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Author Topic:   Genetic 'Bottlenecks' and the Flood
Me
Inactive Member


Message 1 of 59 (16178)
08-28-2002 2:15 PM


I am wondering about the genetic bottlenecks which some of the paeleo-geneticists(?) have proposed. I understand that mitochondrial Eve need not necessarily have been the only woman alive at the time, but do not some of the theories suggest a very small breeding group of humans at some time in the past?

If this is the case, then there is an opportunity for the creationists to prove a point. The dates of such a bottleneck ought to match those for Noah and his family. Furthermore, there should be a similar bottleneck for all other animals, except fishes, matching the human dates.

I don't know if domestication and human breeding would upset such calculations - perhaps we would need to select cells from uncontrolled groups like wild birds. Would this be a sensible, credible and practical experiment?


Replies to this message:
 Message 2 by John, posted 08-28-2002 2:51 PM Me has responded

  
John
Inactive Member


Message 2 of 59 (16180)
08-28-2002 2:51 PM
Reply to: Message 1 by Me
08-28-2002 2:15 PM


quote:
Originally posted by Me:
/b]

Exactly right. Creationists should be able to find bottlenecks in every species of plant and animal dated to the same time-frame, ie the flood.

quote:
I don't know if domestication and human breeding would upset such calculations - perhaps we would need to select cells from uncontrolled groups like wild birds. Would this be a sensible, credible and practical experiment?

On the scale like that of the flood, I don't see how human activity could skew the data.

Definitely a credible experiment. Wonder why the creationists haven't already carried it out? It would prove their point once and for all, after all.

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 1 by Me, posted 08-28-2002 2:15 PM Me has responded

Replies to this message:
 Message 3 by Me, posted 08-28-2002 3:12 PM John has responded

  
Me
Inactive Member


Message 3 of 59 (16182)
08-28-2002 3:12 PM
Reply to: Message 2 by John
08-28-2002 2:51 PM


[QUOTE]Originally posted by John:
Definitely a credible experiment. Wonder why the creationists haven't already carried it out? It would prove their point once and for all, after all.
[/B][/QUOTE]

I was hoping to get some idea of the difficulties and costs involved. For instance, I believe there was a need to take samples from a large number of humans spread over a wide geographic area. I was thinking that samples could be taken from migrating birds to minimise the amount of travel involved. This might give access to a large breeding population easily, but I am not sure of the detailed requirements.

If some estimates of the actual costs could be made, based on a proposed methodology, we could formally invite one of the Creation Institutes to undertake the experiment, or get a University interested. There would need to be a lot of consideration of the issues first, of course.

One line that might be taken is that the genetic mechanisms which were used for this dating were not valid in some way. So agreement would need to be achieved that what was being proposed would be a sensible test.


This message is a reply to:
 Message 2 by John, posted 08-28-2002 2:51 PM John has responded

Replies to this message:
 Message 4 by John, posted 08-28-2002 3:45 PM Me has not yet responded

  
John
Inactive Member


Message 4 of 59 (16183)
08-28-2002 3:45 PM
Reply to: Message 3 by Me
08-28-2002 3:12 PM


quote:
Originally posted by Me:
I was hoping to get some idea of the difficulties and costs involved.

It should be easy enough to do. The data is probably already available. If you could find five or six species with a bottleneck at 6000bce, the snowball would start rolling and no-one could stop it.

Just challenge the Creationists orgs to find ten species with such a bottleneck.

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 3 by Me, posted 08-28-2002 3:12 PM Me has not yet responded

Replies to this message:
 Message 5 by Mammuthus, posted 08-29-2002 4:32 AM John has responded

  
Mammuthus
Member (Idle past 3890 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 5 of 59 (16216)
08-29-2002 4:32 AM
Reply to: Message 4 by John
08-28-2002 3:45 PM


Hi John,
I don't believe that would prove much if you found 6 species with evidence of a bottleneck 6K years ago. How would a flood at that time account for all the species that show no evidence of genetic bottlenecks? Take for example Pan troglodytes. Chimps have at least 4 times the nuclear and mtDNA variation as a group as humans. Gorillas are also highly genetically diverse. There are other exceptions as well. For such a test to have any relevance EVERY single species on Earth would have to have a genetic bottlneck and a coalescence time of 6000 years before present. Actually, out of curiosity, can anyone find a single example of a species that has been identified where the genetic bottleneck dates back to 6000 years ago? There may be but it is nothing I have looked for or seen widely reported.

