Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
4 online now:
Newest Member: popoi
Post Volume: Total: 915,817 Year: 3,074/9,624 Month: 919/1,588 Week: 102/223 Day: 13/17 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   No genetic bottleneck proves no global flood
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


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?
Bottlenecks and founder effects - Understanding Evolution
Population bottleneck - Wikipedia
Edited by AdminPhat, : No reason given.

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

Replies to this message:
 Message 3 by jar, posted 03-09-2012 9:54 AM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 6 of 140 (655734)
03-13-2012 3:54 AM


.....bump.....

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

Replies to this message:
 Message 7 by RAZD, posted 03-13-2012 9:05 AM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


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:
 Message 9 by Perdition, posted 03-13-2012 12:50 PM Tangle has not replied
 Message 10 by New Cat's Eye, posted 03-13-2012 2:05 PM Tangle has replied
 Message 13 by RAZD, posted 03-13-2012 2:15 PM Tangle has not replied
 Message 15 by anglagard, posted 03-15-2012 12:24 AM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


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

This message is a reply to:
 Message 10 by New Cat's Eye, posted 03-13-2012 2:05 PM New Cat's Eye has replied

Replies to this message:
 Message 12 by New Cat's Eye, posted 03-13-2012 2:14 PM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 26 of 140 (720295)
02-21-2014 11:54 AM


A comment on the radio just prompted me to make a proper scientific prediction.
The comment was that Australia's epidemic population of rabbits are descended from just 13 ( some sources say 24) rabbits in 1859.
There will therefore be a distinct bottleneck - after all, that's only 150 or so years ago.
In the spirit of declaring all results of hypothesis testing even if they disprove it, I offer this:
Abstract
The well documented historical translocations of the European rabbit (Oryctolagus cuniculus) offer an excellent framework to test the genetic effects of reductions in effective population size. It has been proposed that rabbits went through an initial bottleneck at the time of their establishment in Australia, as well as multiple founder events during the rabbit's colonization process. To test these hypotheses, genetic variation at seven microsatellite loci was measured in 252 wild rabbits from five populations across Australia. These populations were compared to each other and to data from Europe. No evidence of a genetic bottleneck was observed with the movement of 13 rabbits from Europe to Australia when compared to French data. Within Australia the distribution of genetic diversity did not reflect the suggested pattern of sequential founder effects. In fact, the current pattern of genetic variation in Australia is most likely a result of multiple factors including mutation, genetic drift and geographical differentiation. The absence of reduced genetic diversity is almost certainly a result of the rabbit's rapid population expansion at the time of establishment in Australia. These results highlight the importance of population growth following a demographic bottleneck, which largely determines the severity of genetic loss.
Just a moment...
So no bottleneck. And the rabbits are still rabbits, damn it.
By the 1920s, less than 70-years since its introduction, the rabbit population in Australia ballooned to an estimated 10 billion, reproducing at a rate of 18 to 30 per single female rabbit per year. The rabbis started to migrate across Australia at a rate of 80 miles a year. After destroying two million acres of Victoria's floral lands, they traversed across the states of New South Wales, South Australia, and Queensland. By 1890, rabbits were spotted all way in Western Australia.
They introduced myxomatosis and knocked out about 90% and continue to trap and shoot them so the levels are nowhere near what they where in 1920s but there are still hundreds of millions.
ps Faith, note that genetic diversity was not lost by isolation - in this case at least.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

Replies to this message:
 Message 27 by NosyNed, posted 02-21-2014 1:03 PM Tangle has replied
 Message 31 by Faith, posted 02-21-2014 3:23 PM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 28 of 140 (720306)
02-21-2014 1:16 PM
Reply to: Message 27 by NosyNed
02-21-2014 1:03 PM


Re: Bottleneck
nosyned writes:
note that genetic diversity was not lost by isolation - in this case at least.
So the arc coulda happened and not shown a bottleneck?
Well the rabbits certainly could have been on the ark and not show a bottleneck - according to these findings. Speed of reproduction and an empty ecosystem seems to be a big consideration.
Animals with slower reproduction, say elephants, could be different.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 27 by NosyNed, posted 02-21-2014 1:03 PM NosyNed has not replied

