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Author Topic:   No genetic bottleneck proves no global flood
Tangle
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Posts: 4397
From: UK
Joined: 10-07-2011
Member Rating: 2.8


Message 61 of 140 (720689)
02-26-2014 2:16 PM
Reply to: Message 56 by Faith
02-25-2014 9:49 PM


There's far too much I don't understand about genetics for me to make much more progress on this and I don't like making stuff up.

What we have evidence for though is that bottlencks do not necessarily reduce gentic diversity in the long term. The main requirement for recovery is the ability to breed freely and often.

We have not seen any new species or even sub-species arise as a result of a bottleneck in the sort of timescales you are imagining. (Very long term of course, this does occur as a result of dift and or mutation.)

Cheetah's are an exceptional example as science says that they went through 2 bottlenecks, one very ancient and one recent c10,000 years ago. The cheetah's genetic diversity is compared - exageratedly - to lab mice that are almost clones of each other.

Cheetahs have other problems too, they're top of the food chain so there aren't many able to be in the same area, have low sperm count and poor infant mortality so they're not in a great place to recover. Notedly, they are still recognisably cheetahs after two bottlenecks and a long time.


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:
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RAZD
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Posts: 18240
From: the other end of the sidewalk
Joined: 03-14-2004
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Message 62 of 140 (720706)
02-26-2014 6:04 PM
Reply to: Message 60 by Tangle
02-26-2014 1:54 PM


Re: heterozygosity measurements - part 2
I don't know yet.

Wake me up when you do ;-)

Well the article does go into this a little bit:

Population Bottlenecks: Heterozygosity vs. Allelic Diversity ... continued ...

quote:
Another consideration is the duration of the bottleneck. For how many generations is the population size reduced? How does this affect heterozygosity and allelic diversity? We can calculate the expected proportion of heterozygosity retained after a bottleneck with population size N lasting for t generations:

{1 - 1/(2N)}t

Where t is the number of generations. This would generate an exponential decay curve ... assuming that the population size is static and there are no new mutations, both questionable assumptions, especially with rabbits ... ("had to keep telling the rabits, only two only two" - Bill Cosby on Noah ) ...

Back to the article:

quote:
Allendorf used computer simulations to examine the effect of multiple generations on allelic diversity. For each set of parameter values (N, n and t) the simulation was run 1,000 times, and the means of these simulations are graphed below. Each graph represents a different population size, N, with t on the x-axis and A on the y-axis. The different colored lines represent different numbers of alleles present (n) prior to the bottleneck (n = 2, 5, or 10). The dashed line represents the expected loss of heterozygosity (E(H)) for a population of size N over t generations. (Graphs redrawn from Allendorf 1986; values for A estimated from same).



Again it appears that the expected proportion of heterozygosity is a first approximation and the allelic diversity calculation is more representative ...

... however there is no reference to numbers of offspring, which I would think would be critical to hold on to the alleles from the original bottleneck population.

Instead these calculations seem to assume that the following generation is another bottleneck from the previous generation ???

Seems the models are missing something: I would expect that cheetahs would have a much larger bottleneck impact than rabbits due to the difference in numbers of offspring.

Edited by RAZD, : formula clarity


we are limited in our ability to understand
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Tangle
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Posts: 4397
From: UK
Joined: 10-07-2011
Member Rating: 2.8


(1)
Message 63 of 140 (720708)
02-26-2014 7:12 PM
Reply to: Message 62 by RAZD
02-26-2014 6:04 PM


Re: heterozygosity measurements - part 2
RAZD writes:

Seems the models are missing something: I would expect that cheetahs would have a much larger bottleneck impact than rabbits due to the difference in numbers of offspring

That absolutely must be the case. The rabbits were able to go from a dozen to 10 billion in a few years - the cheetahs can't do anything like that because they are top predators in niche with a lion and a fertility problem. (lions kill 90% of cheetah cubs).

It occurs to me that Australia could both save the cheetah from extinction and solve its rabbit problem by introducing cheetahs. Just a thought.


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 62 by RAZD, posted 02-26-2014 6:04 PM RAZD has acknowledged this reply

  
Faith
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Posts: 23949
Joined: 10-06-2001
Member Rating: 1.0


Message 64 of 140 (720717)
02-27-2014 2:26 AM
Reply to: Message 58 by RAZD
02-26-2014 7:49 AM


Yes there could have been all those varieties in the original population, but the effect of a change in gene frequencies is that you DO get more of some and less of others and you DO get completely new combinations, more mottled fur with fewer green eyes or whatever. The point isn't that you get something that never existed before but that you get combinations that now CHARACTERIZE this new population and distinguish it from the mother population, a new "look," not brand new traits.