Cheers,
Mammuthus

quote:
Originally posted by John:
quote:
Originally posted by Me:
I was hoping to get some idea of the difficulties and costs involved.

It should be easy enough to do. The data is probably already available. If you could find five or six species with a bottleneck at 6000bce, the snowball would start rolling and no-one could stop it.

Just challenge the Creationists orgs to find ten species with such a bottleneck.



This message is a reply to:
 Message 4 by John, posted 08-28-2002 3:45 PM John has responded

Replies to this message:
 Message 6 by John, posted 08-29-2002 5:23 AM Mammuthus has not yet responded
 Message 7 by Me, posted 08-29-2002 6:15 AM Mammuthus has not yet responded

  
John
Inactive Member


Message 6 of 59 (16220)
08-29-2002 5:23 AM
Reply to: Message 5 by Mammuthus
08-29-2002 4:32 AM


quote:
Originally posted by Mammuthus:
Actually, out of curiosity, can anyone find a single example of a species that has been identified where the genetic bottleneck dates back to 6000 years ago? There may be but it is nothing I have looked for or seen widely reported.

Ah... and that is exactly my point. Why bother with analyzing every species when you can't find even a few?

Conversely, even one species that does not show such a bottleneck derails the whole thing.

------------------
www.hells-handmaiden.com

[This message has been edited by John, 08-29-2002]


This message is a reply to:
 Message 5 by Mammuthus, posted 08-29-2002 4:32 AM Mammuthus has not yet responded

Replies to this message:
 Message 8 by Quetzal, posted 08-29-2002 7:06 AM John has not yet responded

  
Me
Inactive Member


Message 7 of 59 (16222)
08-29-2002 6:15 AM
Reply to: Message 5 by Mammuthus
08-29-2002 4:32 AM


quote:
Originally posted by Mammuthus:
Hi John,
I don't believe that would prove much if you found 6 species with evidence of a bottleneck 6K years ago. For such a test to have any relevance EVERY single species on Earth would have to have a genetic bottlneck and a coalescence time of 6000 years before present.

That's our point - the creationist theory predicts that all species should show this evidence.

In practice, of course, it would not be necessary for them to test all species. By the time they had got 6, 10 or 100 with such a bottleneck they would have very powerful evidence, and mainstream science would pick up on it. We are, I presume, quite open to being proved wrong in our assumption that there was no world-wide flood which brought all species down to 1 (or 7) breeding pairs?

Creationists do have a reasonable chance with this one. All populations vary in breeding size, and there must be some species which show a population dip at around the right time. Of course, it will not be enough to show that a single species has a dip - they must show that no species exhibits no dip.

[B][QUOTE]
Actually, out of curiosity, can anyone find a single example of a species that has been identified where the genetic bottleneck dates back to 6000 years ago? [/b][/quote]

Here is where we make a call to the creationists on the board. What I suspect will happen is that the techniques which are used to determine these bottlenecks will be questioned. So another part of this thread involves asking creationists if they accept the validity of these tests and their interpretation. Since the tests depend loosely on what we might call micro-evolution, which I undestand even the YE group accept, we should be able to pin down a position where they are forced to disagree with directly testable evidence.


This message is a reply to:
 Message 5 by Mammuthus, posted 08-29-2002 4:32 AM Mammuthus has not yet responded

  
Quetzal
Member (Idle past 3287 days)
Posts: 3228
Joined: 01-09-2002


Message 8 of 59 (16226)
08-29-2002 7:06 AM
Reply to: Message 6 by John
08-29-2002 5:23 AM


There IS evidence from at least one species of a genetic bottleneck around (very roughly) the right approximate timeframe. The cheetah (Acinonyx jubatus) is every conservation biologists' favorite example. The bottleneck equated to a reduction of the species to less than seven (some people claim a single pregnant female) individuals. I wonder if this corresponds to the cheetah being put on the ark as 7 specimens? Anyway, cheetahs are some 97% genetically monomorphic(the same as genetically “pure” strains of lab mice). The bottleneck is variously dated from a low of 4000 ya to 10-12,000 ya. The latter figure is probably most accurate. The point, of course, is that something similar MUST be observed in all/nearly all organisms for the massive genetic bottleneck represented by the ark to be even remotely possible.

