irrelevant and wrong.I didn't say I was studying genetics in general. I study what I feel I need to grasp for my argument. I'm not going to become a geneticist or a biologist. You've missed a lot of things I've said. There has to be some sort of mutation involved.I'll have to come back to the rest. I'm on my way out.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

Many would think that understanding the words in what you study would be required.

Hi Faith,You're not the only one having trouble following these long posts that cover a lot of territory, but one thing in HBD's last post was both clear and straightforward. It's something that though it's been asked many times here, it's never been answered: I suggest addressing just this for now.

If the question is simply where did the alleles come from above and beyond the two for each locus that had to have been in the individuals on the ark, I've said there had to have been a form of mutation to account for them. A very reliable form of mutation I might add, that actually formed alleles instead of mistakes, unfunctioning alleles or diseases, a mutation rather different from that we know today.And as far as the "markers" go I'll just take HBD's word for it that they are a reliable indicator of numbers of alleles, though I will probably never understand how the markers work.But I've gone on to the problem of trying to explain why additive processes, like mutation, migration, gene flow, cross breeding and so on, can't lead to macroevolution.