Furthermore, in "standard Mendelian combinations" there is no mathematical reason for these to suddenly all become sorted into certain individuals that would then become reproductively isolated within the rest of the population sufficiently to form such a sub-population.

"Suddenly" is not a word I've used; "sorted into certain individuals" also reflects nothing I've said; and you have it backwards, saying that after such sorting "then" these "sorted individuals" "become reproductively isolated," which gets everything out of order that I've been talking about. Reproductive isolation of a portion of a population is the FIRST thing that happens in my scenario, although in reality there may not be such perfect isolation; but isolation all by itself should produce the effects I'm talking about, because it gives you new gene frequencies that now work their way through the new isolated population.

I thought it was pretty well understood that a change in gene frequencies is a definition of evolution so that merely from such a change you should expect new phenotypes; it's rather surprising to see this foundational principle challenged and misrepresented.

Nor would there be an evolutionary cause for this - there would be no positive selection for such combinations in an ecology with static selection pressure, and sexual selection would much more likely act to reduce the numbers of such random occurrences of such mathematically rare combinations.

New combinations that form a new characteristic look to a subpopulation are not necessarily "mathematically rare," at least the components of the combinations are not although the particular combination MAY be brand new, based on as many as half a dozen or more traits in a combination that didn't occur in the parent population, or maybe very occasionally did but was overwhelmed by combinations that occurred in greater frequency there. The new "look" is based on a new mix of alleles. This is elementary, RAZD, you really shouldn't be fighting it.

You may or may not ALSO have positive selection working on the population. You'll get a new population whether you do or don't. In a population of mice, or any small creature vulnerable to predators, or other circumstances that challenge the fit between creature and environment, selection may well be a big factor, but it is possible to get a new population without positive selection. In fact it is inevitable as long as the genetic diversity in the original population was reasonably good.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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Tangle
Member
Posts: 4397
From: UK
Joined: 10-07-2011
Member Rating: 2.8


Message 65 of 140 (720719)
02-27-2014 3:51 AM


Another way a recovery from a bottleneck can happen is by immigration. It's wrong to imagine that the separation of populations is always permanent.

Abstract

Mammal species characterized by highly fluctuating populations often maintain genetic diversity in response to frequent demographic bottlenecks, suggesting the ameliorating influence of life history and behavioral factors. Immigration in particular is expected to promote genetic recovery and is hypothesized to be the most likely process maintaining genetic diversity in fluctuating mammal populations.

Most demographic bottlenecks have been inferred retrospectively, and direct analysis of a natural population before, during, and after a bottleneck is rare. Using a continuous 10-year dataset detailing the complete demographic and genetic history of a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis), we analyzed the genetic consequences of a 4-year demographic bottleneck that reduced the population to seven adult squirrels, and we evaluated the potential ‘‘rescue effect’’ of immigration.

Analysis of six microsatellite loci revealed that, while a decline in allelic richness was observed during the bottleneck, there was no observed excess of heterozygosity, a characteristic bottleneck signature, and no evidence for heterozygote deficiency during the recovery phase. In addition, we found no evidence for inbreeding depression during or after the bottleneck. By identifying immigrants and analyzing their demographic and genetic contributions, we found that immigration promoted demographic recovery and countered the genetic effects of the bottleneck, especially the loss of allelic richness. Within 3 years both population size and genetic variation had recovered to pre-bottleneck levels, supporting the role of immigration in maintaining genetic variation during bottleneck events in fluctuating populations.

Our analyses revealed considerable variation among analytical techniques in their ability to detect genetic bottlenecks, suggesting that caution is warranted when evaluating bot- tleneck events based on one technique

I have to admit to being very confused by this statement:

Analysis of six microsatellite loci revealed that, while a decline in allelic richness was observed during the bottleneck, there was no observed excess of heterozygosity, a characteristic bottleneck signature, and no evidence for heterozygote deficiency during the recovery phase.

Heterozygosity increase after a bottleneck?


