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The Long Term Evolution Experiment ( Ltee )


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#1 deadlock

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Posted 24 August 2008 - 07:56 AM

The Long Term Evolution Experiment (LTEE) has been going on since 1988, and its goal was to study how related mutations can accumulate.They used Escherichia Coli because it can metabolize citrate internally during aerobic growth on other substrates.The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.Indeed , atypical E.Coli that grow aerobically on citrate have been isolated from agricultural and clinical settings, and were found to harbor plasmids, presumably acquired from other species, that encode citrate transporters.So, the ability to digest citrate depends on related mutations.
They started out with 12 individual, identical E.Coli bacteria making 12 colonies.They fed them glucose and citrate, and gave them 12.2 times more citrate than glucose.The expectation was that if the E.Coli did evolve into a form that could digest citrate, that new variety would flourish in the citrate -rich environment and drive the old variation to extinction.
So, it took more than 30.000 generations to fully evolve a capability that was already almost there, and it only happened in 1 out of 12 populations.In human terms 30.000 generations is 600.000 years.The scientists don´t know how many mutations are related to the trait yet, but let´s imagine that were 1000 mutations.So, we had 1000 beneficial mutations accumulated in 30.000 geneations.The difference between human and chimps genetic code is 4%, 120 millions of mutations. The numbers of generations necessary to accumulate 120 millions of mutations woul be : ( ( 120 * 10^6 ) / 10^3 ) * 30 * 10^3 = 36 * 10^8 generations.In years terms it would be : 36 * 10^8 * 20 = 72 billions of years.

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#2 rbarclay

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Posted 24 August 2008 - 01:23 PM

The Long Term Evolution Experiment (LTEE) has been going on since 1988, and its goal was to study how related mutations can accumulate.They used Escherichia Coli because it can metabolize citrate internally during aerobic growth on other substrates.The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.Indeed , atypical E.Coli that grow aerobically on citrate have been isolated from agricultural and clinical settings, and were found to harbor plasmids, presumably acquired from other species, that encode citrate transporters.So, the ability to digest citrate depends on related  mutations.
They started out with 12 individual, identical E.Coli bacteria making 12 colonies.They fed them glucose and citrate, and gave them 12.2 times more citrate than glucose.The expectation was that if the E.Coli did evolve into a form that could digest citrate, that new variety would flourish in the citrate -rich environment and drive the old variation to extinction.
So, it took more than 30.000 generations to fully evolve a capability that was already almost there, and it only happened in 1 out of 12 populations.In human terms 30.000 generations is 600.000 years.The scientists don´t know how many mutations are related to the trait yet, but let´s imagine that were 1000 mutations.So, we had 1000 beneficial mutations accumulated in 30.000 geneations.The difference between human and chimps genetic code is 4%, 120 millions of mutations. The numbers of generations necessary to accumulate 120 millions of mutations woul be : ( ( 120 * 10^6 ) / 10^3 ) * 30 * 10^3 = 36 * 10^8 generations.In years terms it would be : 36 * 10^8 * 20 = 72 billions of years.

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Deadlock

I have read this newsletter and think is a great article (I enjoy reading their newsletter). Thank you for bring it up here on the forum.

Bob Barclay

#3 A.Sphere

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Posted 24 August 2008 - 05:22 PM

So, it took more than 30.000 generations to fully evolve a capability that was already almost there, and it only happened in 1 out of 12 populations.In human terms 30.000 generations is 600.000 years.The scientists don´t know how many mutations are related to the trait yet, but let´s imagine that were 1000 mutations.So, we had 1000 beneficial mutations accumulated in 30.000 geneations.The difference between human and chimps genetic code is 4%, 120 millions of mutations. The numbers of generations necessary to accumulate 120 millions of mutations woul be : ( ( 120 * 10^6 ) / 10^3 ) * 30 * 10^3 = 36 * 10^8 generations.In years terms it would be : 36 * 10^8 * 20 = 72 billions of years.

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Surely you see the obviously wrong assumption in this calculation don't you?

#4 deadlock

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Posted 25 August 2008 - 03:53 AM

Surely you see the obviously wrong assumption in this calculation don't you?

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No, explain me

#5 Stereotomy

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Posted 25 August 2008 - 09:09 PM

I don't know what answer Sphere intends to give, but here's two from me:

-You haven't taken population size into account. Larger population = faster evolution
-You've assumed no simultaneity of evolution. There's no reason two beneficial traits couldn't emerge in a group- or even two groups, then after intermating between organisms with one beneficial trait and those with the other, end up with some with both (who then become dominant)

Also, 12 seems like an incredibly small sample size.

