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Author Topic:   No genetic bottleneck proves no global flood
Tangle
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Message 1 of 140 (655298)
03-08-2012 6:39 PM


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.

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.)

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.

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.

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. 

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.

So what's wrong with it?

http://evolution.berkeley.edu/...o101/IIID3Bottlenecks.shtml
http://en.wikipedia.org/wiki/Population_bottleneck 

Edited by AdminPhat, : No reason given.


Life, don't talk to me about life - Marvin the Paranoid Android

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Message 2 of 140 (655300)
03-09-2012 8:30 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the No genetic bottleneck proves no glbal flood thread in the Proposed New Topics forum.
    
jar
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(3)
Message 3 of 140 (655311)
03-09-2012 9:54 AM
Reply to: Message 1 by Tangle
03-08-2012 6:39 PM


Origin of the example.
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.

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.

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.

Here is the detailed description of the first argument (the genetic bottleneck).

quote:
In the version of the myth found in Genesis 6 God instructs Noah to:

quote:
19 You are to bring into the ark two of all living creatures, male and female, to keep them alive with you. 20 Two of every kind of bird, of every kind of animal and of every kind of creature that moves along the ground will come to you to be kept alive. 21 You are to take every kind of food that is to be eaten and store it away as food for you and for them."

In the version of the myth found in Genesis 7 we see similar (close but not the same) instructions:

quote:
2 Take with you seven of every kind of clean animal, a male and its mate, and two of every kind of unclean animal, a male and its mate, 3 and also seven of every kind of bird, male and female, to keep their various kinds alive throughout the earth.

We also find similar explanations of what will be destroyed in Genesis 6 it says:

quote:
7 So the LORD said, "I will wipe mankind, whom I have created, from the face of the earth—men and animals, and creatures that move along the ground, and birds of the air—for I am grieved that I have made them."

and in Genesis 7:

quote:
4 Seven days from now I will send rain on the earth for forty days and forty nights, and I will wipe from the face of the earth every living creature I have made."

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).

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.

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.


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

Edited by jar, : an ---> and appalin spallin as usual

Edited by jar, : fix quote boxes


Anyone so limited that they can only spell a word one way is severely handicapped!

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Wounded King
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Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 4 of 140 (655317)
03-09-2012 11:46 AM
Reply to: Message 3 by jar
03-09-2012 9:54 AM


Re: Origin of the example.
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.

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.

Throw a little 'Salty' Davison style chromosomal rearrangements into the mix and I'm sure after a few generations we could have you a nicely assorted set of genetically diverse organisms, admittedly for humans and a flood date ~2304 BCE this only gives us about 215 generations to play with assuming a generation time of about 20 years. But I'm sure with a positive attitude and a little bit of imagination we could come up with something.

As to the ignoring of evidence that makes such ad hoc explanations blatantly counterfactual, what were you expecting from creationists?

TTFN,

WK

P.S. Now I have this dark urge to do a Lam and start trolling the forum as a creationist/Idist.


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Taq
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Message 5 of 140 (655325)
03-09-2012 12:31 PM
Reply to: Message 4 by Wounded King
03-09-2012 11:46 AM


Re: Origin of the example.
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.

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. Also, most estimates put the number of pseudogenes between 20k and 100k compared to around 30k functional genes.

What would we expect in the introns of functional genes for the above scenario?


This message is a reply to:
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Tangle
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Posts: 4530
From: UK
Joined: 10-07-2011
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Message 6 of 140 (655734)
03-13-2012 3:54 AM


.....bump.....

Life, don't talk to me about life - Marvin the Paranoid Android

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RAZD
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Message 7 of 140 (655741)
03-13-2012 9:05 AM
Reply to: Message 6 by Tangle
03-13-2012 3:54 AM


Perhaps a discussion of what a bottleneck looks like:

quote:
Population Bottleneck:

A population bottleneck (or genetic bottleneck) is an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing.[1]

A slightly different sort of genetic bottleneck can occur if a small group becomes reproductively separated from the main population. This is called a founder effect.