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 66 by Faith, posted 02-27-2014 5:44 AM Tangle has responded

  
Faith
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Posts: 23949
Joined: 10-06-2001
Member Rating: 1.0


Message 66 of 140 (720724)
02-27-2014 5:44 AM
Reply to: Message 65 by Tangle
02-27-2014 3:51 AM


With a bottleneck you can get such depleted genetic diversity that breeding with other members of the pseices has become impossible, unless the others are reintroduced very soon after the bottleneck. But in the examples I focus on I've specifically ruled out immigration because that is only putting back formerly lost genetic material, it is not new genetic material. I've specifically said this many times. Gene flow keeps genetic diversity up. I'm trying to highlight what happens when the processes that bring about evolution are happening, the isolating and selecting processes. That's when you get reduction of genetic diversity, through the processes of evolution. Sure you can prevent loss of genetic diversity in many ways, and that's what conservationists try to do when a species has low genetic diversity, they try to reintroduce others of the species to bring it back up.

There is only ONE process that supposedly adds new genetic material, new alleles, and that's mutation, which I don't believe does any such thing.

I don't understand any of gthat about microsatellite loci, still have to spend some time on it.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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herebedragons
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Posts: 1251
From: Michigan
Joined: 11-22-2009
Member Rating: 5.6


Message 67 of 140 (720732)
02-27-2014 9:10 AM
Reply to: Message 66 by Faith
02-27-2014 5:44 AM


With a bottleneck you can get such depleted genetic diversity that breeding with other members of the pseices has become impossible

But changing allele frequency alone is not enough to make two sub-species reproductively incompatible.

There is only ONE process that supposedly adds new genetic material, new alleles, and that's mutation, which I don't believe does any such thing.

I hope you are going to follow my Genetic and Cellular Mechanisms and Variation thread.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


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RAZD
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Posts: 18240
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.9


(1)
Message 68 of 140 (720738)
02-27-2014 10:35 AM
Reply to: Message 64 by Faith
02-27-2014 2:26 AM


Yes there could have been all those varieties in the original population, but the effect of a change in gene frequencies is ...

What causes the change in gene frequencies Faith? If there is no difference in selection pressure from one generation to the next then there is no cause for a change in gene frequencies (other than drift which occurs over many generations).

Gene frequencies don't change spontaneously.

... the effect of a change in gene frequencies is that you DO get more of some and less of others and you DO get completely new combinations, ...

In response to selection pressure that favors some more and others less, without such pressure there is no mechanism to cause changes in frequencies.

... and you DO get completely new combinations, more mottled fur with fewer green eyes or whatever. ...

Ah the hopeful monster?

If each of these traits exist in the population beforehand, as you claim, but are not expressed frequently then they would necessarily be rare and recessive -- rare so that two matching recessive genes do not occur with any great frequency in the previous population, and recessive so that they can exist in sufficient numbers to stay in the population gene mix.

If these rare recessive genes also was deleterious (selected against) when occurring in both copies then that would also work to keep the allele suppressed in the general population before the bottleneck event.

Having this same scenario repeated for a number of different genes and then somehow magically combining them all into one individual would be a mathematically rare event.

Having it occur with no selection pressure to positively select any of these traits would be highly improbable.

Having it then become a dominant phenotype would be astounding.

... The point isn't that you get something that never existed before but that you get combinations that now CHARACTERIZE this new population and distinguish it from the mother population, a new "look," not brand new traits.

Magically?

What causes this change Faith?

I thought it was pretty well understood that a change in gene frequencies is a definition of evolution so that merely from such a change you should expect new phenotypes; it's rather surprising to see this foundational principle challenged and misrepresented.

In response to selection pressure, in response to changes in the ecology. It is a response mechanism not a causal one. The new phenotype occurs (by mutation) before the frequencies change in the breeding population and they cause the frequency change through selection.

The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities.

"Suddenly" is not a word I've used; "sorted into certain individuals" also reflects nothing I've said; ...

They are implicit in your fantasy. You have a bunch of phenotypic changes all occurring at the same time and forming a subpopulation ... that is suddenly in ecological terms.

... and you have it backwards, saying that after such sorting "then" these "sorted individuals" "become reproductively isolated," which gets everything out of order that I've been talking about. Reproductive isolation of a portion of a population is the FIRST thing that happens in my scenario, although in reality there may not be such perfect isolation; but isolation all by itself should produce the effects I'm talking about, because it gives you new gene frequencies that now work their way through the new isolated population.

And you are the one that has it backwards, Faith.

