Evolution Requires Reduction in Genetic Diversity

I want to try to put together a spin-off from The Origin of Novelty thread because Bolder-dash is pursuing a different objective from mine there and it's getting too confusing to try to keep the arguments separate.

I'll try to pick out the posts from that thread I think best define where this thread should go:

I started my argument there with this brief statement in Message 235:

The fact that shows evolution to be wrong is that the development of varieties or breeds (otherwise known as MICROEVOLUTION) requires the reduction of genetic diversity. That's a FACT. To be true evolution would require the opposite, the increase in genetic diversity. But you can't get a true-breed Hereford if its DNA -- gene pool -- contains Black Angus alleles, you can't get a chihuahua if its DNA contains Great Dane alleles and so on and so forth. The farther out in a true-bred line the less genetic diversity you get. THAT's MICROEVOLUTION. Therefore MACROEVOLUTION couldn't possibly EVER occur. I've argued this many times here, it utterly utterly defeats evolution but forget anybody ever recognizing that fact. So there's your substance.

In Message 323 I said

I don't use the baramin terminology, simply never became familiar with it, but I get that it refers to the same class of things, also called Kinds, that microevolve within their own gene pools, which are considered to belong only to that class and are genetically unrelated to other baramins, Kinds or Species or whatever the terminology is that works best. (If the term "baramin' is useful to keep from this sort of confusion I should learn to use it I suppose.) In any case I see that the usual question gets asked about this that all creationists encounter: Where is the dividing line between the baramins or Kinds, or where is the stopping point beyond which further evolution cannot occur. My own argument is that because reduced genetic diversity MUST accompany the development of new varieties or breeds (within the Kind or baramin) there is a natural point beyond which further variation or "evolution" cannot occur and that is your stopping point or boundary that defines the Kind or baramin. I call this Evolution Defeats Evolution. That is, the very processes that bring about new phenotypes also yultimately lead to genetic depletion for a given line of true breed, which makes further evolution impossible when that point is reached.

In Message 356 I was responding to a post herebedragons made to Bolder but it was partly about my own posts:

I did not say that artificial breeding does not reduce genetic variability. It does and in that she was largely correct. Hip hip hooray. I may have to copy that out, change the font to something formal like Olde English and put it in 72 point and hang it on my wall. Yikes, a tiny little concession. Means SO much. But what she seemed to imply was that breeding is accomplished by eliminating genetic diversity alone. Yes, that is indeed my argument. You do not get new breeds, new phenotypes, either in the wild or under domestication, or keep an established breed pure, without reducing the genetic diversity, or once the breed is established, by keeping the genetic understructure limited to ONLY what expresses the characteristics of that breed. The implication is that all the characteristics we find in dog breeds were originally in the wolf; they were just so well mixed that the phenotype that is expressed is ... a wolf. It just can't be that simple. The alleles that originally existed in the wolf population must have changed sometime during the selection process. This is somewhat of a tangent to the argument I'm making but my guess is that today's wolves have evolved as much as the dogs that bred from the original wolf so that their genetic diversity is also much reduced from that of whatever the original population was, which might have been very much like today's wolves or not as much as we suppose. My argument includes the observation that whenever you isolate a portion of a previous population you get the familiar formula "change in gene frequency" which is what creates the new varieties or breeds and this can affect both the "parent" population and the "daughter" population which in fact can in some cases be hard to differentiate from each other anyway, since the numbers are affected in both cases and the greater the reduction in numbers the more dramatic the remix of alleles and the phenotypes formed from them. The smaller the portion the greater the phenotypic change and the greater the decrease in its collective genetic diversity. Your position is that these alleles did change but that all such changes were actually diseases that humans thought were neat so they breed for that disease. Is that accurate? This doesn't apply to my own argument. In my argument alleles don't change, they just shuffle within the whole population from individual to individual, sometimes creating some interesting new phenotypes, but it is really only when a small number break off from the greater population that such new phenotypes become expressive to any noticeable extent. The problem is that when you try to oversimplify a situation like this it just gets reduced to silliness. Greyhounds were bred for speed, they are the second fastest animal on earth. Do you consider that a loss of function as compared to the wolf? I don't think in such terms myself and Bolder's frame of reference may be getting confused with mine here. I wasn't arguing for a "loss of function" at any point, my argument is that in order to get NEW functions or features, new phenotypes, new traits, you have to isolate the particular alleles for those traits from others that would interfere, and that is what happens when a portion of a population gets reproductively isolated, and the smaller its numbers the greater the phenotypic divergence you should get from the original ALONG WITH a great reduction in genetic diversity. Of course the speed of the greyhound involves no loss of function. What it DOES involve is the isolation or selection of whatever alleles for whatever genes are responsible for creating that speedy bodily structure, which of course means that genes/alleles that would interfere with it are eliminated from the breed, left behind in the "original" population from which it microevolved. It is not. But while breeders are selecting for this gain in function (increased speed) they are inadvertently selecting for less desirable traits like lack of body fat and thin, fragile skin and long, thin bones. Breeders did not intentionally select specifically for these traits, they were by products of the desirable trait - speed. Yes, of course that can happen. The thing I wanted Faith to think about was that there is more going on that just allele frequency or eliminating Great Dane alleles to breed Chihuahuas. The problem here is that I've been working on this for something like eight or ten years now and you aren't going to just casually get me to think about some other alternative until you've shown you understand what I'm arguing, which is far from the case at the moment. Since the rest of this post is clearly responding to Bolder about something that doesn't impinge on my argument at all, I'll stop here.