Population bottlenecks reduce the genetic variation and, therefore, the population's ability to adapt to new selective pressures, such as climatic change or shift in available resources. Genetic drift can eliminate alleles that could have been positively selected on by the environment if they had not already drifted out of the population.[2]

Population bottlenecks increase genetic drift, as the rate of drift is inversely proportional to the population size. The reduction in a population's dispersal leads, over time, to increased genetic homogeneity. If severe, population bottlenecks can also markedly increase inbreeding due to the reduced pool of possible mates (see small population size).

... The golden hamster is a similarly bottlenecked species, with the vast majority descended from a single litter found in the Syrian desert around 1930. And cheetahs are sufficiently closely related to one another that transplanted skin grafts do not provoke immune responses,[9] thus suggesting an extreme population bottleneck in the past.

The genome of the giant panda shows evidence of a severe bottleneck that took place about 43,000 years ago.[10] There is also evidence of at least one primate species, the golden snub-nosed monkey, that also suffered from a bottleneck around this time.

Further deductions can sometimes be inferred from an observed population bottleneck. Among the Galápagos Islands giant tortoises — themselves a prime example of a bottleneck — the comparatively large population on the slopes of Alcedo volcano is significantly less diverse than four other tortoise populations on the same island. DNA analyses date the bottleneck to around 88,000 years before present (YBP).[11]


We can also see that this would apply to any species taken off the endangered species list.

So we have the ability to see bottlenecks in populations: how do they line up in timing?

quote:
Dating the genetic bottleneck of the African cheetah

... The timing of a bottleneck is difficult to assess, but certain aspects of the cheetah's natural history suggest it may have occurred near the end of the last ice age (late Pleistocene, approximately 10,000 years ago), when a remarkable extinction of large vertebrates occurred on several continents. To further define the timing of such a bottleneck, the character of genetic diversity for two rapidly evolving DNA sequences, mitochondrial DNA and hypervariable minisatellite loci, was examined. Moderate levels of genetic diversity were observed for both of these indices in surveys of two cheetah subspecies, one from South Africa and one from East Africa. Back calculation from the extent of accumulation of DNA diversity based on observed mutation rates for VNTR (variable number of tandem repeats) loci and mitochondrial DNA supports a hypothesis of an ancient Pleistocene bottleneck ...


Of course genetic information cannot give you accurate timing (estimates can be made, but they are at best relative dates that tell the sequence of what occurred rather than the dates), so this needs to be tied back to fossil evidence for dating the events.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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Tangle
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From: UK
Joined: 10-07-2011
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Message 8 of 140 (655768)
03-13-2012 12:40 PM


As we don't look likely to get any opinion at all now from the creation side of the argument, can we dream up any defence at all for them?

Is it possible for a genetic bottleneck to be masked?

If we assumed that all life had gone through the bottleneck, maybe what we're looking at when we examine the genomes of existing species IS a bottleneck and the lower variance in the cheetah etc are just anomalies?

I can't find even small straws to grasp here......


Life, don't talk to me about life - Marvin the Paranoid Android

Replies to this message:
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Perdition
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Message 9 of 140 (655769)
03-13-2012 12:50 PM
Reply to: Message 8 by Tangle
03-13-2012 12:40 PM


can we dream up any defence at all for them?

Well, the obvious one would be God. He caused the flood, and wanted the animals to survive, and since a genetic bottleneck can be detrimental to a species, he "fixed" them.

The supposed "Supergenome" combined with extremely different genetic laws in the past, as foreveryoung posited, might solve some of it.

As you say, claiming that since everything has the same genetic bottleneck, you might not notice it since everything would look the same, might work for non-scientists.

Unfortunately, the third claim comes from a misunderstanding of genetics and the first two are offered with no (and in the first one's case, no possible) evidence.


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New Cat's Eye
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Message 10 of 140 (655781)
03-13-2012 2:05 PM
Reply to: Message 8 by Tangle
03-13-2012 12:40 PM


As we don't look likely to get any opinion at all now from the creation side of the argument, can we dream up any defence at all for them?

There's always "magic"...


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Tangle
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Message 11 of 140 (655784)
03-13-2012 2:08 PM
Reply to: Message 10 by New Cat's Eye
03-13-2012 2:05 PM


CS writes:

There's always "magic"...

I was hoping to leave that until last; when all hope of finding a non-fatuous argument had gone. Maybe it's that time now....