#6 deadlock

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Posted 26 August 2008 - 03:41 AM

I don't know what answer Sphere intends to give, but here's two from me:

-You haven't taken population size into account. Larger population = faster evolution


We´re talking about bacterias, no organism in the world would have a population size greater than bacterias.The experience used trillions upon trillions of bacterias in 20 years.

-You've assumed no simultaneity of evolution. There's no reason two beneficial traits couldn't emerge in a group- or even two groups, then after intermating between organisms with one beneficial trait and those with the other, end up with some with both (who then become dominant)


It´s not true. First, Bacterias can give and receive genetic material through plasmids.Second, S@xual reproduction makes more difficult to pass mutations on.A mutated bacteria has 100% of chance of passing its mutations on, while S@xual reproduction because of recombination has only 50%.

Also, 12 seems like an incredibly small sample size.


No, because each population has trillions upon trillions of bacterias.


In reality, the experience maximized all the factors in favor of evolution, and even so it took 30.000 generations to evolve some point mutations.Let´s see them:

1 - 100% of selection :

Bacterias have a generation time of 20 minutes, human has generation time of 20 years.There´s a great probability that a mutated human dies before reproduction. All bacterias survived to reproduction.If a mutation for citrate happened there was citrate to select it.What would be the probability of a mutation favoring citrate happens in a bacteria that has citrate available in the wild ?

2 - Asexual reproduction :
Each bacteria is a clone of its ancestor, so we have 100% of mutations being passed on.Human has S@xual reproduction, so the probability of a mutation be passed on is 50%, if the mutation is in a recessive allele then the probability is very low.Human lived in small separeted groups, what is the probability of a mutated male finds a mutated female , mates her and their mutations are related ?

3 - Incredible population size:
It was used trillions upon trillions of bacterias in 20 years, no mammalian population could reach that number.

It´s very clear that any mammalian group would take more than 30.000 generations to evolve some simple trait, because no organism can evolve faster than bacterias.But, even using the bacterias number the evolution of any mammalian organism is impossible.

#7 BVZ

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Posted 11 November 2008 - 10:29 PM

You are assuming that the 4% divergence between humans and chimps you used in your calculation consists ENTIRELY of beneficial mutations, since you are using the accumulation rate of BENEFICIAL mutations to reach a result of 72 billion years.

If you want to do it correctly you have to use the rate at which ALL mutations accumulate (become fixed), not just beneficial ones.

The reason for this is that the 4% divergence you used contains not only beneficial mutations on humans and chimps, but also netural and deleterous mutations.

You have to take that into account.

I predict your 72 billion year result will drop like a lead balloon.

#8 deadlock

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Posted 12 November 2008 - 02:02 AM

You are assuming that the 4% divergence between humans and chimps you used in your calculation consists ENTIRELY of beneficial mutations, since you are using the accumulation rate of BENEFICIAL mutations to reach a result of 72 billion years.

If you want to do it correctly you have to use the rate at which ALL mutations accumulate (become fixed), not just beneficial ones.

The reason for this is that the 4% divergence you used contains not only beneficial mutations on humans and chimps, but also netural and deleterous mutations.

You have to take that into account.

I predict your 72 billion year result will drop like a lead balloon.

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First, explain me how deleterious mutations can be fixed in a population.Perhaps, it´s a new theory that I dont know.

Second, neutral mutations take longer time to be fixed than beneficial ones.So, explain me how changing beneficial mutations to neutral will drop the result ?

#9 BVZ

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Posted 12 November 2008 - 03:31 AM

Sure no problem.

But before I explain, I want to make sure about something. You said the following:

First, explain me how deleterious mutations can be fixed in a population.Perhaps, it´s a new theory that I dont know.


Whan you say this, are you stating that you think it is impossible for deleterous mutations to become fixed in a population?

Now, the explanation.

Lets look at your argument in the OP.

You examine a positive trait in a population, and you assume that it took 1000 beneficial mutations for that trait to arise. (It's propably a lot less, but that would be a guess on my part.)

It took 30000 generations to get these mutations.

Based on this, you calculate that 72 billion years is neccesary for the divergence between humans and chimps to accumulate.

Here is the problem with this:

You take the rate of beneficial mutations neccesary for a specific trait to come into existance, and then use that to calculate the divergence between humans and chimps. The problem is that the DNA that differs between humans and chimps do not consist 100% out of beneficial mutations, and this means you can't use the rate of beneficial mutation increase to calculate how long this divergence will develop.

Does this make sense?

Also, since chimps and humans developed from a common ancestor (according to evolution theory) you have to divide the divergence by 2 before you do the calculation, since humans and chimps evolved in parralel, and the divergence between them accumulated in parralel.