Replies to this message:
 Message 29 by RAZD, posted 02-21-2014 1:31 PM Tangle has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 30 of 140 (720309)
02-21-2014 1:37 PM
Reply to: Message 29 by RAZD
02-21-2014 1:31 PM


Re: Bottleneck
It would help if someone with access to the full paper and some actual knowledge of genetics (ie not me gave it a read through and translated for us.
On the face of it though, it looks to me like Jar's hypothesis is nfg.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 29 by RAZD, posted 02-21-2014 1:31 PM RAZD has seen this message but not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 32 of 140 (720339)
02-21-2014 5:46 PM


To coin a phrase Faith, they're still rabbits.
There's no more reason to expect rabbits in Australia to change their fur colour or physiology than those in Belgium. It would take an environmental cause to select for a fur colour change in a population. Remember the peppered moth?

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

Replies to this message:
 Message 33 by Faith, posted 02-21-2014 11:42 PM Tangle has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 34 of 140 (720356)
02-22-2014 3:31 AM
Reply to: Message 33 by Faith
02-21-2014 11:42 PM


The paper answers your question.
In fact, the current pattern of genetic variation in Australia is most likely a result of multiple factors including mutation, genetic drift and geographical differentiation. The absence of reduced genetic diversity is almost certainly a result of the rabbit's rapid population expansion at the time of establishment in Australia. These results highlight the importance of population growth following a demographic bottleneck, which largely determines the severity of genetic loss.
The population grew so fast - from 13 individuals to 10 billion in 60 years - that all the known methods of genetic change happened very quickly and recovered genetic diversity.
But the rabbits couldn't have bred that quickly if they were under any selection pressure and we don't expect radical changes in form if an animal is as obviously fit for its environment as the rabbit was/is in Australia.
Regardless, what this study shows is that bottlenecks aren't found in all species that undergo one and isolating a small group of animals does not necessarily lead to long term loss of genetic diversity.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 33 by Faith, posted 02-21-2014 11:42 PM Faith has replied

Replies to this message:
 Message 35 by Faith, posted 02-22-2014 3:46 AM Tangle has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 36 of 140 (720358)
02-22-2014 4:26 AM
Reply to: Message 35 by Faith
02-22-2014 3:46 AM


The reason I didn't rub your face in all the mistakes you made in your first post was because you were making so many and it would have been unkind. I hoped that quoting the piece that I did would be enough. However, if you insist
Faith writes:
The main thing I argued at length was that there was no selection pressure and selection was not a part of my thinking, that any change would be brought about strictly by the change in gene frequencies. I gather you didn't read any of that or if you did it went in one ear and out the other.
No Faith I chose to disregard it because change in gene frequency is the very definition of evolution; I suspect you are confusing this phrase with one of the methods by which a change in gene frequency comes about which is genetic drift.
Genetic drift is hypothesised by the paper as one of the mechanisms of recovering genetic diversity in the isolated population as well as mutation, which is why I quoted that section again for you.
Another thing I said was that recovering genetic diversity through rapid population growth could only be referring to the accumulation of mutations,
Which is incorrect and is why I quoted you that passage again.
And I questioned their method of determining genetic diversity or its loss, wondering how that method is expected to demonstrate that, which wasn't explained and I gather you don't know either. And then I gave my own expectation of how genetic diversity would best be shown by DNA analysis, which would be by looking for reduced heterozygosity at those gene loci where the phenotypic change is occurring if there is any.
Phenotypic change is not necessary to show genetic diversity - the rabbits are still rabbits, remember? You're confusing and conflating dozens of half understood terms.
And as you haven't the first clue about how you would go about deciding the genetic diversity of rabbits I didn't think it worth commenting on, preferring to take the word of those who actually do the work and know which way up to hold a pippette. But as you've pushed me, they used a method called microsatellite loci analysis (again, stated in the Abstract)
Microsatellites, also known as Simple Sequence Repeats (SSRs) or Short Tandem Repeats (STRs), are repeating sequences of 2-6 base pairs of DNA.[1] It is a type of Variable Number Tandem Repeat (VNTR). Microsatellites are typically co-dominant. They are used as molecular markers in STR analysis, for kinship, population and other studies. They can also be used for studies of gene duplication or deletion, marker assisted selection, and fingerprinting.
If you wish to know more, you're going to have to do some work but i'm afraid it will only confuse you more.
Microsatellite - Wikipedia

