Yes you DO get loss of genetic diversity with evolution Part 1

Getting anyone to accept my claim about reduced genetic diversity, obvious though it is, is the real battle here unfortunately. So let's go back to my last thread on the subject at EvC and see if it's possible to make any headway on it:

Here's Percy's opening gambit on the subject on that thread:

Genetic diversity can go in any direction after reproductive isolation. For example, consider a relatively homogeneous population that becomes divided in two when a river changes course. There are now two populations, both with pretty much the same alleles and allele frequency. Mutations experienced in one population will no longer be shared with the other and the populations will evolve along different paths. If this continues for a sufficient period then they could lose their mutually interfertile quality and become two species.

Let's take it step by step:

Genetic diversity can go in any direction after reproductive isolation.

Of course I am claiming that genetic diversity can NOT go in "any direction" after reproductive isolation. It CAN remain more or less stable for long periods, but otherwise it can ONLY decrease; it can NOT increase. This is of course based on the Creation Model I've spelled out in earlier blog posts, that denies the mutations which are needed by the Evolution Model. Mutations are the ONLY way it could increase.

But to get off the hypothetical and bring this down to a question of evidence and fact, I'm claiming that it DOESN'T increase, and that ought to be provable with the DNA sampling test I've suggested.

For example, consider a relatively homogeneous population that becomes divided in two when a river changes course. There are now two populations, both with pretty much the same alleles and allele frequency.

Of course if you posit a split into two populations that retain the same character as the original I wouldn't expect to see much change either. This is not a scenario that leads to evolution and all I'm talking about is how evolution -- or variation or the production of a new phenotype -- leads to reduced genetic diversity.

This situation would exist if the two new populations are appreciably different in size and/or have appreciably different gene frequencies -- which is in fact more likely to occur in a smaller population. That's when you get the beginnings of the phenomenon I'm talking about. The larger may change too to some degree because its gene frequencies will have changed also, but not to the extent of the smaller one.

But evolution always has to invoke (beneficial) mutations, those imaginary changes in the DNA that fuel the changes the theory requires.

Mutations experienced in one population will no longer be shared with the other and the populations will evolve along different paths. If this continues for a sufficient period then they could lose their mutually interfertile quality and become two species.

Of course there is no evidence that this happens at all. And the Creation Model has no need of them as there are plenty of built-in genes and alleles to bring out all kinds of variations in any Species.

1. Mutation is not needed, the original genetic endowment of each Species fuels all possible variations of that Species.
2. There is no evidence for it, it's purely an article of faith.
3. Where there is evidence of its existence, its effect is either neutral or deleterious, which the Creation Model explains as due to the Fall which brought death, disease and deformity to all living things.

If both populations thrive then diversity could increase in both.

There is no way that GENETIC diversity ever increases after reproductive isolation -- not just "diversity" as PHENOTYPIC diversity is something else, and as my formula has it, phenotypic diversity increases as genetic diversity decreases. I don't know how to prove this as making charts of combinations of genes and alleles quickly gets beyond me, but keeping the Creation Model in mind ought to make it intuitively obvious. One argument I've made is that it ought to be obvious that increases in genetic diversity would prevent ever establishing a domestic breed as its character would always be threatened by the input of new alleles.

As I quote in a post below, from the Wikipedia article on Zygosity:

True breeding organisms are always homozygous for the traits that are to be held constant.

Homozygosity for an entire population is of course the extreme of genetic depletion, also known as "fixed loci" in which there is only one allele in the entire population for the given gene. It's the same situation that Nature has brought about in the cheetah and the elephant seals and the North American bison. It's the FORMULA for getting a new phenotype. It's EVIDENCE that what i'm saying is correct, that you MUST have reduced genetic diversity IF you are to get EVOLUTION.

And again it pertains not just to domestic breeding but also to varieties in the wild -- the beaks of Darwin's finches couldn't be counted on to be stable even if they had been brought about by Natural Selection, they'd always be subject to change that would interfere with their relationship to their environmental niche. In other words an increase in genetic diversity ALWAYS interferes with EVOLUTION. You get evolution or the development of new phenotypes / varieties as you lose alleles for competing traits, which means a decrease in genetic diversity. For a finch population to be characterized by a beak that can crack nuts means it has to NOT have the alleles for beaks that can penetrate small narrow spaces. It could be that an all-purpose beak would work fine and dandy, but the theory says that you get these specialized beaks by natural selection so that they can adapt to their particular ecological niche and since that does appear to be the case they must have alleles FOR their particular adaptation and NOT have the alleles for the other adaptations.

I know I argued this to death on that thread to deaf ears and here I've barely gotten through this one post from Percy. Oh well, might as well keep at it for a while at least.

But if one or both populations suffer some disaster such as flood or famine or an invasive predator or disease that greatly reduces population size, then diversity would be reduced. It all depends upon what happens to the populations.

No, it doesn't ALL depend on that although such events would certainly have an impact. The point I want to keep in mind here is CHANGE IN GENE FREQUENCIES. Many things can bring this about; what brings it about isn't the important thing but simple population splits are usually quite enough for the purpose.

Speciation + Evolution = LOTS of Trait Diversity with LOSS of Genetic Diversity leading to end of ability to evolve

Another one from RAZD at EvC, Speciation + Evolution = More Diversity

The scene: sitting at computers all over the world ...