So even WITHOUT taking the mistake I pointed out into consideration, we can already halve the 72 billion years to 36 billion years.

After this is done, considering the fact that beneficial mutations are pretty rare when compared with neutral ones, you will find that the resulting time value will decrease dramatically.

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Posted 12 November 2008 - 10:40 AM

The problem in the OP is that it doesn't take into account actual rates of mutations. There's a paper on this very experiment which calculates the estimated rate of beneficial mutations at 4x10^-9 per cell per generation (here: http://www.pubmedcen...gi?artid=14717). Doesn't sound like much, but if you extrapolate this rate to human evolution (I've done just that, but I'll have to dig up the numbers) you get quite a number of beneficial mutations that could have occurred in human evolution.

The OP also assumes (as others have pointed out) that all divergence between humans and chimps is strictly beneficial, ignores parallel divergence, and also assumes all divergence is from only point mutations. Not to mention the rather arbitrary 1000 mutations to evolve a trait number.

Taking all that into account, that 72 billion year number doesn't mean much.

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Posted 12 November 2008 - 11:19 AM

First, explain me how deleterious mutations can be fixed in a population.Perhaps, it´s a new theory that I dont know.


Hitchhiking. Basically, a deleterious mutation "hitchhikes" along with a benficial mutation. The beneficial mutation is selected for outweighing the deleterious mutation, and the deleterious mutation spreads along with it.

You can also get situations where mutations may be beneficial or deleterious depending on context. An example would be the sickle-celled mutation where environmental context plays a huge role in how that mutation is spread in the population.

Second, neutral mutations take longer time to be fixed than beneficial ones.So, explain me how changing beneficial mutations to neutral will drop the result ?


Fixation is less relevant than accumulation. If you have two discrete populations that evolve with strictly neutral mutations occuring every generation, you'll wind up with a net genetic difference between the two populations.

#12 deadlock

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Posted 12 November 2008 - 01:57 PM

Sure no problem.

But before I explain, I want to make sure about something. You said the following:
Whan you say this, are you stating that you think it is impossible for deleterous mutations to become fixed in a population?


Yes

You take the rate of beneficial mutations necessary for a specific trait to come into existance, and then use that to calculate the divergence between humans and chimps. The problem is that the DNA that differs between humans and chimps do not consist 100% out of beneficial mutations, and this means you can't use the rate of beneficial mutation increase to calculate how long this divergence will develop.


Can´t I ? As I said beneficial mutations get fixed faster than neutral ones, if I use neutral mutations things will get worse to evolution.Does this make sense?

Also, since chimps and humans developed from a common ancestor (according to evolution theory) you have to divide the divergence by 2 before you do the calculation, since humans and chimps evolved in parralel, and the divergence between them accumulated in parralel.So even WITHOUT taking the mistake I pointed out into consideration, we can already halve the 72 billion years to 36 billion years.


I dont have to divide by 2 because we dont know the proportion that the mutations acumulated in each lineage.But we can see that the chimp phenotype is closer to our supposed ancestor than human phenotype.So, it´s obvious that the major part of divergence is on our side and chimps had little change.But I wont fight for this point, I can accept 36 billion years.

After this is done, considering the fact that beneficial mutations are pretty rare when compared with neutral ones, you will find that the resulting time value will decrease dramatically.


No, it wont because we are not discussing the frequency that mutations happen but the time they take to get fixation.

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Posted 12 November 2008 - 02:22 PM

But we can see that the chimp phenotype is closer to our supposed ancestor than human phenotype.So, it´s obvious that the major part of divergence is on our side and chimps had little change.


Difference in phenotype is irrelevant since there is discordance between changes to the genome and changes to the phenotype. It's possible to have large divergence genetically with little change to the phenotype and vise-versa.

#14 deadlock

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Posted 12 November 2008 - 02:50 PM

The problem in the OP is that it doesn't take into account actual rates of mutations.  There's a paper on this very experiment which calculates the estimated rate of beneficial mutations at 4x10^-9 per cell per generation (here: http://www.pubmedcen...gi?artid=14717).  Doesn't sound like much, but if you extrapolate this rate to human evolution (I've done just that, but I'll have to dig up the numbers) you get quite a number of beneficial mutations that could have occurred in human evolution.


I couldnt acess the link, but the reference I have about mutation rates is 10^-10.SANDWALK.I think you are making confusion between mutation rates and rates of beneficial mutation.Beneficial mutations are so rare that nobody knows its rate.

The OP also assumes (as others have pointed out) that all divergence between humans and chimps is strictly beneficial,


Using beneficial mutations I´m helping evolution.

ignores parallel divergence


As I said I can accept 36 billion years

, and also assumes all divergence is from only point mutations.