The topic then took a turn as PaulK wanted me to account for the effect of mutations:

PaulK in message 359 writes: If, after working for eight or more years, your argument that evolution must reduce genetic diversity still has no more support than "'cause I say so!" then I suggest that it is very likely that you are going down a blind alley. At the least you ought to have some evidence that mutations do not occur sufficiently quickly to make up for lost diversity. But I've never seen any hint of that.

To which I responded in Messages 369 and 376:

(Message 369) If mutations occurred the way you think they do, you could not establish a new breed or maintain a breed, and that I HAVE argued at some length. Mutations as a matter of fact INTERFERE with the normal processes of evolution. (Message 376 in response to Taq who said mutations are found to be very necessary and gave some genetic information) In the context of population genetics, you cannot have mutations constantly cropping up or you will never get a new variety let alone speciation. The development of new varieties does depend upon establishing an isolated gene pool, and once established keeping the gene pool isolated from new genetic material, otherwise known as gene flow, but mutation would have the same effect. Whatever you find in the laboratory about mutations is really another subject.

Message 380 in answer to PaulK

If mutations occurred the way you think they do, you could not establish a new breed or maintain a breed, and that I HAVE argued at some length. Mutations as a matter of fact INTERFERE with the normal processes of evolution. No, that's absolutely false. Indeed it's not even true of selective breeding. If a mutation considered desirable should appear then breeders will incorporate it into their program, as they did with the Scottish Fold cat. But then you would be CHANGING your breed for some other breed. What I'm talking about is maintaining an established breed where you do not want novelty, you want purity. You want a PERFECT Tonkinese cat or Friesian horse, you do not want imperfections and most mutations produce imperfections. It's very very rare that you get one that you want to incorporate. And I also dispute that what are called mutations are really mutations anyway. I believe that most phenotypic occurrences that show up here and there within an established breed are nothing more than a new combination of a rare allele that has always been in the gene pool. In fact mutations are the "fuel" of evolution and absolutely essential to the process. This is only an assumption or an article of faith, and for the most part a matter of definition since what you call a mutation, if it IS desirable, is most likely not a mutation at all but a normally occurring allelic variant.

PaulK answer to above Message 384

quote: But then you would be CHANGING your breed for some other breed. So it would be evolution. That's supposed to be a problem ? quote: What I'm talking about is maintaining an established breed where you do not want novelty, you want purity. That isn't evolution. Selection and gene flow can stabilise a population but there's no objective to keep a "pure" population in evolution. quote: You want a PERFECT Tonkinese cat or Friesian horse, you do not want imperfections and most mutations produce imperfections. It's very very rare that you get one that you want to incorporate. Evolution isn't about maintaining some artificial idea of "PERFECT" breeds. quote: This is only an assumption or an article of faith, and for the most part a matter of definition since what you call a mutation, if it IS desirable, is most likely not a mutation at all but a normally occurring allelic variant. No, it's what the theory SAYS happens. So it's what you've got to argue against. Arguing that the way that you think evolution ought to work wouldn't work is a bit pointless.

Taq answer to my last message387 saying the same thing PaulK was saying:

But then you would be CHANGING your breed for some other breed. Exactly. You have novel changes arising from mutations that are then selected for. We call this evolution.