"Why don't creationists understand evolution -- it is so simple," the evolutionist wails:

1. Evolution - the change in hereditary traits in populations from generation to generation - is an observed and documented fact, a process that occurs constantly in the natural world around us, and

2. Speciation - the division of parent populations into reproductively isolated daughter populations - is also an observed and documented fact, a process that occurs frequently in the natural world around us.

These two simple processes are sufficient to explain the diversity of life we know, from the world around us, from history, from prehistory and archeology, from geology and physics and paleontology and the fossil record, and from chemistry and the genetic record.

Well, it sounds good on paper, I guess, as theory at least, but unfortunately it fails in reality. Yes, there is an "evolution" by which heritable traits change from generation to generation, but this has never been observed beyond what we call "micro" evolution, or evolution within the genetic limits that define each species, and in fact it can't occur beyond microevolution for the reasons I've given over and over here, which are the same reasons there is no evolution beyond speciation. And yes, speciation is also a documentable fact, but it always occurs with loss of genetic diversity, even to the extreme of fixed loci or total homozygosity for some traits in the population, which makes further evolution beyond speciation purely a pipe dream.

But RAZD just goes on asserting the theory, the pipe dream, as if it were reality, as they all do.

We can even see how evolution causes speciation with Ring Species:

1. the species forms a band made up of several varieties around some barrier to their survival ability,

2. each of the varieties has slightly different hereditary traits from their neighbors,

3. each reproduces with their neighbors in hybrid zones that show a mixing of the hereditary traits of the two neighbors, except that

4. when they meet on the other side of the barrier, the two ends do not mate.

Evolution results in different hereditary traits developing in each of the areas dominated by the different varieties, differences that do not hinder mating until they reach a certain threshold - the difference between the end varieties.

Yes, pretty much but as long as he sticks to the level of traits -- of the phenotypes, of the different observable characteristics between the populations -- he misses the reason what happens happens: The splitting of the populations changes the gene frequencies. When new traits emerge this is because alleles for competing traits have been reduced which can proceed after many population splits to the point that they are completely lost to the new population. After a series of splits the genetic diversity may be quite drastically reduced, and the main reason there is no interbreeding between the first and last populations is the genetic incompatibility that has developed by then.

Again, my prediction is that if you sampled the DNA of the first and last populations (better done in a laboratory where you can sample the first before it too undergoes change), you should find much greater genetic diversity in the first and much reduced diversity in the last, more heterozygosity in the first, more homozygosity in the last, particularly for the traits that are most characteristic of the populations.

Remove any one of the intermediate varieties, so that the band is broken, and you have two distinct species.

We now have more species than before, so life is more diverse. It is so simple:

Evolution + Speciation = Diversity

Way TOO simple, RAZD. Yes you do have more diversity of TRAITS, but you are simultaneously getting REDUCED diversity of GENETIC POSSIBILITIES. This is all just the usual evolutionist daydream based on surface facts completely ignoring what is going on genetically, which is the NECESSARY reduction of genetic diversity, which occurs with EACH splitting off of a portion of the population to form a new population. This is a trend that can keep producing new phenotypes for some time by losing more alleles, but can ultimately arrive at such genetic depletion that no further phenotypic change is possible, a condition like that of the cheetah. Not that this degree of depletion is inevitable, but reduction in that direction certainly is.

This little scenario depicts, I believe, the state of many debates between creationists - people that predominantly use faith to understand the world - and "evolutionists" - people that predominantly use science to understand the world.

What "this little scenario" actually depicts is evolutionist reliance on wishful thinking as they spell out what they THINK happens, because they haven't really faced the GENETIC PICTURE which is working against their all-too-sanguine expectation that change in traits can just go on and on without genetic cost. It really is a daydream, a fantasy. And it's quite the joke that they are constantly claiming to appeal to EVIDENCE and accusing creationists of relying only on faith.

(I skipped his caricature of the creationist response to the above because it is a distraction from what I'm trying to say here.)

Where does "large" change come from? - the change that makes giraffes so different from kangaroos? Simple:

Speciation - the division of parent populations into reproductively isolated daughter populations - is also an observed and documented fact, a process that occurs frequently in the natural world around us, and

Evolution- the change in hereditary traits in populations from generation to generation - is an observed and documented fact, a process that occurs constantly in the natural world around us.

SO simple as long as he just goes on daydreaming about the surface traits and imagining that there are no limits to change.

Speciation + Evolution = More Diversity
After speciation has occurred, the daughter populations no longer share genes through reproduction, and they are free to evolve completely different traits.

Yes, and this lack of sharing of genes means a LOSS OF GENETIC DIVERSITY. Yes, they ARE "free to evolve copletely different traits" but this is ALWAYS made possible by the loss of competing alleles for those traits, which is completely ignored by evolutionists. You can always get new traits BY LOSING competing alleles, but if the population splits that bring this about continue to occur, eventually a point will be reached where you can't get new traits any more because you'll be completely out of alleles. Speciation may not always mean genetic depletion but it certainly means genetic reduction from earlier populations particularly where the main new traits are emerging.

The likelyhood is high that one of them will become quite different, either to inhabit a new ecology that the other is not as well suited to (could have caused the original split), or to make use of the existing ecology in a different way, and this will lessen competition between the two species rather than drive one to extinction.

Lotta sheer conjecture there. It really isn't even necessary to posit environmental or situational reasons for trait changes or even the population splits themselves. Migration will bring about splits and the splits alone will bring about trait changes. The fewer individuals at the start of a new population the bigger the observable trait changes, the ecology is not likely to have much to do with it. It may be that both populations still have sufficient genetic variability even to undergo several further splits if necessary, but since he's completely ignored the whole question of what happens to the genes while focusing on the traits and fantasizing endless change he's going to miss the state of genetic depletion also when it does finally occur after more population splits.

