Jump to content


Photo

The Long Term Evolution Experiment ( Ltee )


  • Please log in to reply
85 replies to this topic

#21 Guest_shpongle_*

Guest_shpongle_*
  • Guests

Posted 12 November 2008 - 03:52 PM

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.


Here is the link again: http://www.pubmedcen...cgi?artid=14717

And it's disingenuous to automatically dismiss a paper before you've even read it.

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


From the Nature paper: http://www.nature.co...ature04072.html

On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total 90 Mb. This difference corresponds to 3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies63, 64, 65, 66, 67. Of course, the number of indel events is far fewer than the number of substitution events (5 million compared with 35 million, respectively).

It looks like indel events occur at 14% the rate of substitutions (5 million versus 35 million). The reason they cause more differences is due to the fact that they affect more base pairs. I.e., a substitution will affect 1 base pair, but a single indel could affect many base pairs.

#22 BVZ

BVZ

    Junior Member

  • Advanced member
  • PipPip
  • 98 posts
  • Age: 27
  • Christian
  • Theistic Evolutionist
  • South Africa

Posted 12 November 2008 - 10:39 PM

Yes


Okay.

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?


No. Using beneficial mutations ONLY when doing the calculation you did in the OP will increase the time dramatically. Including ALL mutations in the calculations will decrease the time dramatically.We know that beneficial mutations are much rarer than neutral ones. So excluding the fixation rates of neutral and even deleterous mutations from your calculation seems like a baseless thing to do.

I dont have to divide by 2 because we dont know the proportion that the mutations acumulated in each lineage.


Actually I agee with you. The value we will have to divide by will not be EXACTLY two. I don't know enough to tell you how this value could be estimated. Others on this board might know.

Either way, the value will most definitely NOT be 1.

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.


Okay. It's a start.

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

View Post


The value WILL decrease from 32 billion years a a mich lower number.

The mutation fixation rate in chimps, as well as the mutation fixation rate in humans since the common ancestor between the two determine the divergence between the two.

Lets take the common ancestor as the baseline, with 0 divergence.

If chimps alive today have X mutations in thier DNA that the common ancestor did not have, and humans alive today have Y mutations in thier DNA that the common ancestor did not have, then the divergence between chimps and humans today, will be X+Y.

So, if you want to calculate how long ago the common ancestor existed, you take X and divide it with the mutation fixation rate of chimps (dX), or you take Y and divide it by the mutation fixation rate in humans (dY).

Both should give you the same value.

Now, the trick is to figure out what dX or dY is.

It is important to realise that both contain the fixation rate of ALL mutations, not just beneficial ones.

For argument sake, dX might have a consistency like this: 1% beneficial, 0.1 deleterous, and 98.9% neutral.

If you ONLY use the beneficial muttions in the calculation, dX will have a MUCH lower value. And remember, since you are dividing by dX, the lower dX, the higher your result will be.

Which is why you got such a high result. Does this explain why including other types of mutations (neutral and deleterous) decreses the result of you calculation?

#23 Guest_shpongle_*

Guest_shpongle_*
  • Guests

Posted 13 November 2008 - 12:13 AM

I thought I'd just post some more from the paper "Initial sequence of the chimpanzee genome and comparison with the human genome": http://www.nature.co...ature04072.html

First the abstract:

Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.

(emphasis mine)

Some key points:

Genotype vs phenotype:

Genetic basis for human- and chimpanzee-specific biology

Given the substantial number of neutral mutations, only a small subset of the observed gene differences is likely to be responsible for the key phenotypic changes in morphology, physiology and behavioural complexity between humans and chimpanzees.


...

As a result, the extent of phenotypic variation between organisms is not strictly related to the degree of sequence variation. For example, gross phenotypic variation between human and chimpanzee is much greater than between the mouse species Mus musculus and Mus spretus, although the sequence difference in the two cases is similar. On the other hand, dogs show considerable phenotypic variation despite having little overall sequence variation (0.15%). Genomic comparison markedly narrows the search for the functionally important differences between species, but specific biological insights will be needed to sift the still-large list of candidates to separate adaptive changes from neutral background.