Life, don't talk to me about life - Marvin the Paranoid Android

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New Cat's Eye
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Message 12 of 140 (655786)
03-13-2012 2:14 PM
Reply to: Message 11 by Tangle
03-13-2012 2:08 PM


CS writes:

There's always "magic"...


I was hoping to leave that until last; when all hope of finding a non-fatuous argument had gone. Maybe it's that time now....

No, that's cool. We can just leave it alone and wait for a creationist response. And/or redirect to here from another topic where it gets brought up again. I'll edit my last post to that Rob guy to bring any arguments about it here.


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RAZD
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Message 13 of 140 (655787)
03-13-2012 2:15 PM
Reply to: Message 8 by Tangle
03-13-2012 12:40 PM


Hi Tangle,

As we don't look likely to get any opinion at all now from the creation side of the argument, ...

Not really a surprise, imho: first they need to understand the process, and they are not likely to get that information from creationist sources.

... can we dream up any defence at all for them?

Well, just from this information in Message 7 we have two possibilities:

(1) a bottleneck "about 43,000 years ago" in the Giant Panda lineage, and
(2) a bottleneck "approximately 10,000 years ago" in the Cheetah lineage.

For the creationist this means that (a) either the age measurements are off (SOP - as both these need to be crammed into ~5,000 years ago), or there is something else for which they don't have a clue.

Is it possible for a genetic bottleneck to be masked?

Well, I would think that the "approximately 10,000 years ago" event could mask the effects of the "about 43,000 years ago" ... if we found more evidence of bottleneck events at this later period.

Of course, then we go to the Toba Event

http://en.wikipedia.org/wiki/Toba_catastrophe_theory

quote:
The Toba supereruption (Youngest Toba Tuff or simply YTT[1]) was a supervolcanic eruption that occurred some time between 69,000 and 77,000 years ago at Lake Toba (Sumatra, Indonesia). It is recognized as one of the Earth's largest known eruptions ...

The Toba event is the most closely studied supereruption. In 1993, science journalist Ann Gibbons first suggested a link between the eruption and a bottleneck in human evolution. Michael R. Rampino of New York University and Stephen Self of the University of Hawaii at Manoa quickly lent their support to the idea. The theory was further developed in 1998 by Stanley H. Ambrose of the University of Illinois at Urbana-Champaign.


So now the ~10,000 year ago and the ~43,000 year ago events mask the ~70,000 year ago event, and further analysis of the bottleneck patterns in other species will likely produce older dates for their most recent bottleneck events, creating an ever increasing problem for the YEC timing issues.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
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jar
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Message 14 of 140 (655788)
03-13-2012 2:17 PM


hominid genomes
Well, we have DNA samples analyzed for hominids going back at least 50,000 years now, from several different species and no evidence of any super genome has ever been found. It is also true that genetic evidence from plants, fungi, insects, animals, fish, just about every critter ever sequenced shows no evidence of any super genome.

Until someone presents evidence of some super genome I think that idea can be set aside.


Anyone so limited that they can only spell a word one way is severely handicapped!

  
anglagard
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Posts: 2157
From: Big Spring, TX, USA
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(2)
Message 15 of 140 (655930)
03-15-2012 12:24 AM
Reply to: Message 8 by Tangle
03-13-2012 12:40 PM


Pardon Me
Tangle writes:

As we don't look likely to get any opinion at all now from the creation side of the argument, can we dream up any defence at all for them?

If we so-called evolutionists have to create the talking points for ICR, AIG, DI and the like, they may as well raise the white flag.

Yup, that good ol' DNA. Darwin predicted it, scientists use it to create cladistic diagrams which, oh my seem to so often completely agree with evolution derived from ancestry using physiology, and now we have all that evidence against a simultaneous bottleneck in the genetic code of all multicellular life.

After being at war with geology and biology what will they declare war on next? chemistry? physics?... mathematics?

Oh, pardon me, I see they already have.

Now do they really expect us to come up with arguments for them?

Next thing you know they will expect us to read the Bible for them.

Oh. pardon me, I see they already have.


Read not to contradict and confute, not to believe and take for granted, not to find talk and discourse, but to weigh and consider. - Francis Bacon

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