Here’s a good on-line discussion of the ~10k date
Menotti-Raymond, M. and O’Brien, S.J. 1993. Dating the genetic bottleneck of the African cheetah. PNAS 90.

There are several other organisms that exhibit evidence of more recent genetic bottlenecks, including the Canadian grizzly (see, Implications of preliminary genetic findings for grizzly bear conservation in the central canadian rockies), the northern elephant seal, the baleine whale, florida panther, Illinois prairie chicken, black-footed ferret, etc. However, as would be expected by a standard evolutionary explanation, these bottlenecks are widely separated in time and wildly variable in causation – meaning there’s no way possible to attribute the collection of bottlenecks to a single, one-year-long point event like a global flood. There’s lots of good info in “Conservation Biology” and “Conservation Ecology” journals, as well as all over the web if anyone's interested in this issue (which has significant implications for conservation, preservation, and reintroduction of species). A fascinating topic.

[edited for grmayr an speeling]
[edited again to fix link]
Fixed 2nd link (You missed one, Q) - Adminnemooseus

[This message has been edited by Quetzal, 08-29-2002]

[This message has been edited by Quetzal, 08-30-2002]

[This message has been edited by minnemooseus, 09-20-2002]


This message is a reply to:
 Message 6 by John, posted 08-29-2002 5:23 AM John has not yet responded

Replies to this message:
 Message 9 by Me, posted 08-29-2002 11:53 AM Quetzal has not yet responded
 Message 10 by Mammuthus, posted 08-29-2002 12:25 PM Quetzal has responded

  
Me
Inactive Member


Message 9 of 59 (16242)
08-29-2002 11:53 AM
Reply to: Message 8 by Quetzal
08-29-2002 7:06 AM


quote:
Originally posted by Quetzal:
There IS evidence from at least one species of a genetic bottleneck around (very roughly) the right approximate timeframe. The cheetah (Acinonyx jubatus) is every conservation biologists' favorite example. .... The bottleneck is variously dated from a low of 4000 ya to 10-12,000 ya

Thanx - just what we were looking for. I wonder why creationists are not citing the cheetah as an example of the Ark's cargo - it looks like it could have been the only one! Of course, with hindsight, we should expect the only survivor on the ark to be a predator, and a single one rather than a pack animal.

By the way, the link you provided to the Menotti-Raymond, M. and O’Brien, S.J. paper does not work for me. I have tried unsuccessfully to find another - is there one you know?


This message is a reply to:
 Message 8 by Quetzal, posted 08-29-2002 7:06 AM Quetzal has not yet responded

Replies to this message:
 Message 11 by John, posted 08-29-2002 12:26 PM Me has not yet responded
 Message 55 by Nuggin, posted 08-17-2007 3:13 AM Me has not yet responded

  
Mammuthus
Member (Idle past 3890 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 10 of 59 (16244)
08-29-2002 12:25 PM
Reply to: Message 8 by Quetzal
08-29-2002 7:06 AM


Hi Quetzal,
I am aware of the more recent bottleneck examples as well as much older bottleneck examples i.e. Homo sapiens. Many of my colleagues worked for the WCS (wildlife conservation society) so I got to see lots of seminars on the subject of bottlenecks. I had thought Steve O'Brien had put the cheetah bottleneck in recent historical times with one single breeding pair owned by a Maharaja who kept exotic pets and bred the cheetahs (I could be wrong...I read it somewhere about 12 years ago). But an example of a bottleneck really spot on dating to the mythical flood has not been demonstrated to my knowledge.