This is pretty unwieldy I guess but I'm going to post it as is and will probably come back to try to improve it.

(For reference as the thread proceeds, I want to keep the link to the Introduction to Genetics thread available. It was started but never finished though there was some good discussion there.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : TO ELIMINATE SNARKY SENTENCE

Edited by Faith, : Add link to Intro to Genetics thread

Can this get promoted?

As you say, it is unwieldy. Would it be possible to compose a shorter opening post that is original (rather than cut-n-pastes) and doesn't contain lines like, "So there's your substance and now you can bring on your stupid answers as usual. Ho hum."

The part of your argument that I think is understood is that since sub-subspecies such as Herefords (of cattle) and chihuahuas (of wolves) have reduced genetic diversity, and since new species begin from isolated populations consisting of a subspecies or sub-subspecies, that therefore speciation can only occur from a reduction of genetic diversity. I don't think many would have a problem with a discussion based upon this style of speciation. It's fairly representative and it's unarguably true since by definition a subset is always an incomplete representation of the full set.

The part that isn't clear is your view of the role of mutations. You appear to be arguing that if mutations really had the effect that evolution claims then species would be inconstant and perpetually changing, which is precisely what evolution does claim based upon the available evidence. I think discussion would center around this and not around the initial reduction in genetic diversity that can be associated with speciation.

If the above is a sufficiently accurate representation of your views then I can just promote this now and you wouldn't have to attempt a rewrite of the opening post. I'll be checking back in in a few hours.

I did want to have the whole basic argument on the table at least which i guess you are saying is possible. And I'm amazed that you agree with that much of it, even, since I don't recall that ever happening when I argued it many times before. But best not to look a gift horse in the mouth.

Yes that part can just be left as is and I'll go cut out that offending line if you want {ABE: Just did so}. I do think you stated my view pretty well, so the topic to be pursued at the moment is the questions about mutations raised by PaulK and Taq.

So I'm happy if you're willing to promote as is.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Thread copied here from the Evolution Requires Reduction in Genetic Diversity thread in the Proposed New Topics forum.

I think that the best way to start this discussion is with a very simple explanation of how evolution is meant to work. There are many, many complications but we need to agree the basics first.

Adaptive evolution is held to be the interplay of two processes, mutation and selection. Mutation provides a stream of variations while selection is the directional aspect, culling diversity. Evolution has no definite endpoint other than extinction.

Selection is quite simple to understand. All life inherits some traits from it's parents or parent. Variation in these traits leads to variation in fitness which is defined in terms of producing offspring who manage to reach the point of reproducing themselves. Those individuals with the greatest fitness will tend to produce more offspring, and therefore their traits will tend to become more common in the population. Fitness is also affected by the environment - a trait may be good in some environments and bad in others - and environments do change over time.

If we are going to compare natural selection to a dog breeder the nearest equivalent would be a pragmatic breeder of working dogs. A breeder who is concerned with the practical benefits of the traits he can select, and not with any abstract idea of breeds. A breeder who is happy to take in the new, and adapt to changing demands, rather than pursuing an aesthetic "perfection".

Faith writes: I did want to have the whole basic argument on the table at least which i guess you are saying is possible. And I'm amazed that you agree with that much of it, even, since I don't recall that ever happening when I argued it many times before. But best not to look a gift horse in the mouth.

If you're referring to the part about one route to speciation beginning with a subpopulation that possesses only a subset of all alleles of the species, then I think most everyone has always agreed about this.

Disagreement only arises when it is declared that increasing diversity is impossible, at which point discussion of mutations and selection begins. But the problem isn't whether increasing diversity is possible. The problem, given that reproduction involves imperfect copying, is how one would ever prevent increasing diversity?

--Percy

If you're referring to the part about one route to speciation beginning with a subpopulation that possesses only a subset of all alleles of the species, then I think most everyone has always agreed about this.

Odd then that it has never before been expressed to me. While I'm quite willing to keep the focus at least at first on the questions raised about mutations, I do have to say that nobody in my recollection in discussing this subject before has ever acknowledged that i am right about my claim that evolution in ANY context whatever leads to reduced genetic diversity.