Thats the most common mutation, so it´s obvious that the great majority are point mutations.But be free to show the numbers of other types of mutation and how they change the math.

  Not to mention the rather arbitrary 1000 mutations to evolve a trait number.


We have millions of mutations to explain.It´s irrelevant if we have one million traits of 26 point mutations or 26 thousand traits of one thousand mutations.

Taking all that into account, that 72 billion year number doesn't mean much.


All you took in account are wrong, but you could at least show the math instead of making unsupported claims.

#15 deadlock

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Posted 12 November 2008 - 02:53 PM

Difference in phenotype is irrelevant since there is discordance between changes to the genome and changes to the phenotype.  It's possible to have large divergence genetically with little change to the phenotype and vise-versa.

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What do mean ? Homology in phenotype is not equal homology in genotype ?

#16 deadlock

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Posted 12 November 2008 - 02:57 PM

Hitchhiking.  Basically, a deleterious mutation "hitchhikes" along with a benficial mutation.  The beneficial mutation is selected for outweighing the deleterious mutation, and the deleterious mutation spreads along with it.

You can also get situations where mutations may be beneficial or deleterious depending on context.  An example would be the sickle-celled mutation where environmental context plays a huge role in how that mutation is spread in the population.


We are talking about fixation.sickle-celled mutation is not fixed in human population.Show me a deleterious mutation that is fixed in human specie.

Fixation is less relevant than accumulation.  If you have two discrete populations that evolve with strictly neutral mutations occuring every generation, you'll wind up with a net genetic difference between the two populations.


Of course not, all the differences between human and chimps are fixed in each specie.So, you have to explain the fixation of those differences.And I´m not saying that neutral mutations cannot be fixed in population I´m saying that they take longer to fix than beneficial ones.

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Posted 12 November 2008 - 03:08 PM

I couldnt acess the link, but the reference I have about mutation rates is 10^-10.SANDWALK.I think you are making confusion between mutation rates and rates of beneficial mutation.Beneficial mutations are so rare that nobody knows its rate.


Uh, the paper I referenced had a rate of beneficial mutations. It's 4x10^-9 per cell per generation.

I think you are confusing the fact that the rates are being quoted with different measures (per nucleotide versus per cell generation). Apples and oranges.

Using beneficial mutations I´m helping evolution.


No you're restricting the differences between genomes to a specific "type" of mutation.

Thats the most common mutation, so it´s obvious that the great majority are point mutations.But be free to show the numbers of other types of mutation and how they change the math.


But the majority of genetic difference is not caused by point mutations. I'll dig up a paperin Nature that shows that the majority of difference is caused by mutations that affect multiple base pairs (i.e. indels and the like), but yet occur far less frequently (10% of the rate compared to point mutations IIRC).

It´s irrelevant, we have millions of mutations to explain.


It's pretty revelant to your math since it inflates your result a thousand fold.

All you took in account are wrong, but you could at least show the math instead of making unsupported claims.


I'll get back to you once I've looked up the relevant papers.

#18 deadlock

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Posted 12 November 2008 - 03:20 PM

Uh, the paper I referenced had a rate of beneficial mutations.  It's 4x10^-9 per cell per generation.

I think you are confusing the fact that the rates are being quoted with different measures (per nucleotide versus per cell generation).  Apples and oranges.


Please, post a valid link.If the paper is saying that, it probably is using circular reasoning.It´s probably assuming evolution is true to estimate how many beneficial mutations should have happened.Like mutation rates that are calculated comparing human and chimps DNA.

No you're restricting the differences between genomes to a specific "type" of mutation.

it´s the faster one.But be free to show other calculation.

But the majority of genetic difference is not caused by point mutations.  I'll dig up a paperin Nature that shows that the majority of difference is caused by mutations that affect multiple base pairs (i.e. indels and the like), but yet occur far less frequently (10% of the rate compared to point mutations IIRC).


if it´s only 10% of the rate how is it responsible for the majority of differences ?

It's pretty revelant to your math since it inflates your result a thousand fold.


Please show me the math

#19 falcone

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Posted 12 November 2008 - 03:26 PM

Please, post a valid link


Deadlock, the link puts an unnecessary ")" at the end of the URL. Remove this and refresh and you'll get to the paper.

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Posted 12 November 2008 - 03:32 PM

What do mean ? Homology in phenotype is not equal homology in genotype ?

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Yes (assuming you mean what I think you mean).

The gist of it is this: you can have lots of genetic changes but these changes might not have a big affect on the phenotype. On the other hand, you can have a single mutation that causes a big change in the phenotype.




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