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


Message 16 of 59 (16400)
09-02-2002 7:05 AM
Reply to: Message 15 by Quetzal
08-30-2002 5:15 AM


[B][QUOTE]Originally posted by Mammuthus:

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.

[/B][/QUOTE]

I think we have established a new view on living conditions in the Ark with as much assurance as the creationists usually work with. We have now 'proved' that the Ark was launched, but that the predators got out of control and ate all the specimens, leaving a single cheetah pair surviving. They probably climbed the mast while the carnage was taking place below, and ate all the monkeys. Perhaps we could start our own religion on the strength of this astounding insight!


This message is a reply to:
 Message 15 by Quetzal, posted 08-30-2002 5:15 AM Quetzal has responded

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Quetzal
Member (Idle past 3371 days)
Posts: 3228
Joined: 01-09-2002


Message 17 of 59 (16415)
09-02-2002 9:53 AM
Reply to: Message 16 by Me
09-02-2002 7:05 AM


[QUOTE]Originally posted by Me:
I think we have established a new view on living conditions in the Ark with as much assurance as the creationists usually work with. We have now 'proved' that the Ark was launched, but that the predators got out of control and ate all the specimens, leaving a single cheetah pair surviving. They probably climbed the mast while the carnage was taking place below, and ate all the monkeys. Perhaps we could start our own religion on the strength of this astounding insight![/B][/QUOTE]

That is a seriously good idea! The only problem I see is showing how one pair of cheetahs "microevolved" into the 11+ million species of life (including plants) alive today in only 4000 years. Oh, why not? It works for the creationists...


This message is a reply to:
 Message 16 by Me, posted 09-02-2002 7:05 AM Me has not yet responded

Replies to this message:
 Message 18 by Mammuthus, posted 09-02-2002 10:21 AM Quetzal has not yet responded

  
Mammuthus
Member (Idle past 3974 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 18 of 59 (16418)
09-02-2002 10:21 AM
Reply to: Message 17 by Quetzal
09-02-2002 9:53 AM


Is it not fantastic to finally realize that cheetahs and sea monkeys and chia pets are all related by the carnivores running amok on a boat 6000 years ago I'm glad that phylogenetic tree of life has finally been resolved here once and for all

[QUOTE]Originally posted by Quetzal:
[B][QUOTE]Originally posted by Me:
I think we have established a new view on living conditions in the Ark with as much assurance as the creationists usually work with. We have now 'proved' that the Ark was launched, but that the predators got out of control and ate all the specimens, leaving a single cheetah pair surviving. They probably climbed the mast while the carnage was taking place below, and ate all the monkeys. Perhaps we could start our own religion on the strength of this astounding insight![/B][/QUOTE]

That is a seriously good idea! The only problem I see is showing how one pair of cheetahs "microevolved" into the 11+ million species of life (including plants) alive today in only 4000 years. Oh, why not? It works for the creationists...

[/B][/QUOTE]


This message is a reply to:
 Message 17 by Quetzal, posted 09-02-2002 9:53 AM Quetzal has not yet responded

  
John
Inactive Member


Message 19 of 59 (17910)
09-20-2002 10:07 PM
Reply to: Message 14 by Quetzal
08-30-2002 4:24 AM


quote:
Originally posted by Quetzal:
Thanks John. Appears I had an extra "http://" in there.

If one is good, you'd think two would be better.

Bump.....

I was liking this one.

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


This message is a reply to:
 Message 14 by Quetzal, posted 08-30-2002 4:24 AM Quetzal has not yet responded

  
Alec
Inactive Member


Message 20 of 59 (41324)
05-25-2003 10:30 PM


Me:

quote:
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?

It is true that the evidence from mtDNA does not necessarily prove that one woman was alive at the time, but simply means that only one woman's mtDNA has prevailed. However, it is consistent with Genesis also.

Evidence in the human genome is suggesting a very significant population bottleneck (a period in time when a population was almost wiped out, but then rebounded). This evidence is called long-range linkage disequilibrium (LD). LD simply means that genes are inherited together--they're not evenly shuffled out. Because they're inherited in large haplotypes (basically, chunks of them), and because we find this evidence in humans, it means that they underwent a recent population bottleneck. Because the genes aren't very shuffled, there hasn't been a great deal of time since this event.

quote:
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.

