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Beneficial Mutations


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#1 PhilC

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Posted 29 June 2010 - 01:59 AM

I’ve been thinking again about beneficial mutations, and have noticed the following:

1. We only see mutations that have large effects.
2. Large effects are more likely to be deleterious.
3. Small mutations are also likely to be deleterious.
4. We have few examples of small deleterious mutations.
5. Beneficial mutations are most likely to be small in effect.
6. We are unlikely to find many cases of beneficial mutations.

Asking to see beneficial mutations is like asking to see minor bad ones. We don’t see them because their effect is likely to be small. Sickle cell anaemia is used because it is a major effect.

Here is another and in this case, because of the beauty of the experiment, it is empirical and repeatable.

In 2008, Lenski and his collaborators reported on a particularly important adaptation that occurred in one of the twelve populations: the bacteria evolved the ability to utilize citrate as a source of energy. Wild type E. coli cannot transport citrate across the cell membrane to the cell interior (where it could be incorporated into the citric acid cycle) when oxygen is present. The consequent lack of growth on citrate under oxic conditions is considered a defining characteristic of the species that has been a valuable means of differentiating E. coli from pathogenic Salmonella. Around generation 33,127, the experimenters noticed a dramatically expanded population-size in one of the samples; they found that there were clones in this population that could grow on the citrate included in the growth medium to permit iron acquisition. Examination of samples of the population frozen at earlier time points led to the discovery that a citrate-using variant had evolved in the population at some point between generations 31,000 and 31,500. They used a number of genetic markers unique to this population to exclude the possibility that the citrate-using E. coli were contaminants. They also found that the ability to use citrate could spontaneously re-evolve in populations of genetically pure clones isolated from earlier time points in the population's history. Such re-evolution of citrate utilization was never observed in clones isolated from before generation 20,000. Even in those clones that were able to re-evolve citrate utilization, the function showed a rate of occurrence on the order of once per trillion cells. The authors interpret these results as indicating that the evolution of citrate utilization in this one population depended on an earlier, perhaps non-adaptive "potentiating" mutation that had the effect of increasing the rate of mutation to citrate utilization to an accessible level (with the data they present further suggesting that citrate utilization required at least two mutations subsequent to this "potentiating" mutation). More generally the authors suggest that these results indicate (following the argument of Stephen Jay Gould) "that historical contingency can have a profound and lasting impact" on the course of evolution.


http://en.wikipedia....tion_experiment

#2 OneHourPhoto

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Posted 29 June 2010 - 05:51 AM

Phil, can I just say your posting evidence relating to micro evolution, you know from other threads that you have participated in on the very subject the kind of reponse you are going to recieve, I hope you are not "baiting" anyone here. Other than that it's an interesting thread and the article is a good read.

#3 gilbo12345

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Posted 29 June 2010 - 05:59 AM

I’ve been thinking again about beneficial mutations, and have noticed the following:

1. We only see mutations that have large effects.
2. Large effects are more likely to be deleterious.
3. Small mutations are also likely to be deleterious.
4. We have few examples of small deleterious mutations.
5. Beneficial mutations are most likely to be small in effect.
6. We are unlikely to find many cases of beneficial mutations.

Asking to see beneficial mutations is like asking to see minor bad ones.  We don’t see them because their effect is likely to be small.  Sickle cell anaemia is used because it is a major effect.

Here is another and in this case, because of the beauty of the experiment, it is empirical and repeatable.
http://en.wikipedia....tion_experiment

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Nice find :huh:

Though I have never heard of this experiment..lol perhaps they should put this one in my texbook instead of that stupid malaria resistance from sickle cell annemia... <_<

Though the citrate eating gene (or whatever lol ), could have come from a plasmid? Or perhaps this is a form of variation / adaption... As the ability to eat citrate doesn't change the function / form of the bacteria... Since they are meant to be natures recyclers :D

Anyway at least I have something else to ponder :D

#4 PhilC

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Posted 06 July 2010 - 01:27 PM

Phil, can I just say your posting evidence relating to micro evolution, you know from other threads that you have participated in on the very subject the kind of reponse you are going to recieve, I hope you are not "baiting" anyone here. Other than that it's an interesting thread and the article is a good read.

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Thanks for the warning. I'm not baiting anyone (though I'm sure someone will point out that these are still bacteria). I'm only trying to show that beneficial mutations do occur, and this is an example which is repeatable and empirical.