Continued evolution of daughter populations along different ecological paths results in increased diversity - difference - between them over time. That is how the small amount of difference we seen below can become the amount of difference we see between other bird species.

Again, overrated influence from the environment but this is really a side issue, but anyway, the increased diversity is completely the result of the change in gene frequencies brought about by the population split. If the environment contributes an influence that further impacts the population numbers or reproductive isolation and therefore the gene frequencies, then it will contribute to the trait differences between the populations as well, but again, there is no need for this to happen in order for even great differences to come about as the change in gene frequencies alone will do it.

Continued evolution causes more change - in each population, from generation to generation to generation

Along with change in gene frequencies which can rapidly reduce and even eliminate some alleles as the changes continue, to the point that you run out of alleles for enough traits that further change is impossible, probably a very interesting new population with new traits but no more genetic variability.

That should be enough for starters. There is more to discuss about where change occurs, but this is long enough for now. This thread is about evolution after speciation.

A total pipe dream I'm afraid, as speciation is most likely to occur at the very outer edges of the genetic variability of the species, thus preventing further evolution.

Loss of Genetic Diversity same as Loss of Information: Both prevent macroevolution. Evolution Defeats Evolution

[NoNukes says]: A creationist might state that nature cannot create the "information" required to produce novel features and "macroevolution" . Dog breeding includes human intervention which can be viewed as being similar to an ID agent stepping in to add information allowing new features like wiener-dog legs.

I don't really grasp the context of the issue of "novel" characteristics so I'm not sure how to address that, but I can respond to the idea of "information" at least.

Apparently this is easily misunderstood, and I have to agree that the very term "information" is vague or even cryptic in a way. The idea is really pretty simple though, from a creationist point of view anyway. You have a given built-in genetic recipe from the Creation for each species, so the possibility of that species evolving into another would require the addition of whatever is lacking in the first that the second needs. That's the "information" that would have to be added to the genome for it to macroevolve. Perhaps I don't even need to invoke the original Created species for this to make sense. It should be apparent to all that each species does have its own genome, many of which are in the process of being sequenced, and they are being sequenced AS being specific to the particular species they belong to. The DNA for each species has its own characteristics peculiar to that species, genes that aren't found in some other species but only this one, a certain number of chromosomes particular to the species and so on and so forth, with of course occasional exceptions. The genes pertain to the particular trait, perhaps eye color, the alleles define the different qualities of that trait, in this case the color. Wherever there are many alleles for a trait you can get a great variety from the genome as given for that species, you don't need to add alleles. Macroevolution requires getting from these recognizable species to something completely outside the particular genetic recipe, whether you think of them as having evolved to their present identity or been created independently at the Creation. You still have to posit the addition of NEW information that is not already present in the current genome.

New genes at least. New alleles isn't enough. New alleles for extant genes could only give variation to the trait the gene instructs for.

So has anybody ever shown the formation of a new gene? Is there even a theory about how that might come about?

In any case, the whole idea of the need for more information really starts as an observation that the processes of evolution ELIMINATE INFORMATION rather than adding it, and that fact means that evolution is moving in a direction that makes evolution less rather than more possible.

But I think it's clearer to say that evolution reduces genetic diversity. It's really the same observation. Evolution eliminates alleles at the very least and at some extremes may eliminate ALL alleles for a given gene which effectively kills the gene and most probably makes it a corpse in the genetic graveyard known as Junk DNA.

This IS the natural direction of all evolutionary processes. In order to get a new phenotype, especially one that sticks and becomes characteristic of a new population or variation or breed, other alleles for the same traits that give a different character MUST GO. That's LOSS OF INFORMATION, or REDUCED GENETIC DIVERSITY.

THIS LOSS IS THE VERY MACHINE OF EVOLUTION ITSELF.

Now here comes RAZD answering NoNukes:

Curiously, the mutations that cause short legs are fairly common in many species, including humans - it's called Dwarfism.

So is RAZD saying these mutations are NEW information?

I must ask, how does he know these are mutations? He gives no evidence, he merely CALLS the allele that bring about this trait mutations. Evidence please. I'm willing to consider this a mutation myself just because dwarfism must be thought of as a disease process, which I KNOW mutations produce. But are all shorter legs caused by dwarfism or is it simply possible to get a combination of naturally occurring (built-in) genes/alleles that naturally produce shorter legs? Evidence please.

The difference is between a random mutation occurring and it being spread into the breeding population is selection.

Pure theory, which is all evolution ever has to offer. Is he talking about useful / beneficial mutations, and if so nobody has ever shown that they even occur except in very rare and problematic instances, they are merely ASSUMED to be the source of all change in the genome. But if we are talking about nondeleterious variations the most likely scenario is that a rare normal allele simply comes to expression, and then yes, it will spread in the population if it is selected in the reproductive lottery. If not, it won't. But to call it a mutation is simply to beg the usual questions.

Within the ecological challenges and opportunities imposed by artificial selection, there is a survival and reproductive benefit to having short legs for the dogs being bred that have them, and not having them would be detrimental. This is a rather demanding ecology to survive in, yes?

Could be, depends I suppose. But we still don't know if this is a mutation or simply a normal-occurring healthy allele.