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 35 by Faith, posted 02-22-2014 3:46 AM Faith has replied

Replies to this message:
 Message 38 by Faith, posted 02-22-2014 2:20 PM Tangle has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 37 of 140 (720359)
02-22-2014 5:06 AM


Another study on rabbits and bottlenecks, this time in the UK where myxomatosis killed 99.9% of rabbits, comes to the same conclusions:
It is often assumed that, when a population goes through a severe bottleneck, random genetic drift will induce a massive loss of genetic variability. Despite the extremely large mortality induced by myxomatosis, much variation is still observed within rabbit populations, with average heterozygosity being 0.520. The reduction in heterozygosity induced by a population bottleneck depends not only on bottleneck size but also on the rate of population growth after the bottleneck, with rapid growth limiting the severe effects of drift to a few generations. However, the loss of alleles is largely dependent on bottleneck size only (Nei et al., 1975), because the bottleneck tends to eliminate many low-frequency alleles from the population. It is proposed that the rabbit's short generation time, together with high fecundity leading to a rapid population growth rate, could account for the degree of heterozygosity observed in present populations, despite the severity of the bottleneck. On the other hand, despite the degree of variation still observed in European wild rabbit populations, there can be no doubt that a disease such as myxomatosis resulting in the death of 99.9% of a population must have a significant effect on the genetic structure of that population.
This time the full paper is available in Heredity, but sadly above my pay grade.
Population structure and genetic variation of European wild rabbits (Oryctolagus cuniculus) in East Anglia | Heredity
It's quite interesting that this paper talks of genetic drift creating 'massive loss of diversity' following a bottleneck due to the loss of low frequency alleles. Which seems contradictory.
Edited by Tangle, : No reason given.
Edited by Tangle, : No reason given.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

Replies to this message:
 Message 39 by Faith, posted 02-22-2014 3:03 PM Tangle has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 40 of 140 (720415)
02-23-2014 4:27 AM
Reply to: Message 38 by Faith
02-22-2014 2:20 PM


All of this has been gone over many times with you but you just keep making the same assersions and errors.
Population splits/isolations/speciation events do not necessarily lead ultimately to a loss of genetic diversity. That's just one of your fantacies and it's shown here very clearly that even in extreme bottlenecks, it's possible for a species to recover extreemly quickly if the circumstances are right.
I'm simply focusing on observable traits because they ARE observable and they are what should be expected of a population of anything founded on low numbers, and the low founding numbers usually imply reduced genetic diversity
Phenotypic trait changes are NOT to be expected in a population of low numbers - it takes environmental pressure to select for a change or genetic drift over great periods of time. We would actually expect a population of low numbers to die out quickly but if they survived in circumstances like the rabbits we would expect them to reproduce in the normal way and produce rabbits just like their parents.
Yes, I had already looked up the definition myself. Besides being written in technical language which is hard for me, nothing there explains how genetic diversity can be shown by this method.
Besides it being the method used by geneticists to measure genetic diversity you mean? The fact that it's hard for you isn't an argument.
And I still get the impression you don't know either. Anyway I'm not discussing these things with Wikipedia, and it would help if you'd just explain anything you DO understand, in your own words.
Of course I don't know, i've said exactly that. I'm not a practicing geneticist, but unlike you, I have the sense not to declare things wrong that i don't understand just because i don't like the conclusion. Have a bit of humilty for god's sake.
Edited by Tangle, : No reason given.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 38 by Faith, posted 02-22-2014 2:20 PM Faith has replied

Replies to this message:
 Message 42 by Faith, posted 02-23-2014 1:50 PM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 41 of 140 (720416)
02-23-2014 5:34 AM
Reply to: Message 39 by Faith
02-22-2014 3:03 PM