Me, however, is very correct in saying that creationists with no background in biology, genetics, or any other science will say that the methods used for determining bottlenecks or lack thereof are wrong so in effect it does not matter. On the other hand I am very certain if an example dating to the mythical flood were found for
even one species of landsnail the creationists would jump up and down about how the same methods they don't believe in vindicate their position

Of course there are plenty of species that underwent such a strong bottleneck that that went extinct long before the mythical flood such as Mammuthus primigenius

Cheers,
Mammuthus

quote:
Originally posted by Quetzal:
There IS evidence from at least one species of a genetic bottleneck around (very roughly) the right approximate timeframe. The cheetah (Acinonyx jubatus) is every conservation biologists' favorite example. The bottleneck equated to a reduction of the species to less than seven (some people claim a single pregnant female) individuals. I wonder if this corresponds to the cheetah being put on the ark as 7 specimens? Anyway, cheetahs are some 97% genetically monomorphic(the same as genetically “pure” strains of lab mice). The bottleneck is variously dated from a low of 4000 ya to 10-12,000 ya. The latter figure is probably most accurate. The point, of course, is that something similar MUST be observed in all/nearly all organisms for the massive genetic bottleneck represented by the ark to be even remotely possible.

Here’s a good on-line discussion of the ~10k date
Menotti-Raymond, M. and O’Brien, S.J. 1993. Dating the genetic bottleneck of the African cheetah. PNAS 90.

There are several other organisms that exhibit evidence of more recent genetic bottlenecks, including the Canadian grizzly (see, Implications of preliminary genetic findings for grizzly bear conservation in the central canadian rockies), the northern elephant seal, the baleine whale, florida panther, Illinois prairie chicken, black-footed ferret, etc. However, as would be expected by a standard evolutionary explanation, these bottlenecks are widely separated in time and wildly variable in causation – meaning there’s no way possible to attribute the collection of bottlenecks to a single, one-year-long point event like a global flood. There’s lots of good info in “Conservation Biology” and “Conservation Ecology” journals, as well as all over the web if anyone's interested in this issue (which has significant implications for conservation, preservation, and reintroduction of species). A fascinating topic.

[edited for grmayr an speeling]

[This message has been edited by Quetzal, 08-29-2002]


Fixed links (I think) - Adminnemooseus

[This message has been edited by minnemooseus, 09-20-2002]


This message is a reply to:
 Message 8 by Quetzal, posted 08-29-2002 7:06 AM Quetzal has responded

Replies to this message:
 Message 15 by Quetzal, posted 08-30-2002 5:15 AM Mammuthus has not yet responded

  
John
Inactive Member


Message 11 of 59 (16245)
08-29-2002 12:26 PM
Reply to: Message 9 by Me
08-29-2002 11:53 AM


quote:
Originally posted by Me:

By the way, the link you provided to the Menotti-Raymond, M. and O’Brien, S.J. paper does not work for me. I have tried unsuccessfully to find another - is there one you know?

This one should work.

http://www.pnas.org/cgi/reprint/90/8/3172.pdf

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 9 by Me, posted 08-29-2002 11:53 AM Me has not yet responded

Replies to this message:
 Message 14 by Quetzal, posted 08-30-2002 4:24 AM John has responded

  
derwood
Member (Idle past 680 days)
Posts: 1455
Joined: 12-27-2001


Message 12 of 59 (16246)
08-29-2002 12:42 PM


As far as mtEve goes, any emphases mine:

*************************************************
Science 1995 Dec 22;270(5244):1930-6
The myth of Eve: molecular biology and human origins.

Ayala FJ.

University of California, Irvine, USA.

It has been proposed that modern humans descended from a single woman, the "mitochondrial Eve" who lived in Africa 100,000 to 200,000 years ago. The human immune system DRB1 genes are extremely polymorphic, with gene lineages that coalesce into an ancestor who lived around 60 million years ago, a time before the divergence of the apes from the Old World monkeys. The theory of gene coalescence suggests that, throughout the last 60 million years, human ancestral populations had an effective size of 100,000 individuals or greater. Molecular evolution data favor the African origin of modern humans, but the weight of the evidence is against a population bottleneck before their emergence. The mitochondrial Eve hypothesis emanates from a confusion between gene genealogies and individual genealogies.