We know the bottleneck must have been relatively recent because of the long range of the LD. However, a specific date would require a known recombination rate, and this is somewhat random.

I haven't studied bottlenecks in other animals, but I do know that low genetic diversity is present within animals such as the cheetah, elephant seal, and some rhinos, for example. Koalas alos have low genetic diversity in their mtDNA.

Mammuthus:

quote:
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.

There has been talk of animals not having evidence of a population bottleneck. What genomes have been mapped that do not? Also, wouldn't the bottleneck be for about 5,000 years ago, the supposed time of the Flood? I do know that Mitochondrial Eve has been dated back to about 6000 years, using faster, actualy measured mutation rates, in an artice in Science.

John:

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

Not necessarily. For example, species of amphibians, fish, and insects would not necessarily have genetic evidence of a bottleneck in them because they wouldn't have all died during the Flood of Noah. It is significant to note that the animals that would have gone on the ark--mammals, reptiles, and bird--have a lower averge heterozygosity than the animals that wouldn't have needed to go on the ark.

I'm just throwing around ideas here that I think would be fun to discuss.

-Alec


Replies to this message:
 Message 21 by crashfrog, posted 05-25-2003 10:57 PM Alec has not yet responded
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 Message 31 by Mammuthus, posted 05-27-2003 11:38 AM Alec has not yet responded

  
crashfrog
Inactive Member


Message 21 of 59 (41326)
05-25-2003 10:57 PM
Reply to: Message 20 by Alec
05-25-2003 10:30 PM


For example, species of amphibians, fish, and insects would not necessarily have genetic evidence of a bottleneck in them because they wouldn't have all died during the Flood of Noah.

Actually, for reasons that have been covered a few times, they would have died if they weren't on the ark.

Fish would have been killed by the change in salinity and temperature caused by flooding. Most species of insects are so adapted to their environments that drastic flooding would have elminiated them. For that matter, aquatic mammals would have died from starvation - baleen whales wouldn't be able to strain the thick mud of the flood and the destruction of fish species would have left the other cetaceans with nothing to eat either.

At any rate, a lack of bottleneck in any animal that should have been on the ark would be sufficient evidence against the flood model.


This message is a reply to:
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wj
Inactive Member


Message 22 of 59 (41329)
05-25-2003 11:33 PM
Reply to: Message 20 by Alec
05-25-2003 10:30 PM


quote:
I do know that Mitochondrial Eve has been dated back to about 6000 years, using faster, actualy measured mutation rates, in an artice in Science.

Please provide a citation to support this assertion.


This message is a reply to:
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Replies to this message:
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TrueCreation
Inactive Member


Message 23 of 59 (41330)
05-25-2003 11:45 PM
Reply to: Message 22 by wj
05-25-2003 11:33 PM


Chase Nelson (I believe) has also used something like this in one of his articles:

http://www.promisoft.100megsdns.com/OYSI/Articles/Chase%20Nelson/demographic.htm

You can check his reference list.

-------------------

[This message has been edited by TrueCreation, 05-25-2003]


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Andya Primanda
Inactive Member


Message 24 of 59 (41337)
05-26-2003 4:09 AM
Reply to: Message 20 by Alec
05-25-2003 10:30 PM


quote:
Not necessarily. For example, species of amphibians, fish, and insects would not necessarily have genetic evidence of a bottleneck in them because they wouldn't have all died during the Flood of Noah. It is significant to note that the animals that would have gone on the ark--mammals, reptiles, and bird--have a lower averge heterozygosity than the animals that wouldn't have needed to go on the ark.

Chimps have a greater heterozygosity than humans, which were "obviously" on the ark. Would that mean chimps can survive a flood without taken aboard the ark?


This message is a reply to:
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Alec
Inactive Member


Message 25 of 59 (41417)
05-26-2003 6:50 PM


Crashfrog:

quote:
Actually, for reasons that have been covered a few times, they would have died if they weren't on the ark.