Now the problem with the creationist\IDologist claim about information is that they don't define what the concept means

Well, it's difficult, but I believe I may have succeeded in defining it above. And I vote for substituting the concept of reduction or loss of genetic diversity as being easier to grasp.

or even more importantly, how it can be measured.

As I've proposed, do a DNA sampling of the first and last populations in a ring species, one you find in nature or one you create in the lab. You should find obvious reduced genetic diversity in the last population and probably a progression of reduction in intermediate populations as well. Lots of homozygosity in the last population, a lot more heterozygosity in the first. Go gather a bunch of salamanders from the California ring species, label them and sample their DNA especially the genes for the patterns on their skin.

He goes on to give an irrelevant self-fulfilling chart he claims falsifies the claim about loss of information. He's probably misreading a built-in allelic possibility as new information but it's all just an exercise in proving what he wants to prove.

No, do what I suggest above, see that there really is loss of genetic diversity (same as loss of information) when species evolve. That kills MACROevolution right there.

Evidence for Reduced Genetic Diversity as Necessary Component of Evolution

You want some evidence for the claim that evolutionary processes always involve the reduction of genetic diversity? It's pretty simple, OUGHT to be obvious, and it's all about the reduction of heterozygosity to homozygosity or even less: This is from Wikipedia on Zygosity:

A cell is said to be homozygous for a particular gene when identical alleles of the gene are present on both homologous chromosomes.[2] The cell or organism in question is called a homozygote. True breeding organisms are always homozygous for the traits that are to be held constant.

In nature the same thing applies. Once you get a new variety, a subpopulation that is reproductively isolated from its parent population or other populations of the same species, even the result of a "speciation" event, and especially after it has inbred over some generations, its traits are going to be or become fixed. For a new trait to stick, or continue to characterize the new population, competing alleles for that trait must have been eliminated from that gene pool. THIS IS THE NECESSARY REDUCTION IN GENETIC DIVERSITY THAT ALLOWS A NEW TRAIT TO COME TO CHARACTERIZE A NEW BREED OR POPULATION IN THE WILD, THIS MUST OCCUR FOR A NEW TRAIT TO DEVELOP AND STICK IN A NEW POPULATION.

If they are "true breeding", they will be homozygous for their characteristic traits. This HAS to be true whether the population is the result of natural processes such as natural selection or genetic drift, migration and so on, or domestic breeding decisions.

HOMOZYGOSITY MEANS ONLY ONE ALLELE FOR THE GENE, ALL THE OTHER ALLELES HAVING BEEN ELIMINATED FROM THAT PARTICULAR GENE POOL. THAT'S THE SEVEREST CASE OF DECREASED GENETIC DIVERSITY (except for hemizygosity and nullizygosity, mentioned in the article below) AND IT'S NECESSARY TO GETTING A "TRUE BREED." AND WHAT IS A TRUE BREED BUT A NEW PHENOTYPE OR "SPECIES," A SPECIATION EVENT IN ITSELF, THE SUPPOSED STEP ON THE WAY TO OPEN-ENDED EVOLUTION FROM ONE SPECIES TO ANOTHER ACCORDING TO EVOLUTIONISTS.

Take dogs. If you want a Dachshund you have to eliminate all the alleles that specifically produce Great Danes or Golden Retrievers or Chihuahuas etc. If any of those alleles show up in the Dachshund breeding program you'll get a less perfect Dachshund. They make the breed less than what it is supposed to be.

It works the same way in nature, maybe through Natural Selection but probably more often through random events that simply happen to separate a population into two or more subpopulations. A particularly marked salamander emerges because the other markings are genetically decreased by comparison to those for the new marking. The markings of the last species to develop in a ring species of such salamanders should be genetically homozygous. Same with the genetics underlying the last species in the ring of green warblers and so on. You should find decreased genetic variability and probably a lot of homozygosity, just because this is what evolution DOES.

It's NECESSARY to evolution, and if evolutionists weren't always imagining nonexistent mutations into the mix it ought to be obvious even to THEM. The only mutations that are involved are those that contribute diseases to the mix and interfere with the health of the most genetically reduced populations, even to extinction in some cases.

In nature the introduction of disease elements may simply eliminate a new variety, Natural Selection in operation at its most severe, but if the new variety finds a niche it can adapt to it will survive just as a good domestic breed will.

The new variety necessarily comes through a reduction in genetic diversity. That's how evolution WORKS, really, though such an obvious necessity, that must lead to LESS ability to evolve, is simply ignored by believers in evolution who go on spinning evolution out of imaginary mutations.

To repeat the point: If circumstances are such that the populations remain reproductively separate, meaning without gene flow or the sharing of alleles between them, each will develop its own particular characteristics, and as long as there remains no gene flow or reproductive contact between the populations those characteristics will remain. For them to remain means that the alleles for different characteristics have been eliminated. That's what decreased genetic diversity MEANS. This may amount to actual speciation, but at least certainly at the extremes you do get speciation, where the new characteristics are preserved because there is a complete lack of interbreeding with former populations.

Evolutionists regard bottlenecks as events that interfere with the processes of evolution, but they shouldn't. The elephant seal and the cheetah which were produced by severe bottlenecks -- reduction of their former populations to just a few individuals -- that severely reduced their genetic diversity -- really ought to be considered to be examples of speciation, nature doing what domestic breeders do. Bottlenecks are really just one way new varieties or breeds are brought about in nature or in domestic breeding. ALL the processes of evolution tend in the same direction, genetic drift, migration, natural selection, just not as rapidly. Domestic breeding in the past could be described as the artificial creation of genetic bottlenecks for the purpose of developing desired traits for new breeds. You select the desired character and take pains to breed only with others that possess that character. Since a rigid adherence to this formula also usually brings disease problems into the breed, breeders today take care to avoid the most severe bottleneck methods with the most severely decreased genetic variability by mixing with more vigorous but less desirable animals as far as the target trait is concerned, but if it weren't for the threat of disease, these severe methods would be considered the most reliable way of producing the best breeds. SPECIATION.