Deleterious mutation fixation in human populations:

Our comparative analysis suggests that the patterns of molecular evolution in the hominids are typical of a broader class of mammals in many ways, but distinctive in certain respects. As with the murids, the most rapidly evolving gene families are those involved in reproduction and host defence. In contrast to the murids, however, hominids appear to experience substantially weaker negative selection; this probably reflects their smaller population size. Consequently, hominids accumulate deleterious mutations that would be eliminated by purifying selection in murids. This may be both an advantage and a disadvantage. Although decreased purifying selection may tend to erode overall fitness, it may also allow hominids to 'explore' larger regions of the fitness landscape and thereby achieve evolutionary adaptations that can only be reached by passing through intermediate states of inferior fitness149, 150.

(emphasis mine)

Basically, I just wanted to reinforce what was said earlier about most divergence being neutral, some being deleterious, and the fact that small changes to the genotype can significantly change the phenotype.

There's lots of good stuff in the paper about the differences between humans and chimps and evolutionary mechanisms related to that. It's a pretty technical read, however, but worth slogging through for those interested in this stuff.

#24 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 02:10 AM

Before I answer the posts it´s essencial that you both understand what fixation means.

In population genetics, fixation occurs when every individual within a population has the same allele at a particular locus. The allele, such as a single point mutation or whole gene, will be initially rare (e.g. originating in one individual), but can spread through the population by random genetic drift and/or positive selection. Once the frequency of the allele is at 100%, being possessed by each member, it is said to be "fixed" in the population. Similarly, genetic differences between taxa are said to have been fixed in each species.

You are both confusing the rate that neutral and deleterious mutations happen with the time they take to reach fixation or if they reach fixation. Although, neutral mutations are more frequent they take much longer to reach fixation because they dont have selective value.

#25 BVZ

BVZ

    Junior Member

  • Advanced member
  • PipPip
  • 98 posts
  • Age: 27
  • Christian
  • Theistic Evolutionist
  • South Africa

Posted 13 November 2008 - 02:52 AM

I know what fixation means. My post (#22) I refer to fixation a few times. Did you read this post?

#26 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 05:38 AM

I know what fixation means. My post (#22) I refer to fixation a few times. Did you read this post?

View Post


So, you must show how many mutations are neutral in the difference between man and chimps and how it will decrease the time I calculated.Please, using numbers.

#27 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 05:42 AM

I thought I'd just post some more from the paper "Initial sequence of the chimpanzee genome and comparison with the human genome": http://www.nature.co...ature04072.html

First the abstract:

(emphasis mine)

Some key points:

Genotype vs phenotype:
...
Deleterious mutation fixation in human populations:

(emphasis mine)

Basically, I just wanted to reinforce what was said earlier about most divergence being neutral, some being deleterious, and the fact that small changes to the genotype can significantly change the phenotype.

There's lots of good stuff in the paper about the differences between humans and chimps and evolutionary mechanisms related to that.  It's a pretty technical read, however, but worth slogging through for those interested in this stuff.

View Post


I want empirical evidence.Showing speculations about Human And Chimps differences assuming evolution is true is circular reasoning.I want you to show me an allele in human population that is deleterious and is shared by all the individuals of human specie.

#28 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 05:48 AM

Lets take the common ancestor as the baseline, with 0 divergence.

If chimps alive today have X mutations in thier DNA that the common ancestor did not have, and humans alive today have Y mutations in thier DNA that the common ancestor did not have, then the divergence between chimps and humans today, will be X+Y.

So, if you want to calculate how long ago the common ancestor existed, you take X and divide it with the mutation fixation rate of chimps (dX), or you take Y and divide it by the mutation fixation rate in humans (dY).

Both should give you the same value.

Now, the trick is to figure out what dX or dY is.


You are making a simple logic mistake here.We dont have the genetic code of the common ancestor to calculate X and Y.What we have are the genetic codes of humans and chimps.When we find a difference between humans and chimps, it´s counted as one difference, not two differences.So, it´s not necessary to divide the number of differences by 2.

#29 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 05:57 AM

It is important to realise that both contain the fixation rate of ALL mutations, not just beneficial ones.