Woodmorappe [1996, pp. 143-144] discusses some evidence he believes contradicts this assertion. I quote (a long quote):

"... fish can gradually become accustomed to a wide range of ambient salinities... For example, goldfish will die within two to three hours if place suddenly in half-strength salt water [35 parts per thousand], but will survive indefinitely in that medium if gradually acclimated to it. There are also some salt water mollusks which, if allowed to acclimate to waters of decreasing salinity, will tolerate pure fresh water [fewer than one-half of one salt part per thousand], and some fresh water mollusks which, if transferred gradually, will tolerate full-strength salt water. Amphibians also have greater salinity tolerances if allowed to acclimate gradually to waters of different salinities..."

He also discusses other animals which live in both salt and fresh water. There is even a great deal of variation in salinity among species of the same genus. In addition to this he notes of amphibians:

"... there are many reports of amphibians being found in brackish water or even seawater...salinity tolerances of amphibians vary even within species; as within populations of Rana sphenocephala, Salamandra salamandra, and species of Batrachospes. ... the relatively salt-tolerant populations of Salamandra can live in waters ahving as much as 44% of the salinity of salt water, whereas their conspecifics, living inland and away from salt waters, can tolerate only 27% of the salinity of salt water [pp. 151-152]."

He also notes that amphibians could have survived the Flood by (a) mimicking aquatic organisms and living freely in the water, (b) riding as passengers on floating objects (for example, salamanders have been found attached to wooden objects out at sea), or (c) frogs, for example, could have been transported as eggs on mats at sea, etc. If you'd like references for any one fact he gives, I'd be happy to give you the ones he cites. Keep in mind also that I haven't done any research on that issue myself, so I don't know a great deal.

WJ:

quote:
Please provide a citation to support this assertion.

Certainly: Ann Gibbons, "Calibrating the Mitochondrial Clock," Science 279(5347):28-29, 2 January 1998. She gets her information in part from an article which I have not yet been able to get ahold of: T.J. Parsons, et al., "A High Observed Substitution Rate in the Human Mitochondrial DNA Control Region," Nature Genetics 15:363-368, 1997.

The quote from Gibbons is this: ".. researchers have calculated that 'mitchondrial Eve'--the woman whose mtDNA was ancestral to that in all living people--lived 100,000 to 200,000 years ago in Africa. Using the new clock [based on new observed mutation rates], she would be a mere 6000 years old." She immediately qualifies this by saying that at the moment nobody believes this is the actual age, and I think the reason that nobody does is apparent. Also, the experiments were not 100% conclusive--research still needs to be done. However, I believe this is quite interesting evidence regarding mt Eve.

Andya:

quote:
Chimps have a greater heterozygosity than humans, which were "obviously" on the ark. Would that mean chimps can survive a flood without taken aboard the ark?

What is this estimate based on? I'm not questioning you, but I know that we don't know near as much about the chimp genome. Perhaps there are mechanisms that aid diversification. Also, I know that the human reference database has alot of people like Koreans and Europeans--both not very diverse--but very few Africans, who are much more diverse. For example, Nigerians are more diverse than other humans, and LD is less-ranging in them.

Reference:

Woodmorappe, John, Noah's Ark: A Feasibility Study, (ICR, 1996).


Replies to this message:
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Alec
Inactive Member


Message 26 of 59 (41418)
05-26-2003 6:53 PM


Also, I've been hearing that there's new evidence that mtDNA could also be inherited paternally. Does anyone know a reference for this that I could look up (preferrably in Science, Nature, or PNAS)?
  
crashfrog
Inactive Member


Message 27 of 59 (41421)
05-26-2003 7:33 PM
Reply to: Message 25 by Alec
05-26-2003 6:50 PM


Woodmorappe [1996, pp. 143-144] discusses some evidence he believes contradicts this assertion. I quote (a long quote):

Yeah, some fish might have survived. That's a long, long way from all species of fish. Or even most. So far you've got mullusks, goldfish, and salmon. It's pretty apparent that the ability to survive multiple levels of salinity is a specific adaptation in most species, not the rule.

Coral reefs die if the temperature or salinity change by more than a fraction of a percent. And they grow so slowly that it's ludicrous to suggest that modern coral reefs are younger than 4000 years.

but will survive indefinitely in that medium if gradually acclimated to it.

Is that consistent with a sudden, global deluge? It doesn't seem so to me.

Also you didn't address insect populations. Many insects have lifespanse shorter than a year, and need specific, dry places to lay their eggs. A year's global flood would have wiped out the vast majority of insect species.