Yet here we have RAZD at EvC carrying on as if the evolution processes just go on and on producing new phenotypes or varieties or breeds, even past speciation which he treats as the end point of microevolution and beginning of macroevolution, but afterward the same changes continue without a hitch in his scenario.

What separates (micro) evolution from the macro view of evolution (macroevolution) is the process of speciation, as evolution occurs within the breeding population, and nested hierarchies are formed by speciation events, and macroevolution is just a macro view of what occurs over several generations via evolution and speciation.

If we look at the continued effects of evolution over many generations, the accumulation of changes from generation to generation may become sufficient for individuals to develop traits that are observably different from the ancestral parent population. This lineal change within species is sometimes called phyletic change in species. This is also sometimes called arbitrary speciation in that the place to draw the line between linearly evolved geneological populations is subjective and because the definition of species in general is tentative and sometimes arbitrary.

See, he's simply ASSUMING the open-endedness of evolution, the phenotypic changes just go on and on, a neverending ACCUMULATION of changes. He has no evidence for this, though he has charts that give it an aura of authority that are simply meaningless reflections of his false belief. Actually, they are ILLUSTRATIONS of what he believes, they provide nothing in the way of evidence for any of it. And everything he says is also all assumption without evidence. Dawkins does the same thing with his ridiculous computer models of how evolution works, simply programming in his own bias, his assumption of open-ended changes. Sometimes you'll see an evolutionist acknowledging that reduced genetic diversity can sometimes be a problem but they keep that information off in a separate mental compartment, it's something that occurs only with bottlenecks, in extreme scenarios that interfere with evolution, not with evolutionary processes themselves.

Just for the record, here is the most pertinent part of the Wikipedia article on Zygosity:

Types
The words homozygous, heterozygous, and hemizygous are used to describe the genotype of a diploid organism at a single locus on the DNA. Homozygous describes a genotype consisting of two identical alleles at a given locus, heterozygous describes a genotype consisting of two different alleles at a locus, hemizygous describes a genotype consisting of only a single copy of a particular gene in an otherwise diploid organism, and nullizygous refers to an otherwise-diploid organism in which both copies of the gene are missing.

Homozygous
A cell is said to be homozygous for a particular gene when identical alleles of the gene are present on both homologous chromosomes.[2] The cell or organism in question is called a homozygote. True breeding organisms are always homozygous for the traits that are to be held constant.

An individual that is homozygous-dominant for a particular trait carries two copies of the allele that codes for the dominant trait. This allele, often called the "dominant allele", is normally represented by a capital letter (such as "P" for the dominant allele producing purple flowers in pea plants). When an organism is homozygous-dominant for a particular trait, the genotype is represented by a doubling of the symbol for that trait, such as "PP".

An individual that is homozygous-recessive for a particular trait carries two copies of the allele that codes for the recessive trait. This allele, often called the "recessive allele", is usually represented by the lowercase form of the letter used for the corresponding dominant trait (such as, with reference to the example above, "p" for the recessive allele producing white flowers in pea plants). The genotype of an organism that is homozygous-recessive for a particular trait is represented by a doubling of the appropriate letter, such as "pp".

Genetic Evidence of the Bottleneck at Noah's Flood Part 2

The thread continues:

Wounded King Message 4 loves remembering my contributions on this topic at EvC, not that he remembers them lovingLY of course, but here he's claiming there are many possible ways of coming up with a supposed super genome:

(Quoting JAR): First, even if there was some super genome if the Biblical flood stories were true there would still only be at best 14 copies of it to work with and that is still a bottleneck.

(WK): This seems to totally miss the entire point of the 'Supergenome' gambit. It might technically be a bottleneck if we assume that the survivors of the flood were typical of the pre-flood populations but allowing for a 'Supergenome' it is a bottleneck in a population with, by definition, a genetic composition drastically different to what we are used to analysing and the signature of such a bottleneck might be expected to be similarly drastically different.

I can come up with plenty of ad hoc pseudoscientific Supergenome explanations that could account for this. In fact when this topic came up on Faith's The End of Evolution By Means of Natural Selection thread she ended up, with a little help from me, proposing a hypothetical post flood population whose members were all superpolyploid acting as massive reservoirs of genetic variation and this was subsequent to her previous proposal that all of the extra required alleles would have been found in what is now 'junk' DNA.

Yes, that was one of the first things I was playing with as a possible structure for the original genome (and well before WK offered his help on that thread by the way) since of course it MUST have had much more genetic variability than the genome now.

But I found out not too long ago that the original genome really doesn't have to be different structurally from the genome now because it doesn't take much ordinary heterozygosity, or many alleles per gene, to produce all the variations / breeds / races we see today, only 6.7% heterozygosity in the whole population in fact which is the percentage we have now, as I mention in the previous post.