You are carefully defining the context here in terms of "one route to speciation" through a subpopulation, which is fine because it's true, so I appreciate that much acknowledgment, but I particularly appreciate what herebedragons said, which I include in the OP, which had me wanting to frame it and hang it on my wall BECAUSE even that much had never been acknowledged before.

Your description of the idea of course reserves the implicit claim that other routes do not encounter this problem of reduced genetic diversity. Since my argument is that there are no other routes I will at some point have to try to prove it. But we don't have to start there.

Edited by Faith, : No reason given.

Adaptive evolution is held to be the interplay of two processes, mutation and selection. Mutation provides a stream of variations while selection is the directional aspect, culling diversity. Evolution has no definite endpoint other than extinction.

The theory I've been pursuing for years is that it does, and I realize it's my job to prove it.

Selection is quite simple to understand. All life inherits some traits from it's parents or parent. Variation in these traits leads to variation in fitness which is defined in terms of producing offspring who manage to reach the point of reproducing themselves. Those individuals with the greatest fitness will tend to produce more offspring, and therefore their traits will tend to become more common in the population. Fitness is also affected by the environment - a trait may be good in some environments and bad in others - and environments do change over time.

There is no argument with this basic notion except perhaps to suggest that it is overemphasized in the range of actual occurrences in nature.

If we are going to compare natural selection to a dog breeder the nearest equivalent would be a pragmatic breeder of working dogs. A breeder who is concerned with the practical benefits of the traits he can select, and not with any abstract idea of breeds. A breeder who is happy to take in the new, and adapt to changing demands, rather than pursuing an aesthetic "perfection".

For my purposes it doesn't matter which context you choose, including nature's own "selections" by the fairly frequent and often accidental occurrences that bring about reproductive isolation of separated portions of a population, leading to new phenotypes by reduced genetic diversity there as in all other cases.

But this is all just by way of preliminary statement that can be discussed as we go along.

I want to officially start this thread by answering the last two posts I include in the OP, about mutations.

Edited by Faith, : No reason given.

Faith writes: Odd then that it has never before been expressed to me. While I'm quite willing to keep the focus at least at first on the questions raised about mutations, I do have to say that nobody in my recollection in discussing this subject before has ever acknowledged that i am right about my claim that evolution in ANY context whatever leads to reduced genetic diversity.

No, no, you've misunderstood. It isn't evolution in the form of mutation and natural selection that causes reduced genetic diversity. It's the distribution of the population of an entire species into subpopulations across distinct geographical regions with differing environments that results in reduced diversity in the subpopulations when compared to the entire species. That's what I meant earlier when I used the term "by definition." Practically by definition any subset of a population will have less diversity than the entire population.

The actual process of evolution by means of mutation and natural selection can only lead to increased diversity because there is nothing to prevent the imperfect copying of reproduction.

Your description of the idea of course reserves the implicit claim that other routes do not encounter this problem of reduced genetic diversity. Since my argument is that there are no other routes I will at some point have to try to prove it. But we don't have to start there.

Of course there are other ways that speciation can happen. A homogenous population can be split in two by some geologic or environmental event, such as a river changing course, and then the two subpopulations, each with equal diversity, would evolve according to the requirements of the environments of the newly separated regions.

Or a population of a species can simply evolve over time into a new species.

--Percy

Hi Faith

Faith writes: Hip hip hooray. I may have to copy that out, change the font to something formal like Olde English and put it in 72 point and hang it on my wall. Yikes, a tiny little concession. Means SO much.

Lol. I am more than happy to agree with you whenever you are right. Seriously though, I try to be honest and objective. I am not going to disagree just to disagree.

Faith writes: The problem here is that I've been working on this for something like eight or ten years now and you aren't going to just casually get me to think about some other alternative until you've shown you understand what I'm arguing, which is far from the case at the moment.

Personally, I come to forums like this to help develop my own skills in rhetoric and logic ... I have no illusions that I will change anyone's mind. It also helps me learn as I make sure that anything I post is as well thought out and researched as I can (in any reasonable amount of time )

I am not totally sure where to start with this topic. It is true that genetic events like bottlenecks (a severe reduction in population size), the founder effect (the founders of a new population have only a small proportion of the genes from the original population) or inbreeding (this is essentially the effect artificial selection will have on gene frequency) will reduce genetic diversity. But that is not the whole story.

from Message 459

Faith writes: I believe there was an enormous lot of variability built into the original genome of each creature so that this is what is playing out over time. Novelty is a pretty standard occurrence in this scenario as there is so much variability new features and functions can come to expression through normal sexual recombination in newly reproductively isolated populations.