For argument sake, dX might have a consistency like this: 1% beneficial, 0.1 deleterous, and 98.9% neutral.


Please, show from where you took these numbers.

If you ONLY use the beneficial muttions in the calculation, dX will have a MUCH lower value. And remember, since you are dividing by dX, the lower dX, the higher your result will be.

Which is why you got such a high result. Does this explain why including other types of mutations (neutral and deleterous) decreses the result of you calculation?


No.The fixation rate of neutral mutations is equal to neutral mutations rate, because neutral mutations dont have selective value.So, if all mutations were neutral the fixation rate would be 10^-10.So, each neutral mutation would have to happen 10^10 times to reach fixation.It will increase my calculation.

#30 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 06:26 AM

http://www.nature.co...ature04072.html

On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total 90 Mb. This difference corresponds to 3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies63, 64, 65, 66, 67. Of course, the number of indel events is far fewer than the number of substitution events (5 million compared with 35 million, respectively).

It looks like indel events occur at 14% the rate of substitutions (5 million versus 35 million).  The reason they cause more differences is due to the fact that they affect more base pairs.  I.e., a substitution will affect 1 base pair, but a single indel could affect many base pairs.

View Post


Ok, We can use 40 millions instead of 120 millions, let´s see it :

( 40 * 10^6 ) / 10^3 ) * 30 * 10^3 = 12 * 10^8 generations.In years terms it would be : 12 * 10^8 * 20 = 24 billions of years.

Not so Good for evolution.

#31 MRC_Hans

MRC_Hans

    Member

  • Banned
  • PipPipPip
  • 576 posts
  • Age: 59
  • no affiliation
  • Agnostic
  • Denmark

Posted 13 November 2008 - 06:57 AM

Ok, We can use 40 millions instead of 120 millions, let´s see it :

( 40 * 10^6 ) / 10^3 ) * 30 * 10^3 = 12 * 10^8 generations.In years terms it would be : 12 * 10^8 * 20 = 24 billions of years.

Not so Good for evolution.

View Post

The formula assumes that events take place in series. That is, obviously, wrong. In a population of, say, a million individuals, in principle a million events can take place at the same time (same generation).

Hans

#32 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 07:12 AM

The formula assumes that events take place in series. That is, obviously, wrong. In a population of, say, a million individuals, in principle a million events can take place at the same time (same generation).

Hans

View Post


No, it doesnt. The calculation is based on the experience made with E.Coli for 30 years.Go to the beginning of the thread and you´ll see it.

#33 Guest_shpongle_*

Guest_shpongle_*
  • Guests

Posted 13 November 2008 - 08:43 AM

I want empirical evidence.Showing speculations about Human And Chimps differences assuming evolution is true is circular reasoning.I want you to show me an allele in human population that is deleterious and is shared by all the individuals of human specie.


This isn't speculation, these are the actual differences based on genetic analysis. If you are going to talk about human-chimp evolution, the crux of it is analysing the differences between the two species to determine how they differ. Only then can you actually say anything about how they evolved. Ignoring this isn't helping your position.

#34 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 08:55 AM

Here is the link again: http://www.pubmedcen...cgi?artid=14717

And it's disingenuous to automatically dismiss a paper before you've even read it. 


The mistake in this paper is how they identify beneficial mutations :

"Determination of Fitness Parameter m. The Malthusian fitness parameter m can be determined from the frequency increase of the carrier of the advantageous mutation "

It´s a flawed assumption.If you look at Green eye allele you´ll see it has low frequency compared to black eye or brown eye.Using their reasoning, black eye or Brown eye are beneficial mutations.I have green eyes and I can assure you it´s not disadvantageous.

Despite of that, the paper only confirms what I´m saying.They got the rate of 4 beneficial mutations for every 1 billion individuals.So, it means that 1.000 beneficial mutations need 250 billions of births.

#35 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 13 November 2008 - 08:58 AM

This isn't speculation, these are the actual differences based on genetic analysis.  If you are going to talk about human-chimp evolution, the crux of it is analysing the differences between the two species to determine how they differ.  Only then can you actually say anything about how they evolved.  Ignoring this isn't helping your position.