There's so many inconsitencies with the flood/ark model I don't know where to begin. The ark's too small to result in speciation on the scale we see it today unless you're willing to grant rates of mutation and speciation totally at odds with what we see today. There's no room for all the food that those animals would have consumed. There's no way that such small populations could survive in the post-flood world - a virtual waterlooged wasteland. There's no way an ark constructed with "antidiluvian" technology could have survived - and there's certainly no reason one big ark would have been the sole survivor, especially among fishing communities.

There's the fossil sorting problem - fossils are sorted in ways that have nothing to do with flood survivability (complexity of shell suture, for instance.) There's the total lack of flood sediment in certain areas of the world (the Canadia shield, for instance). There's the apparent lack of genetic bottlenecks in most species, as far as I'm aware.

The flood is a myth. It's thematic similarity to the flood myths of other cultures suggests that it's simply another version of the same fairy tale. Belief in the flood narrative as a historical account is only possible if you throw out basic information from a wide variety of fields such as engineering, biology, geology, literary criticism, and even theology.


This message is a reply to:
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Alec
Inactive Member


Message 28 of 59 (41429)
05-26-2003 11:54 PM


crashfrog:

quote:
Yeah, some fish might have survived. That's a long, long way from all species of fish. Or even most. So far you've got mullusks, goldfish, and salmon. It's pretty apparent that the ability to survive multiple levels of salinity is a specific adaptation in most species, not the rule.

Coral reefs die if the temperature or salinity change by more than a fraction of a percent. And they grow so slowly that it's ludicrous to suggest that modern coral reefs are younger than 4000 years.


Multiple levels of salinity is an adaptation--exactly. As is, in the creationist model, the adjustment to one level of salinity. Woodmorappe cites these example to show that it is possible to be adapted to both conditions. It then follows that in a creationist model these animals would have had the adaptation to different conditions in the past. Fish have since adapted to certain environments.

Coral reefs are a good point: you've got me there. I haven't studied them at all, so I don't know.

quote:
Is that consistent with a sudden, global deluge? It doesn't seem so to me.

I think it is. The salt would not have all been immediately stirred up in the Flood, to my knowledge. It would have been more gradual, and it's possible that different depths would have different salinities.

quote:
Also you didn't address insect populations. Many insects have lifespanse shorter than a year, and need specific, dry places to lay their eggs. A year's global flood would have wiped out the vast majority of insect species.

I also don't know much about this. It occurs to me that many insects could have survived on or in the water, on meaning on mats, etc. There also seems no reason to me that insects couldn't have simply gotten on the ark, hitching a ride with other animals that came came on, in the food supply, in the cargo, etc. Beyond that, good point also.

quote:
There's so many inconsitencies with the flood/ark model I don't know where to begin. The ark's too small to result in speciation on the scale we see it today unless you're willing to grant rates of mutation and speciation totally at odds with what we see today. There's no room for all the food that those animals would have consumed. There's no way that such small populations could survive in the post-flood world - a virtual waterlooged wasteland. There's no way an ark constructed with "antidiluvian" technology could have survived - and there's certainly no reason one big ark would have been the sole survivor, especially among fishing communities.

As far as speciation: We're finding different mechanisms all the time of rapid speciation that could have happened post-Flood. For example, introns (usally labelled Junk DNA) could have played a role. Depending on where the cell begins transcription, different genes can be produced. The founder effect also stimulated variation, for example it alters pleiotropic balance, and founder populations have a great range of variation. Inbreeding depression would have selected for animals that would have been more fit early, also. Genes are highly interactive, and rapid post-Flood variation would have been possible.

Fossils are not my field. I do know, for instance, that we find marine fossils near the top of Everest, for example. As far as the lack of bottlenecks in most species, that can't be asserted. We haven't mapped a great deal of genomes, and making accurate conclusions without doing so is questionable.

I would think that Flood myths all over the world lend support to the historical fact of a literal, global Flood. It must have its roots in history, don't you think?

-Alec


Replies to this message:
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crashfrog
Inactive Member


Message 29 of 59 (41431)
05-27-2003 1:55 AM
Reply to: Message 28 by Alec
05-26-2003 11:54 PM


As is, in the creationist model, the adjustment to one level of salinity.