Reproductive isolation does not happen spontaneously, nor is it necessarily are result from geographic isolation. Reproductive isolation is something that occurs by accumulated changes in breeding subpopulations when gene flow is interrupted or severely restricted. Ring species demonstrate this: several subpopulations in a ring, spreading from an original population around a geological feature, forming subpopulations capable of reproduction with the neighboring subpopulations, but gene flow between these subpopulations is less than inside each subpopulation, and where two ends meet they do not interbreed.

New combinations that form a new characteristic look to a subpopulation are not necessarily "mathematically rare," ...

This is you not understanding what you are saying.

... at least the components of the combinations are not although the particular combination MAY be brand new, based on as many as half a dozen or more traits in a combination that didn't occur in the parent population, ...

Which would be a mathematically rare occurrence in the parent population and no different in the bottleneck population without selection pressure cause them all to be positively selected -- also a mathematically rare occurrence.

... or maybe very occasionally did but was overwhelmed by combinations that occurred in greater frequency there. The new "look" is based on a new mix of alleles. ...

ie -- rare and recessive traits in the original population ... suddenly all getting sorted together with no causal pressure.

... This is elementary, RAZD, you really shouldn't be fighting it.

No Faith, it is fantasy, made up hokum. Phenotypic change of a single trait spread in a breeding population can occur in response to selection for that trait. A couple of traits selected at the same time would be unusual (ie Galapagos\Darwin Finches only changed beak size), and "as many as half a dozen or more traits" would be astounding.

And to have a whole subpopulation form with such traits in the absence of any selection pressure would be magic, not evolution.


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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Tangle
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Posts: 4397
From: UK
Joined: 10-07-2011
Member Rating: 2.8


(2)
Message 69 of 140 (720747)
02-27-2014 12:47 PM
Reply to: Message 66 by Faith
02-27-2014 5:44 AM


Faith writes:

With a bottleneck you can get such depleted genetic diversity that breeding with other members of the pseices has become impossible, unless the others are reintroduced very soon after the bottleneck. But in the examples I focus on I've specifically ruled out immigration because that is only putting back formerly lost genetic material, it is not new genetic material. I've specifically said this many times. Gene flow keeps genetic diversity up.

Yes, yes, all that is obvious. The point of my post was only to show that isolation does not always mean a permanent bottleneck. Re-introductions via immigration must happen many, many times.

That's when you get reduction of genetic diversity, through the processes of evolution.

No. You get the decrease in diversity via isolation. The process of evolution happens after separation and increases 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 66 by Faith, posted 02-27-2014 5:44 AM Faith has responded

Replies to this message:
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Stile
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Posts: 2848
From: Ontario, Canada
Joined: 12-02-2004
Member Rating: 1.9


(1)
Message 70 of 140 (720753)
02-27-2014 2:53 PM
Reply to: Message 61 by Tangle
02-26-2014 2:16 PM


Increase of genetic information?
Tangle writes:

What we have evidence for though is that bottlencks do not necessarily reduce gentic diversity in the long term. The main requirement for recovery is the ability to breed freely and often.

Is there a reason the term "recovery" is used all the time when referencing this?

It would seem to me that for the genetic diversity to increase, brand new "genetic diversity" would have to be created.

That is:

Let's say genetic diversity was 6.2
Then there was a bottle neck and it dopped to 1.3
Then the genetic diversity worked it's way back up to 6.2 again.

I can see the use of the word "recovery" in this sense.

But I think it's important to note (especially in context with the EvC debate) that the "recovered" genetic diversity is entirely new. It's not "getting back" the same old genetic information from before... it's entirely new genetic information. It's simply the level of diversity that's "recovered..." but brand new genetic information has been created in order for the diversity to get back to that level.

This should be rather simple to prove out as well by comparing the genetic information from before and after... if it's different, then new genetic information was obviously created. If the genetic information is exactly the same... then my idea is falsified.

There's far too much I don't understand about genetics for me to make much more progress on this and I don't like making stuff up.

I know even less than you, I'm sure. So I've probably screwed up a few terms in my post. But I hope I was able to get my idea across?


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Faith
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Posts: 23949
Joined: 10-06-2001
Member Rating: 1.0


Message 71 of 140 (720756)
02-27-2014 3:16 PM
Reply to: Message 69 by Tangle
02-27-2014 12:47 PM


That's when you get reduction of genetic diversity, through the processes of evolution.

No. You get the decrease in diversity via isolation. The process of evolution happens after separation and increases diversity.