View Post


They are speculating what is and what is not deleterious mutations comparing the human and chimps genomes, assuming they have a common ancestor.First, you must prove that deleterious mutations can be fixed in a population, using real deleterious mutations, not supposed deleterious mutations.

#36 Guest_shpongle_*

Guest_shpongle_*
  • Guests

Posted 13 November 2008 - 09:22 AM

Before I answer the posts it´s essencial that you both understand what fixation means.

In population genetics, fixation occurs when every individual within a population has the same allele at a particular locus. The allele, such as a single point mutation or whole gene, will be initially rare (e.g. originating in one individual), but can spread through the population by random genetic drift and/or positive selection. Once the frequency of the allele is at 100%, being possessed by each member, it is said to be "fixed" in the population. Similarly, genetic differences between taxa are said to have been fixed in each species.

You are both confusing the rate that neutral and deleterious mutations happen with the time they take to reach fixation or if they reach fixation. Although, neutral mutations are more frequent they take much longer to reach fixation because they dont have selective value.

View Post


I understand perfectly well what fixation means. I don't see how it's relevant, however, since we we're not talking about which genetic differences become fixed. We're just talking about the gross differences between genomes.

For example, using the mutation rate from the blog you linked earlier, it pegs the rate of mutations at ~130 substitutions (single nucleotide) per person per generation. Assuming 5 million years of evolution with a mean generation time of 20 years, that means we have 250 000 generations. Assuming strictly neutral evolution, therefore the net accumulated difference from the ancestor to a current individual is going to be just 130x250000 = 32.5 million base pairs.

And if I want to double check this with data from another paper on mutation rates in mammalian genomes I can: http://www.pnas.org/...t/99/2/803.full

In this paper, they compute the average neutral mutation rate to be 2.22x10^-9 substitutions per site per year. Note that this is based on a different unit measure (annual as opposed to generational). Based on the size of the genome (3 billion base pairs) times the rate (2.22x10^-9) times the distance (5 million years), yields a net accumulated difference from the ancestral population of 33.3 million base pairs. How about that?

Furthermore, we don't care which differences are accumulated. Indeed, if the population averages at 100,000 individuals, that means there are a total of 3.25 trillion possible mutations that could have occurred. But the majority of them get weeded out through random genetic drift.

Now this rate is only based on point substitutions. Indels play a huge role in genetic difference (from the Nature paper, 3% of difference from indels vs ~1.2% from point mutations). So this 32.5 million base pairs of substitutions, assuming the same proportion of difference would translate into an additional 114 million base pairs worth of differences.

So now we are at ~146 million base pairs. The net size of the human genome is 3 billion base pairs, so this means the net accumulate differences would be 4.8% from the original ancestor. This is obviously very high for just the human lineage (it implies a net difference of 9.6% between two populations), so obviously there is more to the story (i.e. purifying selection eliminating differences).

But the bottom line is that mutation rates are not an issue for evolution of differences between humans and chimps.

#37 Guest_shpongle_*

Guest_shpongle_*
  • Guests

Posted 13 November 2008 - 09:29 AM

The mistake in this paper is how they identify beneficial mutations :

"Determination of Fitness Parameter m. The Malthusian fitness parameter m can be determined from the frequency increase of the carrier of the advantageous mutation "

It´s a flawed assumption.If you look at Green eye allele you´ll see it has low frequency compared to black eye or brown eye.Using their reasoning, black eye or Brown eye are beneficial mutations.I have green eyes and I can assure you it´s not disadvantageous.

Despite of that, the paper only confirms what I´m saying.They got the rate of 4 beneficial mutations for every 1 billion individuals.So, it means that 1.000 beneficial mutations need 250 billions of births.

View Post


It's not based on frequency. It's based on a statistically significant change in frequency. Basically they are measuring selective sweeps of alleles in the population. That's a key difference in understanding of what they are doing.

Something else I should probably point out is that the rate is based on cell division. In the case of E.coli, they undergo a single cell division when reproducing. But in the case of humans, human gametes undergo more than just 1 cell division. In fact, the blog you referenced talks about this. So you can't do a straight up comparison in rates between E.coli and humans without taking that into account. Just FYI.