So that does lead to considering that the original genome probably simply had a lot more heterozygosity, and since I'd already figured that junk DNA reflects the death of the original DNA you simply think about the genetic power in those 95% of genes when they were still alive, consider also that there could have been many many genes for any given trait and many many alleles for each, and the possibilitieds of genetic variation become astronomical -- without having to postulate some unusual form for the genome such as polyploidy. Just genes and alleles, the basic stuff of today's genome.

Even two individuals with two alleles each for every gene, that's four different alleles between them -- for EVERY gene in the entire genome including the living versions of today's junk DNA -- are going to produce quite an amazing variety of offspring. It would take many generations for all the possibilities to play out to the point of the genetic reduction of the cheetah.

Then we have Taq in Message 5:

(Quoting WK): In fact when this topic came up on Faith's The End of Evolution By Means of Natural Selection thread she ended up, with a little help from me, proposing a hypothetical post flood population whose members were all superpolyploid acting as massive reservoirs of genetic variation and this was subsequent to her previous proposal that all of the extra required alleles would have been found in what is now 'junk' DNA.

(Taq): It would still require hypermutation to produce so many pseudogenes. The overwhelming majority of pseudogenes are the product of MANY mutations, usually not just one.

No mutations, simply original functional DNA built in at the Creation which has been destroyed over the generations because of the Fall, in fact no doubt a lot of it destroyed BY mutations.

***POST UNDER CONSTRUCTION***

Genetic Evidence of the Bottleneck at Noah's Flood Part 1

Well, hi de ho, somebody finally decided to try to have a discussion about the claim that the bottleneck of Noah's Flood should have left genetic evidence that it didn't leave. I've many times wondered exactly what evidence they think they would find, so let's hope somebody finally defines it.

In several threads, Jar has brought up the genetic bottleneck argument against the biblical flood and it appears to me to be a slam dunk of an argument. So I thought it was worth expanding on it and teasing out the details.

Sure, go for it.

Perhaps we should start with when creationists think the flood happened (my bold).

When was Noah’s Flood? 1,981 years to AD 0 plus 967 years to the founding of Solomon’s Temple plus 480 years to the end of the Exodus plus 430 years to the promise to Abraham plus 75 years to Abraham’s birth plus 350 years to Shem’s 100th birthday plus 2 years to the Flood. The Biblical data places the Flood at 2304 BC +/- 11 years.
http://www.answersingenesis.org/...v4/n1/date-of-noahs-flood

So this is about 4,300 years ago. (Maybe other dates around that time will be claimed but a bottleneck should still be apparent.)

I sometimes round it to 4500 years ago but 4300 is more accurate though a couple hundred years isn't going to change the evidence anyway.

Because all existing species have descended from so few individual so recently, their genomes should be very, very similar to each other - simply because all members of the same species would be close cousins.

Species that we know have undergone a bottleneck, such as the elephant seal and the North American bison - which were hunted to near extinction - and the cheetah, which appears to have also gone through a bottleneck 10,000 years ago, show this genetic fingerprint. In the cheetah's case their genetic variance is so small that their immune systems have so much in common that skin grafts aren't rejected between individuals.

So is this the sort of evidence you'd be looking for? Many fixed loci such as the cheetah's? Is this the "genetic fingerprint" you have in mind?

Jar's argument goes that if all animals and plants on earth (with the possible exception of some fish which may have been able to survive salinity changes) were reduced to either pairs, or sometimes a few more of each species (I don't see how 'kinds' could make a difference) we would see the bottleneck fingerprint in pretty much every plant and animal alive today.

The bottleneck should only be applied to creatures on the ark. Plants were not systematically saved on the ark but had to fend for themselves, same with sea creatures and apparently also insects and microorganisms.

But we don't. And because we don't it's not possible that virtually every species on earth was reduced to two or three individuals only a few thousand years ago.

And this should just about do it for the evolutionist side of the argument. I wonder if any creationists there will be up to answering it.

This is rather a unique situation; the proof does not rely on having witnesses around thousand of years ago, partial archaeological records, 'inferences' or any of the usual escape clauses of indirect evidence, it's repeatable, direct, clear, present and obvious.

I agree, it's a nice set-up for your purposes.

So what's wrong with it?
http://evolution.berkeley.edu/...o101/IIID3Bottlenecks.shtml
http://en.wikipedia.org/wiki/Population_bottleneck

"What's wrong with it" coming up. Let's see how the thread goes for a bit and then I'll bring on my answers here. I'll post this and then add to it.

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JAR has now posted his response in Message 3:

IIRC I first presented that idea back in 2005 or 2006 and the beauty of it is that it begins by assuming only what the Bible stories say is true and asks, "If true, what must we see?"

If someone claims that they shot and hit the target, then we must see a hole in the target. If we look at the target and there is no hole, then the claim that the target was hit is falsified.

The test is also independent of when the flood happened; it does not matter if it was yesterday, 4300 years ago or 200,000 years ago.

Regardless of when the flood happened the genetic bottleneck would have been at the same time for every surviving species. The population would have been reduced to at best 14 critters of a kind and at worst 4 critters of a kind.

Actually it was seven and two of the animals and six human beings -- the three sons of Noah and their wives. Noah and his wife had no more children after the Flood so their genes only count in their sons.

But let's not let this go on too far before giving at least a sketchy answer to it: As JAR goes on to anticipate, the answer is in the "super genome" -- but see my previous post in which I've come around to modifying this notion to mean a more fully functional genome in which what is now junk DNA was then alive and contributing many more genes and alleles to the mix.

I also did a post on this some time back as a matter of fact, answering this same challenge from JAR. There ARE markers of the bottleneck in the genomes of all affected, in reduced genetic diversity which is shown in a reduced percentage of heterozygosity for each species.