Faith writes:
But rabbits do appear to be different in having such high heterozygosity. That number IS over 50% heterozygosity, I'm not misreading it am I? That's enormous.
Heterozygosity is measured between 0 and 1 so a measure of .5 seems average to me - but like you, I have no real clue.
Meanwhile, another paper with deer, showing roughly the same effect. I'd love someone who actually knows this stuff to comment.
Background
Within-population genetic diversity is expected to be dramatically reduced if a population is founded by a low number of individuals. Three females and one male white-tailed deer Odocoileus virginianus, a North American species, were successfully introduced in Finland in 1934 and the population has since been growing rapidly, but remained in complete isolation from other populations.
Methodology/Principal Findings
Based on 14 microsatellite loci, the expected heterozygosity H was 0.692 with a mean allelic richness (AR) of 5.36, which was significantly lower than what was found in Oklahoma, U.S.A. (H = 0.742; AR = 9.07), demonstrating that a bottleneck occurred. Observed H was in line with predictions from an individual-based model where the genealogy of the males and females in the population were tracked and the population's demography was included.
Conclusion
Our findings provide a rare within-population empirical test of the founder effect and suggest that founding a population by a small number of individuals need not have a dramatic impact on heterozygosity in an iteroparous species.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 39 by Faith, posted 02-22-2014 3:03 PM Faith has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 43 of 140 (720443)
02-23-2014 2:09 PM


Yes Faith a change in gene frequency is the very definition of evolution but we don't expect to see phenotypic change - rabbits turning blue - just because there's been a bottleneck.
What we expect to see are rabbits being born that are like their parents.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

Replies to this message:
 Message 44 by Faith, posted 02-23-2014 6:19 PM Tangle has replied
 Message 45 by RAZD, posted 02-23-2014 7:21 PM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(2)
Message 46 of 140 (720454)
02-24-2014 3:38 AM
Reply to: Message 44 by Faith
02-23-2014 6:19 PM


However, this discussion about rabbits has been interesting because it shows what could happen when instead of inbreeding working the new frequencies through the whole new population, rabbits go off and start small new populations. Their rapid reproductive rate would keep the worst effects of genetic drift from reducing their genetic diversity while their going off into smaller groups would prevent new phenotypes from becoming characteristic. With herd animals like the wildebeest the new gene frequencies would eventually get worked through the whole herd through some number of generations, but rabbits wouldn't allow that to happen. Nevertheless, barring some other habit or feature that further affects this, we should expect new phenotypes in the population at large.
Biologists do not expect new phenotypes to pop into existence after a bottleneck and the two extreme examples of the rabbits and the deer demonstrate that. Similarly cheetahs, seals and bison are still cheetahs, seals and bison.
This is a factual thing, Faith; if you have examples of new phenotype following a bottleneck, please produce them.
However, this discussion about rabbits has been interesting because it shows what could happen when instead of inbreeding working the new frequencies through the whole new population, rabbits go off and start small new populations. Their rapid reproductive rate would keep the worst effects of genetic drift from reducing their genetic diversity while their going off into smaller groups would prevent new phenotypes from becoming characteristic. With herd animals like the wildebeest the new gene frequencies would eventually get worked through the whole herd through some number of generations, but rabbits wouldn't allow that to happen.
Yes, reproductive rate is identified by both papers as likely being the reason that both the deer and the rabbits recovered gentic diversity. Note that Faith, recovered genetic diversity - not developed new phenotypes.
Nevertheless, barring some other habit or feature that further affects this, we should expect new phenotypes in the population at large.
Nope. Not unless there is selection pressure or long term drift which happen in populations that have not undergone a bottleneck just as much as those that have.
AND both the articles you posted do make it clear that reduced genetic diversity is certainly expected from a bottleneck
Well of course, that's a mathematical certainty!
although the point they are making is that there are circumstances that mitigate this effect. They can't reverse it though.
In the case of the rabbit, genetic diversity recovered to the extent that there was no difference between the host European population and the new Australian population. In the deer, genetic diversity recovered to almost the same level as the Oklahoma population within 70 years - although still different enough to show a bottleneck. (H=.692 vs H=.742). btw, in your earlier post you described the rabbit's H of .5 as 'enormous'.

Life, don't talk to me about life - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 44 by Faith, posted 02-23-2014 6:19 PM Faith has replied

Replies to this message:
 Message 47 by RAZD, posted 02-24-2014 8:32 AM Tangle has replied
 Message 49 by Faith, posted 02-24-2014 10:30 AM Tangle has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024