That doesn't make sense. It takes far, far longer for a species to lose functionality (the adaptation to multiple salinity environments) than it does to gain it because there's no selection pressure for losing things unless their presence is somehow detrimental. For instance, that's why the metabolic pathways of your cells contain the machinery to do primitive anaerobic metabolism as well as the superior aerobic pathways.

Why would fishes have lost their adaptation to multiple salinities? What's the disadvantage in having it? Fish may have lost the ability to adapt to different salinities but it would have taken a lot longer than 4000 years. There's just no selection pressure for it.

The salt would not have all been immediately stirred up in the Flood, to my knowledge. It would have been more gradual, and it's possible that different depths would have different salinities.

In a vast, churning miasma? I don't find that reasonable.

There's a thread here that discusses how the flood would have had to have been simultaneously incredibly violent to deposit sedimentary layers in the way we see them, yet also pretty calm to allow a 600-year-old man and his boat full of animals to survive. The flood explanation just isn't self-consistent.

founder populations have a great range of variation.

Are you sure about this? I don't see how a founder population of two (or even seven) could have any significant amount of genetic diversity - certainly not enough to explain the diversity we see today.

Inbreeding depression would have selected for animals that would have been more fit early, also.

In a population of two, any selection at all ends the species.

I do know, for instance, that we find marine fossils near the top of Everest, for example.

Plate tectonics - ever heard of it? Mount Everest used to be a lot shorter. Used to be under a sea, in fact. (Plates colliding, and all.) I'll wager that you certainly don't find any contemporary sea life on the top of Everest. No whales, for instance.

We haven't mapped a great deal of genomes, and making accurate conclusions without doing so is questionable.

We don't have to map the genomes of every animal. We just have to map the genome of one animal that would have had to have been on the ark to disprove the ark story. I haven't looked, and I'm no geneticist, but I'd be very surprised indeed if there wasn't a mammal (for instance) with no recent genetic bottleneck.

I would think that Flood myths all over the world lend support to the historical fact of a literal, global Flood. It must have its roots in history, don't you think?

I find that the fact that only cultures that live near/on floodplains (or are decended from cultures that did) have flood myths suggests that they're all stories about local floods. Even if they're all stories about the same flood (a proposition that can neither be denied nor accpeted without a time machine), is that any reason to believe in a magically violent-yet-calm global flood? Isn't it much more reasonable to assume that the story is about a local flood that nearly wiped out a burgeoning human population and lives on in the decendants of that population as a legend? It wouldn't have had to be a global flood for the people involved to refer to it as "global". Sometimes your little corner of the world is all the world you have.

The flood model raises way more questions than it addresses, is self-contradictory, and simply fails to be reasonable. I don't really see how it can be taken as anything but a myth. Unless one is motivated by a desire for the Bible to be literally true, and then I would ask you - why do you think it must be so?


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NosyNed
Member
Posts: 8790
From: Canada
Joined: 04-04-2003
Member Rating: 4.1


Message 30 of 59 (41432)
05-27-2003 1:57 AM
Reply to: Message 28 by Alec
05-26-2003 11:54 PM


In a previous exchange:
quote:

but will survive indefinitely in that medium if gradually acclimated to it.

Is that consistent with a sudden, global deluge? It doesn't seem so to me.


It seems to me that this crys out for quantification. How long, days, hours, weeks in "gradually" in the first one? ANd how "sudden" is the second?


As far as speciation: We're finding different mechanisms all the time of rapid speciation that could have happened post-Flood. For example, introns (usally labelled Junk DNA) could have played a role. Depending on where the cell begins transcription, different genes can be produced. The founder effect also stimulated variation, for example it alters pleiotropic balance, and founder populations have a great range of variation. Inbreeding depression would have selected for animals that would have been more fit early, also. Genes are highly interactive, and rapid post-Flood variation would have been possible.

Certainly, we understand that evolution can happen pretty quickly under some circumstances. But there are at least a couple of problems with the idea.
1) The raw speed of the speciation. I've seen some creationist sites that have "kind" at the family level. For there to be no historic record of this happening the full range of speciation would have to have been complete sometime well before 2000 years ago.

2) Why did it stop? There is no suggestion of a mechanism that can turn on and off that extremely.

I'm afraid that an arm waving explanation like this isn't going to hold up under any kind of close examination.


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