JAR is anticipating a much more drastic genetic reduction on the order of the cheetah's and the elephant seal's to near-total HOMOzygosity, but those situations occurred very recently and occurred in gene pools that were already much genetically reduced from the time of the Flood after many generations of population splits. In recent times a severe bottleneck is much more likely to reduce many genes to fixed loci, meaning one allele shared by all the individuals of the bottlenecked population, than would have been the case back at the ark. At that time, assuming the much greater heterozygosity of the far more fully alive genome with very little dead or junk DNA, each individual on the ark would have been heterozygous for enough genes to produce all the variations we see today without the specific markers for reduced genetic variability that JAR is expecting based on TODAY's effects.

As I report in that post I linked above, today's human population has about 6.7% heterozygosity, about which I report one researcher said:

a single human couple with just "6.7% variety" could produce 10 to the 2,017 children ...before they would have to produce an identical twin..."

He goes on to say that the whole spectrum of skin color we see today would be easily produced IN ONE GENERATION with just this 6.7% heterozygosity for that trait. Combining that with the same breadth of possibilities for size, hair or fur color, bone type, muscle type, and so on and so forth, would certainly yield an enormous variety of individuals within each created kind or type.

So I figure this 6.7% heterozygosity is what remained on average to all creatures after the Flood, or perhaps it was somewhat more then and has decreased since then. It's still enough to produce enormous variety, everything we see today.

THEREFORE, at least that much heterozygosity was represented in the passengers on the ark, and since that percentage is standard today there would be no reason to expect to see the usual drastic markers for a bottleneck of the sort that produced the cheetah.

That is, this percentage of heterozygosity we have today IS the marker of the Flood bottleneck. Because of population splits since the Flood that would have reduced it even further, it was no doubt much higher then than it is now, but BEFORE the Flood it would of course have been much much higher. I don't know whether to suppose that ALL genes could have been heterozygous back at the Creation or not, and that would include all the genes that are now in the junk DNA graveyard, but it's not beyond the realm of possibility. For that 100% to have been reduced to 6.7% of the 5% of living DNA still in our genome is a perfectly reasonable expectation of the degree of loss of genetic diversity in the Flood bottleneck.

And THAT's your marker OF the bottleneck. And as I say in that post and imply above as well, so is the great percentage of junk DNA in the genome as well.

There are your markers. But you know what, I know that thread is going to go reeling on without acknowledging this idea. I'm easy to ignore out here in cyber space.

So there really isn't more to say on this subject. However, I'll continue to keep tabs on the thread, including the rest of JAR's post:

But wait, there is more...

one possible way around it has been to invoke some super genome, that the pre-flood genome was somehow different and so allowed for greater variation.

Well, there are two major problems there.

First, even if there was some super genome if the Biblical flood stories were true there would still only be at best 14 copies of it to work with and that is still a bottleneck.

True, but since the mere 6.7% heterozygosity still available in our genome today can account for enormous variety, and AT LEAST that much was represented by the few individuals of each species on the ark, a bottleneck then would have not been reduced to anything like the genetic depletion we expect today. Therefore you are looking for something that fits only your own limited imagination rather than what would really have been the genetic result of such a bottleneck. Just as the early creationist geologists and all of today's geologists persist in looking for evidence of the Flood in all the wrong places.

Second, we have genetic evidence from humans that date to before the 4300 years ago date, from as far back as 30,000 years ago and as far back as 14,000 years ago in the Americas and there is no sign of any super-genome.

I think these two lines of reasoning are pretty solid.

Well, here a creationist simply parts company with the "sciences" that take their mere conjectures about time to be fact. Sorry. The Flood occurred about 4300 years ago and the Creation about 6000 years ago and your age reckonings are nothing but delusion.

And I'm going to skip most of JAR's usual debunkeries of the Bible which usually tend to the blasphemous, and go on to:

In both myths lots of critters get killed, in the myth found in Genesis 6 it seems to be talking about land animals and birds while the myth found in Genesis 7 goes even further and wipes out all living things.

If we play mix and match and take the best scenario from each of the myths we might be able to claim that only the birds and land animals were wiped out based on the passage from the Genesis 6 story and that we have the larger saved population found in Genesis 7.

Based on that mix and match game set we have a situation where all land animals and birds found today will be descended from a population that consisted of at most fourteen critters (seven pairs of clean animals and birds) and at worst case four critters (two pair of unclean animals).

No, take the smallest numbers as I have and only for passengers on the ark, six humans, two unclean animals and seven clean (and remember that most of the clean would have been sacrificed to God by Noah after the ark landed and not have passed on their genes). Sea creatures and plants and others no doubt also perished in great numbers off the ark but we don't have the numbers to calculate in their case.

As for the passengers on the ark, the much greater percentage of heterozygosity in the pre-Flood genome even reduced to a few individuals still accounts for all the variety we see today.

Now that is what I would call a real bottleneck.

We know we can see bottlenecks in the genetic record; a great example is the one in Cheetahs but we even see them in the human genome and most other species.

BUT...

If the flood actually happened we would see a bottleneck in EVERY species of animal living on the land and EVERY bird and EVERY one of the bottlenecks show up in the SAME historical time period.

Talk about a big RED flag.

Yup you're expecting to see the same situation as in TODAY's bottlenecked populations, the extreme homozygosity even to majority fixed loci, instead of the bottleneck markers that really DO exist, the mere 6.7% heterozygosity and the 95% or more junk DNA.