This may be a good place to start. This is what I was wanting you to consider when I said

herebedragons writes: The thing I wanted Faith to think about was that there is more going on that just allele frequency or eliminating Great Dane alleles to breed Chihuahuas.

I know you believe that there was a great flood roughly 4500 years ago. Do you realize the implications of that on your belief that enormous genetic variation was built into the original genome? It would be possible that God created whole populations of critters that contained this enormous amount of diversity, but at the flood there would be a severe (is there a word that means severe times 1000?) bottleneck. All animal populations would be reduced to one breeding pair (ceremonially clean animals would have 7 breeding pairs). At this point there is a maximum of 4 alleles at any locus. Now granted, some alleles control more than one characteristic, but some characteristics are controlled by more than one allele. But the point is there would be virtually no genetic diversity after the flood. Now start removing alleles to produce the various breeds and you quickly run out of alleles.

So you run into a conundrum ... either new alleles must arise in populations (through mutations) or you must abandon the flood bottleneck. I really see no other option. An original population of 1 breeding pair cannot have the kind of genetic diversity that you are thinking of here.

How do you think you could have the amount of genetic diversity it would take to produce all the dog breeds we have today without adding alleles at some point?

HBD

quote:

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The theory I've been pursuing for years is that it does, and I realize it's my job to prove it.

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OK, so we're talking about your theory of evolution, and falsifying it won't have any impact on the standard scientific theory. As far as I know this is the first time you've clearly said this and I don't remember seeing anything that even loosely implied it before recent discussions. The past threads would have likely gone better had you made it clear.

In fact I suggest you come up with some terminology that makes it clear in the future so we know when you're talking about your theory.

quote:

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There is no argument with this basic notion except perhaps to suggest that it is overemphasized in the range of actual occurrences in nature.

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There are, in fact, arguments within evolutionary science as to how far features are the direct products of selection.

quote:

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For my purposes it doesn't matter which context you choose, including nature's own "selections" by the fairly frequent and often accidental occurrences that bring about reproductive isolation of separated portions of a population, leading to new phenotypes by reduced genetic diversity there as in all other cases.

---

The point is that the mechanisms of natural selection are incapable of working towards an abstract ideal, like a "perfect" exemplar of a breed. As a consequence genetic diversity will often tend to increase, as selection fails to remove new variations that have little effect in the current environment.

So, to go back to your theory, you need a selective mechanism which will work the way that your theory requires.

Faith writes: Odd then that it has never before been expressed to me. While I'm quite willing to keep the focus at least at first on the questions raised about mutations, I do have to say that nobody in my recollection in discussing this subject before has ever acknowledged that i am right about my claim that evolution in ANY context whatever leads to reduced genetic diversity. No, no, you've misunderstood. It isn't evolution in the form of mutation and natural selection that causes reduced genetic diversity.

Well, as a matter of fact it is, but I've been too tired all day to get back to this yet. I hope I'm up to answering the mutation statements now.

It's the distribution of the population of an entire species into subpopulations across distinct geographical regions with differing environments that results in reduced diversity in the subpopulations when compared to the entire species. That's what I meant earlier when I used the term "by definition." Practically by definition any subset of a population will have less diversity than the entire population.

Fine, that is true, but again nobody ever acknowledged that fact before, a fact I've hammered away at on more than one thread here, many times trying to keep the subject as oversimplified as you have put it here but still no acknowledgement until now. Nevertheless I do appreciate the acknowledgement even though hyou don't think you are doing anything of the sort.

But you overdefine the situation. The subpopulations can be created by anything that reproductively isolates one from the larger group and that doesn't have to be distinct geographical regions, and believe it or not "differing environments" is NOT what creates the new phenotypes. The genetic situation itself is what creates the new phenotypes, the fact that a new mix of alleles forms the gene pool of the new population compared to the old. That's ALL it takes to produce a new phenotype or variety or breed, or in other words "change in gene frequency." There are a lot of details that need to be discussed about all this and I hope it's going to be possible to get to them before the thread gets swamped in side issues.

The actual process of evolution by means of mutation and natural selection can only lead to increased diversity because there is nothing to prevent the imperfect copying of reproduction.