------------------
"The analysis presented in this study unambiguously shows that chimpanzees are our closest relatives to the exclusion of other primates. This is an important point that cannot be discounted. Further, the functional genetic differences that are represented by nonsynonymous sites also show this relationship. The notion that the great apes form a functional and evolutionary grade is not supported by our analysis. Rather, humans and chimpanzees are a functional evolutionary clade."
http://www.uchicago.edu/aff/mwc-amacad/biocomplexity/conference_papers/goodman.pdf


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Me
Inactive Member


Message 13 of 59 (16249)
08-29-2002 2:09 PM
Reply to: Message 12 by derwood
08-29-2002 12:42 PM


quote:
Originally posted by SLPx:
It has been proposed that modern humans descended from a single woman, the "mitochondrial Eve" who lived in Africa 100,000 to 200,000 years ago... The mitochondrial Eve hypothesis emanates from a confusion between gene genealogies and individual genealogies.

Thanx for the ref. As I said earlier, I understood that MtEve was not necessarily a bottleneck, but I had thought that some other research suggested that there was one somewhere. It is interesting to know that there is no bottleneck detected in Man, and equally interesting to know that there is in some other species. I am wondering what the creationist position may be on the acceptability of this research, given they seem to accept 'microevolution'.

[This message has been edited by Me, 08-29-2002]


This message is a reply to:
 Message 12 by derwood, posted 08-29-2002 12:42 PM derwood has not yet responded

  
Quetzal
Member (Idle past 3287 days)
Posts: 3228
Joined: 01-09-2002


Message 14 of 59 (16290)
08-30-2002 4:24 AM
Reply to: Message 11 by John
08-29-2002 12:26 PM


Thanks John. Appears I had an extra "http://" in there.
This message is a reply to:
 Message 11 by John, posted 08-29-2002 12:26 PM John has responded

Replies to this message:
 Message 19 by John, posted 09-20-2002 10:07 PM Quetzal has not yet responded

  
Quetzal
Member (Idle past 3287 days)
Posts: 3228
Joined: 01-09-2002


Message 15 of 59 (16293)
08-30-2002 5:15 AM
Reply to: Message 10 by Mammuthus
08-29-2002 12:25 PM


quote:
Originally posted by Mammuthus:
Hi Quetzal,
I am aware of the more recent bottleneck examples as well as much older bottleneck examples i.e. Homo sapiens. Many of my colleagues worked for the WCS (wildlife conservation society) so I got to see lots of seminars on the subject of bottlenecks. I had thought Steve O'Brien had put the cheetah bottleneck in recent historical times with one single breeding pair owned by a Maharaja who kept exotic pets and bred the cheetahs (I could be wrong...I read it somewhere about 12 years ago). But an example of a bottleneck really spot on dating to the mythical flood has not been demonstrated to my knowledge.

Actually, you're not wrong. O'Brien's original hypothesis, based on nuclear DNA fingerprinting (around 1983, IIRC) showed a bottleneck about 200-300 years ago. The more recent paper I cited shows the older age, based around comparisons between two subspecies using mtDNA and VNTR divergeance. O'Brien's done a lot of work with cheetahs. Interestingly, the satellite DNA comparisons showed that the nuclear DNA tests were valid as well - indicating the cheetah has undergone two bottlenecks! Given the rapid reduction in cheetah populations today, assuming they survive at all in the wild, future scientists will likely find evidence of a third bottleneck dated around this past Tuesday . It's not a CITES I species for nothing...

quote:
Me, however, is very correct in saying that creationists with no background in biology, genetics, or any other science will say that the methods used for determining bottlenecks or lack thereof are wrong so in effect it does not matter. On the other hand I am very certain if an example dating to the mythical flood were found for
even one species of landsnail the creationists would jump up and down about how the same methods they don't believe in vindicate their position

Totally agree. You've both got it right, that's for sure. In fact, I'm rather surprised the creationists HAVEN'T used the cheetah as "proof" of the flood. Maybe the whole bottleneck thing is too esoteric. Or maybe since it's 10k rather than 4k it isn't close enough to make sense. I should email wmscott - it's right on his timeline. (cackles evilly)


This message is a reply to:
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Replies to this message:
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