That bottleneck signature would be something every geneticists in the world would see. It would be like a neon sign, Broadway at midnight on New Years Eve. It would be something even a blind geneticist could see.

So it seems to me to be a very simple test that will support or refute the Flood.

If that genetic marker is there in EVERY species living on land or bird of the air, then there is support for the flood. It does not prove the flood happened but it would be very strong support.

If on the other hand that genetic marker is NOT there, then the Flood is refuted.

Good try but the marker IS there, in fact TWO markers are there, but you miss them because your expectations are wrong.

And for the second argument see the thread Looking for the Super-Genome. -And it ain't found.

Well, now I do have a different idea of what that original genome would have looked like by which I would expect to find a pre-Flood genome with hardly any junk DNA and a majority of heterozygous genes.

The relevant question is whether it's possible to SEE the genome of ANY creature that lived before the Flood or not, and as far as I know they're all fossilized or destroyed and their DNA is not available. JAR's favorite "Oetzi" is most certainly NOT contemporaneous with Adam and Eve but lived after the Flood despite the preposterously dogmatic claims for his age. He was found in the Alps but his DNA shows him to be related to Corsicans, who most certainly did not exist before the Flood. This is all post-Flood terrain that's being described here. The Alps also did not exist before the Flood but like all the high mountains were formed by tectonic forces set in motion along with the other geologic phenomena associated with the Flood event.

In any case the markers for the Flood bottleneck ARE apparent in today's genomes if 100% or near-100% heterozygosity and no junk DNA characterize the original "super" genome.

Evidence for the Super Genome

Another new creationist at EvC has claimed that the original genome had to have been much larger than today's, which is of course a necessary inference from the creationist claim that all we have genetically is what was given at Creation to the separate Species, no further input since then. This means that an original genetic endowment for each Species has been playing out through all the variations down the centuries, and for that to be possible the original must have been much larger than today's genome.*[see bolded paragraph below about the idea it must be bigger]. And of course the opposition is demanding evidence for this "super genome" which according to their own view of things does not exist.

Considering that THEIR "evidence" consists largely of totally subjective classifications of creatures into "clades" and "nested hierarchies" from which they then infer genetic descent without a shred of ACTUAL evidence; or homologous organs scattered all over the Linnaean classification system that they've imagined into a sequence of genetic descent and called it fact; or purely imaginary made-up tales about how this or that creature came to be, or did or didn't continue to exist; or "beneficial mutations" as the source of all genetic material that in fact exist only in a few highly compromised forms while all the rest are "neutral" or the cause of thousands of genetic diseases; or collections of fossilized dead things in separated strata that are clearly related to one another that they've imagined into evolution from less to more "advanced" over time rather than contemporaneous variation, just 'cause it fits the theory; and the layers of solidified sediments themselves to which they've laughably applied time period designations etc etc etc -- you'd think they might be a LITTLE bit cautious about demanding evidence from others.

Naa.

So what IS the evidence for the super genome? It's an inference from the fact -- provable fact, not imaginary construct -- that population splits tend toward reduced genetic diversity as they also produce new phenotypes. Reason it backwards and you come to, first, the Flood where a huge bottleneck must have brought about a huge decrease in genetic diversity, but not enough to reduce any particular line of variation to fixed loci like the cheetah or the northern seals, because the genome WAS so much bigger then than now, and then back before the Flood to the Creation where you MUST suppose a much much greater genome. Add back in all the genes that died in the Flood and down the centuries that now form the "junk DNA" and that should begin to reconstruct the original genome for you. I used to think that original genome might have been appreciably differently constructed somehow than today's, but now I think that all those reinstated genes with the maximum of alleles for each, fully heterozygous all of them, all combining basically according to Mendelian principles, is quite sufficient to have produced every creature now living and in the fossil Flood Graveyard as well.

*To be accurate, it's probably not right to think of the original genome as "bigger" exactly, simply fully functioning, all of what is now junk DNA fully operational-- a MORE ALIVE genome then. The one we have today, that all the rest of the ark-preserved creatures also have, is something like 90 to 95% dead.

What we have is a model that can explain most of the data and makes sense. We don't have direct evidence of this original fully functional genome, and maybe we can't, but it ought to be recognizable, from the fact that genetic diversity does decrease with phenotypic variation, that such an original is perfectly logical and likely.

Since I just wrote the qualification "ark-preserved" I realized there are other categories, sea creatures that probably survived in different proportions than did the land creatures on the ark, for instance, and bacteria that could have survived just about anything anyway. And the evidence that bacteria DID survive better than other creatures is the fact that they DON'T have a lot of junk DNA. This is of course explained evolution-style HERE:

...which is why bacteria tend to have very little of it.

--but it IS acknowledged that they have very little of it, which according to my version of Creationism means they still have most of their original genetic endowment which the majority of the rest of the creatures don't. Also, this alone should make comparisons between bacterial genetics and the genetics of higher animals highly suspect.

That article, by the way is about how junk DNA IS junk, and how the creationists are wrong who keep trying to find function in it in order to fit their expectation of a perfect Creation in the genome. But as I've said before, junk DNA is much better understood from a creationist point of view as a record of death since the Fall. The original perfect genome would have had no death, there would have been no junk or dead DNA, but since the Fall all life is subject to death, and it makes perfect sense that this would be reflected in the genome. As the article concludes:

The bottom line, though, is the genome is mostly dead, transcriptionally. The junk is still junk.