What you haven't yet grasped is that SELECTION always inevitably reduces genetic diversity. That is the substance of my argument very oversimplified. You can have mutations galore within a population but once you have selection of whatever mix of mutations -- or alleles however formed -- selection reduces genetic diversity in the new population. Selection brings a certain allele mix to expression in the phenotype BY ELIMINATING COMPETING ALLELES from the gene pool. Yes it will take some time to work through this argument.

Your description of the idea of course reserves the implicit claim that other routes do not encounter this problem of reduced genetic diversity. Since my argument is that there are no other routes I will at some point have to try to prove it. But we don't have to start there. Of course there are other ways that speciation can happen. A homogenous population can be split in two by some geologic or environmental event, such as a river changing course, and then the two subpopulations, each with equal diversity, would evolve according to the requirements of the environments of the newly separated regions.

Actually they would evolve according to the particular mix of alleles in their gene pool, which may adapt to peculiarities in their environment certainly, but the environmental factor is not necessarily the driving factor. If you get a finch with a beak that crushes nuts those nuts don't have to be peculiar to the particular environment, it's just that that finch prefers them to the bugs that other finches with slender beaks prefer because they can get at them more easily than the nut-crunching finches can.

Or a population of a species can simply evolve over time into a new species.

Well, yes, this is another way you can get reproductive isolation -- within the population itself -- so that it can evolve over time just as the populations in the other situations can. Not into a completely new species however, just the usual subspecies or variety, because it will be by the same processes that involve the bringing forward of a phenotype along with the reduction of alleles for other phenotypes, which is a reduction in genetic diversity. WHEREVER there is selection of a phenotype there will ALWAYS be a corresponding reduction in genetic diversity as the alleles for other phenotypes get eliminated from the pool.

The decrease in genetic diversity is an INEVITABLE concomitant of the development of new phenotypes, the more dramatic where the selection pressure is heaviest but always present in any situation where a new phenotype gets developed. And this inevitable reduction in genetic diversity can only move in the same direction toward complete genetic depletion, beyond which no evolution at all is possible. This extreme is no doubt rarely reached in nature although I think it sometimes is, but it is easy to reach it in domestic breeding programs if they too aggressively eliminate the competing alleles by reducing the population too severely.

Edited by Faith, : No reason given.

Hi Faith Faith writes: Hip hip hooray. I may have to copy that out, change the font to something formal like Olde English and put it in 72 point and hang it on my wall. Yikes, a tiny little concession. Means SO much. Lol. I am more than happy to agree with you whenever you are right. Seriously though, I try to be honest and objective. I am not going to disagree just to disagree.

I'm SO grateful. Truly, NOBODY ever acknowledged that simple fact here before. They might insist they get what I'm saying but spelling it out and agreeing with it, no. So thanks again. And now I'm sure you'll have plenty of objections anyway.

I am not totally sure where to start with this topic. It is true that genetic events like bottlenecks (a severe reduction in population size), the founder effect (the founders of a new population have only a small proportion of the genes from the original population) or inbreeding (this is essentially the effect artificial selection will have on gene frequency) will reduce genetic diversity. But that is not the whole story.

Yes and no. In a way it IS the whole story which is what my argument is all about, but I'm certainly aware that there are many other situations that have to be considered on the way there.

It is good to get the extreme case of the bottleneck acknowledged because it is an example of the same process of creating a new phenotype by eliminating competing alleles, and in those cases, such as the cheetah which is the classic example, you don't get mutations rushing in to increase the diversity as is claimed happens in all populations. The relevance of the cheetah example is disputed here all the time though, but I like to keep it on the table.

Faith writes: I believe there was an enormous lot of variability built into the original genome of each creature so that this is what is playing out over time. Novelty is a pretty standard occurrence in this scenario as there is so much variability new features and functions can come to expression through normal sexual recombination in newly reproductively isolated populations. This may be a good place to start. This is what I was wanting you to consider when I said herebedragons writes: The thing I wanted Faith to think about was that there is more going on that just allele frequency or eliminating Great Dane alleles to breed Chihuahuas. I know you believe that there was a great flood roughly 4500 years ago. Do you realize the implications of that on your belief that enormous genetic variation was built into the original genome?