#5 PhilC

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Posted 06 July 2010 - 01:31 PM

Nice find :mellow:

Though I have never heard of this experiment..lol perhaps they should put this one in my texbook instead of that stupid malaria resistance from sickle cell annemia...  <_<

Though the citrate eating gene (or whatever lol ), could have come from a plasmid? Or perhaps this is a form of variation / adaption... As the ability to eat citrate doesn't change the function / form of the bacteria... Since they are meant to be natures recyclers :angry:

Anyway at least I have something else to ponder :lol:

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It was only discovered in 2008, so it'll take a while for the books to catch up.

Remember it isn't just one gene, it is a couple, starting with one in about generation 20,000. None of the other 11 'tribes' got this originating mutation, but this particular 'tribe' required at least one other mutation, and possibly more before they could synthesise the citrate.

#6 OneHourPhoto

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Posted 07 July 2010 - 05:47 AM

(though I'm sure someone will point out that these are still bacteria)


You don't think this would be a valid point if it was made?

#7 PhilC

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Posted 07 July 2010 - 06:50 AM

Well, it's an obvious point. I'm not arguing that they aren't. It's like in the Natural Selection observed thread; numerous times people pointed it out to me that they are still fish, as if I was claiming something different.

Of course, this thread is about the fact that we have an empirical, repeatable example of a beneficial mutation, despite the fact that they are unlikely to be seen (more unlikely to be seen than to occur) as said in the OP.

#8 OneHourPhoto

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Posted 08 July 2010 - 05:37 AM

Well, it's an obvious point.  I'm not arguing that they aren't.  It's like in the Natural Selection observed thread; numerous times people pointed it out to me that they are still fish, as if I was claiming something different.

Of course, this thread is about the fact that we have an empirical, repeatable example of a beneficial mutation, despite the fact that they are unlikely to be seen (more unlikely to be seen than to occur) as said in the OP.

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No problems, just wanted to see your thoughts on that.

#9 Adam Nagy

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Posted 20 July 2010 - 01:52 AM

Thanks for the warning.  I'm not baiting anyone (though I'm sure someone will point out that these are still bacteria).  I'm only trying to show that beneficial mutations do occur, and this is an example which is repeatable and empirical.

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The problem, Phil, is not that there is no way to label a mutation beneficial. The very idea of beneficial is so subjective. We need to dig deeper into what it is that is beneficial to the grand tale of evolution.

Being born without feet is a beneficial resistance to athletes feet.

Being born without hair is beneficial to resisting dandruff build up.

Individual findings, like the bacteria which develops an ability to consume citrate, is certainly interesting. However, what does it demonstrate and does it really compel us to ignore the evidence mounting against evolution?

If you want to think about all these little mutations as possibly the reason why we don't see the big ones, ponder this; The best experiment for seeing what the result of mutation accumulation is the 6 billion some walking experiments walking around us every day. Every single person that you come into contact with is accumulating mutations all the time. These mutations run a gamut from neutral to harmful and I suppose a couple could be pin-pointed as beneficial. However, there is an observable net result from the accumulation of these mutations which has a perfectly repeatable result with 100% predictability.

I can predict with 100% certainty that the mutation accumulation that is taking place in your body right now, Phil, is going to certainly result in disease or aging and finally death. The only thing that will beat the mutations to this result is some form of trauma.

Now when you talk about the possibility of the slow accumulation of beneficial mutations, all you have to do is find us an individual which has cheated death for hundreds of years because of the off potential that they have accumulated beneficial mutations. The wheel of chance is in your favor, I mean you have over 6 billion experiments that could be accumulating beneficial mutations in the longer term, against all odds, right? Where are they?

This is exactly the kind of junk that evolution wants to purport as science. Replace the evidence with an anecdote and than demand that all arguments must be framed to disprove that anecdote which has no empirical evidence to support it in the first place (like the 1 in six billion chance that some lucky schmuck is out there cheating death with the accumulation of beneficial mutations.) Well, they could be out there, right? So until we prove that there is nobody out there who is cheating death through the accumulation of beneficial mutations, we must believe that they could be out there and this is evidence for evolution. :huh:

#10 PhilC

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Posted 20 July 2010 - 04:19 AM

Adam, that is a long essay you've written but it doesn't stop one thing being shown here.

Multiple mutations happened that meant the amount of information increased. These were beneficial because they increased the fitness.

Individual findings, like the bacteria which develops an ability to consume citrate, is certainly interesting. However, what does it demonstrate and does it really compel us to ignore the evidence mounting against evolution?


Two of the mainstay things that were said to be against evolution were:

1. Benfefical mutations do not happen.
2. Information does not increase.

This experiment shows both of these are wrong.

