The Genetic Bottleneck challenge to the Flood answered again

On the thread at EvC about how a worldwide flood should have left evidence of severe genetic bottleneck in all living things, it is claimed that there is no such evidence, My answer, which I have given before here, is that they see no evidence for the bottleneck because what they are looking for is what happens to species NOW when there is a bottleneck -- such as the severe homozygosity of the cheetah.

But as I've argued here before, the evidence would simply be a great deal MORE homozygosity after the bottleneck than before, and since we have no way of knowing how much there was before the Flood we can't anticipate how much we should expect to see afterward either. But if there was enormously more heterozygosity before the Flood than there is now, say as much as 75-80% for human beings, as opposed to today's known percentage of 6.7% heterozygosity, then the reduction, the less heterozygosity and greater homozygosity today, wouldn't be noticed, it would be assumed to be normal to the species.

On the usual expectation, Dr. A gives this standard answer to the question how we might determine if there has been a bottleneck in a species:

Well, you look at the size of the population and the amount of genetic diversity within it. In equilibrium (i.e. if the population has been about the same size for a long period of time) the diversity will be proportional to the population size --- there'll be a certain quantity of diversity such that the production of new variants by mutation is just balanced by the elimination of variation by genetic drift.

If there's markedly less diversity than that, this indicates a recent bottleneck.

One clear indicator of reduced diversity is the percentage of homozygosity in the genome: the more homozygosity the less diversity. The problem is that if there was a worldwide Flood, then when you are looking only at today's populations you ARE seeing "markedly less diversity" than would have been the case before the Flood and not recognizing this. Since there is no way to measure the pre-Flood diversity you cannot make this judgment.

HOWEVER, there should be a hint in the fossil record to a much greater pre-Flood diversity, and this does seem to be the case as many species are represented by a huge number of variations. These variations are of course explained by the Theory of Evolution as stages in evolution. But if they were in fact all living populations at the time of the Flood that would in itself demonstrate a very large diversity. There were dozens of different "species" of Trilobites, for instance, and large reptilian sea creatures show an equally great amount of variety, judging from the specimens in the Karoo formation for instance.

The question of the genetics involved, however, seems to me to be most likely answered by the fact I found in Morris and Parker's What Is Creation Science? on page 112, which I quoted in a post on the subject in September of last year, where I quote Parker saying that

human beings are "heterozygous" for 6.7% of their genes, on the average. That means that 6 or 7 times in a 100, the pair of genes for a given trait differ like the genes for brown or blue eyes, or for rolling or not rolling the tongue. Now this may not seem like much. But Ayala calculates 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..."

And I go on to comment that

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.

Well, what does a bottleneck do genetically anyway? Doesn't it produce HOMOZYGOSITY for a number of traits? Isn't that what happened to the cheetah -- it has reached the point genetically where most of its genes are fixed and no variety is possible at all. Since the cheetah is of course descended from the cats on the ark, with their already drastically reduced heterozygosity -- perhaps comparable to the 6.7% of human beings -- a later bottleneck would have reduced it even further to the current state of almost 100% fixed loci, so that each individual is almost a clone of all the others, and further variation is as good as impossible.

6.7% heterozygosity as measured today under the assumptions of the ToE would be taken as the norm for human beings, but it could reflect an enormous reduction from a pre-Flood percentage and therefore represents the bottleneck of the Flood itself.

Just another of the many supposedly unanswerable challenges to the Flood and other creationist claims that have been answered quite nicely though the answer is never recognized and the same old challenges keep being repeated.

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.

===

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.

The Genetic Markers of the Flood Bottleneck

Here comes JAR with his usual wrongheaded assertions (no, no evidence here) against the Flood of Noah.

To mention "fossils" when talking about the Biblical Flood is of course simply silly. The Biblical Flood, if it had happened, was far too recent to have anything to do with fossils.

Too recent to have anything to do with fossils? 4500 years isn't enough time? Even though evolutionists claim that fossils are being formed every day in our own time in far more mundane circumstances than the global biblical Flood? Excuse me? The Flood buried bazillions of living things which would have been made into fossils in a lot less time than 4500 years. I've seen discussions, probably creationist of course since evolutionists are committed to not knowing such things, that show the process occurring in a matter of years in caves that drip calcium carbonate. If I find such a discussion I'll post it.

The Biblical Flood myths say that all the critters on land and in the air with the exception of those critters on the fictional ark were killed during a very short period.

If that were true, then every land and air critter living today, plant or animal, would be descended from the few critters on the ark.

Very true and they are.

That would leave a genetic bottleneck marker in EVERY single living species of plant of animal, and the marker would be only a relatively few generations back.