All the processes of evolution bring about that isolation you acknowledge does cause decrease in genetic diversity. Natural selection produces a new population in much the same way as geographic isolation would, only without moving the population; it simply forms a new population of the selected types. Isolation is more random, but it still forms a new population of the randomly "selected" types as it were. Genetic drift is another form of reproductive isolation, within the population, where unknown or random factors bring about a subpopulation with its own characteristic genetic frequencies, which often involves the elimination of some alleles, just as the other processes do.

Immigration simply remixes the genes that belong to the species already. It's important for recovering genetic diversity when a species is threatened with extinction through a bottleneck.

Again, the ONLY process that could bring about actual increased genetic diversity is mutation, or the formation of new VIABLE genetic sequences or new alleles. It is claimed this happens. I doubt it.

Edited by Faith, : No reason given.


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RAZD
Member
Posts: 18240
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.9


Message 72 of 140 (720758)
02-27-2014 3:33 PM
Reply to: Message 70 by Stile
02-27-2014 2:53 PM


revitalized
Is there a reason the term "recovery" is used all the time when referencing this?

It would seem to me that for the genetic diversity to increase, brand new "genetic diversity" would have to be created.

That is:

Let's say genetic diversity was 6.2
Then there was a bottle neck and it dopped to 1.3
Then the genetic diversity worked it's way back up to 6.2 again.

I can see the use of the word "recovery" in this sense.

But I think it's important to note (especially in context with the EvC debate) that the "recovered" genetic diversity is entirely new. ...

Good point. Perhaps "revitalized" would be better terminology -- it has the connotations of reviving a species from decline without implying return to previous diversity.

... genetic diversity was 6.2

Are you referring to a specific metric that measures this, or just making up numbers?

The metrics I've seen seem to be normalized to numbers between zero (all genes have the same alleles throughout the population) and 1 (all genes have different alleles)

At least this applies to allelic diversity.

This should be rather simple to prove out as well by comparing the genetic information from before and after... if it's different, then new genetic information was obviously created. If the genetic information is exactly the same... then my idea is falsified.

There isn't a large record of before to work from at this time. With the current work on genomes this should not be as much of a problem for future studies.


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:
 Message 70 by Stile, posted 02-27-2014 2:53 PM Stile has responded

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JonF
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Posts: 3483
Joined: 06-23-2003
Member Rating: 2.8


(3)
Message 73 of 140 (720770)
02-27-2014 4:15 PM
Reply to: Message 71 by Faith
02-27-2014 3:16 PM


Again, the ONLY process that could bring about actual increased genetic diversity is mutation, or the formation of new VIABLE genetic sequences or new alleles. It is claimed this happens. I doubt it.

Of course you doubt it. We know. We also know that you (indeed, anybody) have not been able to come up with a viable explanation for the observed increases in genetic diversity. "A rare allele that hung around for thousands of years before it was needed, even against strong selection pressure" doesn't work.

The mainstream explanation does work.

Edited by JonF, : No reason given.


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 Message 71 by Faith, posted 02-27-2014 3:16 PM Faith has responded

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Faith
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Posts: 23949
Joined: 10-06-2001
Member Rating: 1.0


Message 74 of 140 (720772)
02-27-2014 4:26 PM
Reply to: Message 73 by JonF
02-27-2014 4:15 PM


I never said anything like "a rare allele hung around for thousands of years." Rare COMBINATIONS is what I'm talking about, and since there should be millions of possible combinations of traits from just about any genome -- except the severely genetically depleted ones -- you should certainly be able to get rare ones.

However, there is such a thing as an allele being rare in a population but favored in a subpopulation and the example of the pocket mice is an example of that. Also the peppered moths.

It's amazing that you all can maintain your faith in mutations which are not known to produce anything but

  • "neutral" changes that have no clear effects but over time probably deleterious effects when new mutations come along at the same loci,

  • thousands of known genetic diseases that are NOT all selected out before birth, causing all kinds of misery,

  • and highly questionable iffy "beneficial" mutations, all the other "beneficial" mutations being figments of the imagination.

Really touching such a degree of faith.

ABE: There ARE no "observed increases in genetic diversity." Sorry, that's some kind of illusion. /ABE

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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Taq
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Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


(1)
Message 75 of 140 (720776)
02-27-2014 4:39 PM
Reply to: Message 74 by Faith
02-27-2014 4:26 PM


However, there is such a thing as an allele being rare in a population but favored in a subpopulation and the example of the pocket mice is an example of that.

It was rare because it was produced by a mutation, so it was found in only one individual to start with.


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