#11 gilbo12345

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Posted 20 July 2010 - 05:16 AM

Adam, that is a long essay you've written but it doesn't stop one thing being shown here.

Multiple mutations happened that meant the amount of information increased. These were beneficial because they increased the fitness.
Two of the mainstay things that were said to be against evolution were:

1. Benfefical mutations do not happen.
2. Information does not increase.

This experiment shows both of these are wrong.

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Mutations increase genetic information? I thought that mutations changed the EXISTING information into something else? Or is there a mutation that adds entire gene sequences into DNA? :D

#12 evad

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Posted 20 July 2010 - 05:50 AM

Mutations increase genetic information? I thought that mutations changed the EXISTING information into something else? Or is there a mutation that adds entire gene sequences into DNA?  :D

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Gene duplication + mutation of those genes = change in information (but not an increase... just a change).

Why are you so hung up on increasing the information in the genome? What does that prove?

But if you really want examples of an increase in information in the genome (i.e. adding information without deletion):

Charcot-Marie-Tooth disease and Pelizaeus-Merzbacher disease.

If a gene duplicates but creates an error during duplication you have increased the "information" without deleting any existing information.

Google retrotransposon and homologous recombination.

#13 PhilC

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Posted 20 July 2010 - 05:53 AM

Mutations increase genetic information? I thought that mutations changed the EXISTING information into something else? Or is there a mutation that adds entire gene sequences into DNA?


At 35,000 generations there was more information across the 12 tribes than there was at the start. All the original information was there plus the added information to metabolise citrate.

#14 gilbo12345

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Posted 20 July 2010 - 05:54 AM

Gene duplication + mutation of those genes = change in information (but not an increase... just a change).

Why are you so hung up on increasing the information in the genome? What does that prove?

But if you really want examples of an increase in information in the genome (i.e. adding information without deletion):

Charcot-Marie-Tooth disease and Pelizaeus-Merzbacher disease.

If a gene duplicates but creates an error during duplication you have increased the "information" without deleting any existing information.

Google retrotransposon and homologous recombination.

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You're joking right? You're using diseases as evidence for evolution... (a bit like the guy on youtube who was claiming information increases in people who have downs syndrome as they have an extra chromosome)

The word I will pick out of your sentence is "duplication"... The information presented on the total genome is not NEW it is just a copy.

#15 PhilC

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Posted 20 July 2010 - 06:06 AM

Gilbo, you missed my comments.

#16 evad

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Posted 20 July 2010 - 06:12 AM

You're joking right? You're using diseases as evidence for evolution... (a bit like the guy on youtube who was claiming information increases in people who have downs syndrome as they have an extra chromosome)

The word I will pick out of your sentence is "duplication"... The information presented on the total genome is not NEW it is just a copy.

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I am not using this as evidence of evolution. You didn't ask for evidence of evolution. You asked how the information in a genome can increase.

You're starting to border on dishonesty, gilbo. You fail to accept evidence that you've requested and then twist this evidence into strawmen to promote your religious agenda. You have been shown how chromosome numbers can increase and how the number of base pairs can increase. You have been shown the evidence you asked for.

Do you know what a retrotransposon is? If so, how about explaining to me how it DOES NOT increase the information in the genome?

#17 gilbo12345

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Posted 20 July 2010 - 06:17 AM

At 35,000 generations there was more information across the 12 tribes than there was at the start. All the original information was there plus the added information to metabolise citrate.

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What is this from? Citations?

As far as I know bacteria already had this ability. I am not very fluent on this subject as it is relativly new to me, (despite the actual experiments being done over 50 yrs ago, as Jason showed you).

#18 PhilC

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Posted 20 July 2010 - 06:25 AM

Jason showed something else. Look at the experiment that I pointed you to.

In only one tribe did the right mutation occur that meant other mutations would help. If it was a recessive protein then it would have been in the founding population of all the tribes. Look at the actual detail of the experiment.

At about generation 20,000 in one of the tribes new information was formed.

New information was being formed all the time and is being formed all the time, creationists won't accept any evidence unless it is right in front of their face, though. Evolutionists have said this happens and creationists have said it is impossible.

Now we have evidence that even creationists can't deny.

#19 gilbo12345

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Posted 20 July 2010 - 06:38 AM

I asked for citations, for validity...

#20 PhilC

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Posted 20 July 2010 - 07:07 AM

Here is their website:

http://myxo.css.msu.edu/ecoli/

They are now on 50,000 generations!




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