If the Biblical Flood happened, then that marker MUST be there.

It ain't.

Case closed.

I've heard this bit of evolutionist lore many times by now, but I have NEVER ONCE SEEN AN EXPLANATION OF EXACTLY WHAT "MARKER" WOULD POINT TO A BOTTLENECK. Perhaps I merely missed it but I've been looking for some time whenever this subject comes up and all that's offered is this assertion, perhaps some ridicule and choice epithets along with it, BUT NO CLUE AS TO WHAT THE MARKER MIGHT BE THAT WOULD DEMONSTRATE THE BOTTLENECK IN QUESTION.

Now that it's come up again perhaps I'll be motivated to make a more dogged search for such information.

But meanwhile I wanted to highlight JAR's post because of something I just learned about these things that opens up a new answer to the question. I've been rereading Morris and Parker's What Is Creation Science? over the last few days, one of the first books on creationism I read after becoming a Christian, and besides recognizing many points they make that I've made my own in this debate although I'd forgotten their source, I've also run across some points that illuminate some things I hadn't digested and am only now beginning to think about.

One of them suggests an answer to just what WOULD be the genetic indicators of the bottleneck at the Flood and they aren't the sort of "marker" that would jump out at you but something a geneticist today would simply take for granted as the normal state of the genome. Whenever I've gone that far into this part of the debate I find myself wondering about a formerly much bigger genome --polyploidy for instance, which never really fit but now I have a better understanding anyway -- from which it would be easier to imagine descent of all the life forms we see today and extravagantly more varieties before the Flood as well, which certainly must have been the case BECAUSE of such an extreme bottleneck.

No, not a bigger genome, but a different genetic situation along more ordinary lines:

Parker describes how all the varieties of humans and animals are easily accounted for by simple Mendelian genetics combining a given built-in array of genes for various traits. The example he gave was of two parents with "medium" or "average" skin color, expressed as AaBb, with the capital letters representing the darkest and the lower case the lightest, saying that EVERY shade of skin that we see on earth can be produced from those two parents, from the darkest African (AABB)to the lightest Scandinavian (aabb). When you think of every other trait as genetically expressed by the same formula, it becomes clear that an enormous variety of combinations would produce an enormous variety of types or varieties or races -- of people and animals of all kinds -- which would become characteristic of groups as they migrated and became geographically isolated from one another.

And all this incredible variety requires is normal sexual recombination AND HETEROZYGOSITY of the traits.

He also gave this statistic on page 112: "[evolutionist Francisco Ayala] says that human beings are "heterozygous" for 6.7% of their genes, on the average. That means that 6 or 7 times in a 100, the pair of genes for a given trait differ like the genes for brown or blue eyes, or for rolling or not rolling the tongue. Now this may not seem like much. But Ayala calculates 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.

Well, what does a bottleneck do genetically anyway? Doesn't it produce HOMOZYGOSITY for a number of traits? Isn't that what happened to the cheetah -- it has reached the point genetically where most of its genes are fixed and no variety is possible at all. Since the cheetah is of course descended from the cats on the ark, with their already drastically reduced heterozygosity -- perhaps comparable to the 6.7% of human beings -- a later bottleneck would have reduced it even further to the current state of almost 100% fixed loci, so that each individual is almost a clone of all the others, and further variation is as good as impossible.

THERE'S YOUR "MARKER" JAR. Not what you were expecting but there it is. It wouldn't be recognizable in the genome because nobody is looking for it. The average heterozygosity seen today would be accepted as the norm for all human beings for all time. It wouldn't be suspected as a marker of anything, although the basic principle is quite well known.

So instead of the genetic complexities I was trying to imagine to account for the necessity of an enormously greater variety among humans and animals before the Flood, I now appreciate that simple ordinary everyday heterozygosity can account for it all, but presumably there would have been much MORE heterozogosity for a much greater number of genes or traits before the Flood. 100% back at Adam and Eve? 50%?

And to that I would like to add another "marker" of the bottleneck, one of my favorite topics, JUNK DNA -- which makes up something over 90% of the genome. You wouldn't suspect that as a sign of the bottleneck at the Flood, would you, JAR? But if it's what I keep thinking it must be, the record of the genetic death brought about by that bottleneck, as well as all the accumulated death from other causes of course, then its mere existence in the genome is very glaring evidence of the Flood, now to be added to the other marker, the very low incidence of heterozygosity that resulted from all that death. This genetic junkyard or graveyard is a hint at enormously more genetic possibilities at the Creation than exist today.

May I please have my Nobel Prize now?