#38 Guest_shpongle_*

Guest_shpongle_*
  • Guests

Posted 13 November 2008 - 09:36 AM

They are speculating what is and what is not deleterious mutations comparing the human and chimps genomes, assuming they have a common ancestor.First, you must prove that deleterious mutations can be fixed in a population, using real deleterious mutations, not supposed deleterious mutations.

View Post


Again, it's not speculation. Do you understand how they are coming up with that? If not, I can try to explain it for you.

#39 Springer

Springer

    Member

  • Veteran Member
  • PipPipPip
  • 961 posts
  • Age: 53
  • no affiliation
  • Creationist
  • Kalamazoo, MI

Posted 13 November 2008 - 07:03 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.

View Post

I've been waiting for a long time for someone to demonstrate using mathematics how a 4% divergence could be acheived at that mutation rate. We're talking about millions of just the right mutations, resulting in an onward and upward progression, i.e., human intelligence, among other things. I would very much appreciate it if you could show the math that demonstrates that this is possible.

#40 Guest_shpongle_*

Guest_shpongle_*
  • Guests

Posted 13 November 2008 - 08:57 PM

I've been waiting for a long time for someone to demonstrate using mathematics how a 4% divergence could be acheived at that mutation rate.  We're talking about millions of just the right mutations, resulting in an onward and upward progression, i.e., human intelligence, among other things.  I would very much appreciate it if you could show the math that demonstrates that this is possible.

View Post


I'll crunch some numbers, but first I want to clarify a few things:

First, to reiterate the point from the Nature paper on human-chimp genomics I quoted ealier: "we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles". So this notion that it's all about beneficial mutations and nothing else is a wrong way of looking at it. Most of the variation between genomes is not beneficial; indeed most is neutral change.

Second, I already pointed out that mutation rates are not a problem with respect to raw divergence. The question becomes how many beneficial mutations do we truly need. And the truth is the answer is arguably up for debate. We can estimate but we don't really know. Maybe it's only 10,000, maybe 20,000, maybe 100,000. I'll get back to this in a moment.

Third point, the rate from that paper is based on a single experiment involving a single species and single methodology. The authors include a caveat that it may be an underestimate based on the fact they can't necessarily identify every single possible beneficial mutation. So I'd take the number with a grain of salt.

Anyway, onto the calculations:

The rate is given at 4x10^-9 per cell per generation. Human gametes have mutiple cell generations (~30 for female and 400 for male). So the rates of mutation in human gametes are 1.2 × 10^-7 for female (eggs) and 1.6 × 10^-6 for males (sperm). Therefore, the combined rate is 1.72x10^-6.

In a steady population of, oh, 100,000 individuals there will be approximately 0.172 beneficial mutations per generation. This translates to a new benefical mutation every ~5.8 generations or 116 years. Over 5 Mya of evolution between human and chimps, this means approximately 43 thousand beneficial mutations could occur.

I did some quick searching and came across another paper, Positive and Negative Selection on the Human Genome: http://www.genetics....full/158/3/1227

They looked at the makeup of the genome and estimated a rate of 1 advantageous substitution every 200 years:

The large number of amino acid substitutions suggests a high rate of adaptive evolution in primates. The expected number of amino acid substitutions is 2382 (4151 x 70/122) based on the A/S ratio of common polymorphism and the excess is 1278. Therefore, a large proportion, 35%, of amino acid substitutions between humans and old world monkeys are estimated to have been driven by positive selection. Extrapolating this proportion to the total amount of coding DNA in the genome (5 x 10^7 bp) yields an estimate of up to 1 advantageous substitution every 200 years since humans separated from old world monkeys 30 million years ago


Based on their rate, we'd be looking at 25 thousand beneficial mutations in the 5 million years of divergence time between humans and chimps. So the number I crunched is at least ballpark with respect to the number in this paper. The exact right answer though is unknown since all of this is just different ways of estimating it. So far, based on everything I've read about human evolution and the divergence between humans and chimps, I've yet to see anything that would suggest that current mutation rates are a problem.




0 user(s) are reading this topic

0 members, 0 guests, 0 anonymous users