Yes, of course I do, and it's been discussed many times before, here and on my blog as well. I went through a phase of trying to figure out what the original genome would have to be like for this scenario to be true, considering such possibilities as polyploidy, and some here ridiculed the idea of the "supergenome" of course. Eventually I came to a different answer, but I'm not sure this is the time to get into discussing it. Well, you'll see what I have in mind as I answer your next points:

It would be possible that God created whole populations of critters that contained this enormous amount of diversity, but at the flood there would be a severe (is there a word that means severe times 1000?) bottleneck. All animal populations would be reduced to one breeding pair (ceremonially clean animals would have 7 breeding pairs). At this point there is a maximum of 4 alleles at any locus. Now granted, some alleles control more than one characteristic, but some characteristics are controlled by more than one allele. But the point is there would be virtually no genetic diversity after the flood. Now start removing alleles to produce the various breeds and you quickly run out of alleles.

Actually it isn't as dire as all that. The initial diversity before the Flood was so great that enormous diversity remained in the creatures on the ark. This is all speculative of course but I think you need to think of every gene of every individual as being heterozygous, the maximum genetic diversity you could have, two alleles per gene, and different in each individual as well so that you do have four alleles for each pair of animals, and for the human beings you have twelve different alleles for a single gene (the six reproducing human beings, Noah's three sons and their wives). Then if there are many genes for one characteristic and they are all equally heterozygous you obviously have a LOT of genetic diversity that can continue through quite a few generations before being played out.

The clean animals would have even more diversity, EXCEPT that they were used for sacrifice which would have reduced it too.

Of course the population has lost an enormous lot of genetic material, and that's going to show up down the generations, and I haven't completely worked out how that happens but I'm convinced that the huge amount of junk DNA in our genome as well as that of most animals, is THE sign of the eliminated genetic material brought about by the Flood. THAT much death would have to be reflected in the genome and that's how I think it is reflected, but it's going to take thinking through how this plays out down the generations from the ark and I've barely begun to think that through.

So you run into a conundrum ... either new alleles must arise in populations (through mutations) or you must abandon the flood bottleneck. I really see no other option. An original population of 1 breeding pair cannot have the kind of genetic diversity that you are thinking of here.

But it can if we're talking all that junk DNA having been alive before the Flood and functioning in the genome, and such a great percentage of heterozygosity in the genome as well. I keep forgetting this statistic and will no doubt have to look it up again, but I believe our genome now has about 7% heterozygosity, and it's heterozygosity that makes for genetic diversity. I figure that before the Flood the percentage was much bigger, who knows how much, maybe not 100% but even 50% heterozygosity would be enormous.

The idea here is that when you get far out on a breeding line, or you get the situation of the cheetah what you see is a great deal of homozygosity at many different gene loci in the genome. That is the genetic situation that prevents further evolution. A bottleneck now will certainly have such drastic consequences, but back when the genome was so much richer you could have a bottleneck and still maintain enough genetic diversity for many subvarieties to develop down the generations. Nevertheless the TREND is always in the same direction, toward reduced genetic divdersity as new phenotypes or varieties are developed.

How do you think you could have the amount of genetic diversity it would take to produce all the dog breeds we have today without adding alleles at some point?

See above. But again I would point out that even if it were true that new alleles are added by mutation, consider this: a mutation CHANGES an existing allele, it doesn't add something newer than a different expression of that particular gene. If the mutation occurs in a fur color gene it will only affect fur color. You are not going to get anything really new, a new function for instance, through mutation. You are only going to get variations on whatever that gene does. I personally don't think mutations do anything but destroy and deform of course, but even if I'm wrong and they do create useful new alleles what I've said here has to apply.

And then, IF that mutation is SELECTED and proliferates in the population, getting passed on and displacing other alleles for that same gene, then what you have is the reduction of genetic diversity I'm talking about, that is the inevitable concomitant of any -- ANY -- selection process. The selection can be brought about by geographical isolation or mating preference isolation or the actions of a predator on the population or all kinds of things. The point is that getting a phenotype established in a population means that it has to be selected, it has to be reproductively isolated, it has to proliferate, it has to dominate over other allelic competitors, etc etc, and that has to mean that the other alleles are suppressed and ultimately even disappear altogether from the population. There is ALWAYS a loss of genetic diversity wherever you have "evolution."

Edited by Faith, : No reason given.

What you haven't yet grasped is that SELECTION always inevitably reduces genetic diversity.

But isn't the point that whilst selection often reduces diversity, mutation is adding diversity to a population at a greater rate.