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Thread: Humans diverged from chimps, when and how?

  1. #1 Humans diverged from chimps, when and how? 
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    If the claim that Humans and chimps share a common ancestor there must be evidence of that assertion in the genome of both species. This evidence must be discernible and investigable. I do not pretend that any examination here could be exhaustive but there are critical peer reviewed papers that do shed insight into the science of human common descent.


    First issue is to resolve the controversy of actual genome similarities between humans and chimps. A revised assessment of between 70 and 95% has been suggested. (citation on demand)


    First question is how does a downward assessment of similarity affect the chimp human divergence date? Another direct factor is mutation rates in humans and chimps. This also has suffered a reduction by direct empirical measurement.


    How does the layman sort through all the obscuration. Since it is hard to find a paper dealing with both issues of mutation rate and human chimp similarity, I would suggest a paper. I found it included all the variables necessary to calculate a divergence time:


    http://www.genetics.org/content/156/1/297.full


    The original paper was used to calculate a reasonable mutation rate before it was directly measured. Since we now know the actual mutation rate and human chimp similarity we can solve for a new divergence time in terms of number of generations.


    t= number of generations since divergence (Generation =20 years)
    k= percentage of sequence divergence Estimated at 5%
    Ne= effective size of population ~10^4
    (u)=mutation rate 1.1 x 10^-8


    t= .5(k/u-4Ne) from Estimate of the Mutation Rate per Nucleotide in Humans


    Given the values above the divergence in years I calculated: 45 million years


    I went back and verified that values used by the authors of the peer reviewed paper could solve for divergence time, as they found it. Values found on:


    http://www.genetics.org/content/156/1/297/T3.expansion.html


    I verified that no problems presented themselves. The two authors are accepted authorities in evolution science… dispute it with them.


    Michael W. Nachman Susan L. Crowell



    Last edited by GTCethos; September 30th, 2014 at 07:22 PM.
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    Hello!!!

    Try to read this paper... is very long but it is a comparision of human and chimp genome and it talks about divergence rates... Though I don´t know if it is the divergence rates you are interested in.

    Initial sequence of the chimpanzee genome and comparison with the human genome : Article : Nature

    bye


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    I hope it is… The conclusion in the abstract says 175 mutations per generation. This number appears in numerous subsequent papers.
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    Interesting, I had a conversation with one of the authors of that paper…
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    Quote Originally Posted by GTCethos View Post



    Interesting, I had a conversation with one of the authors of that paper…
    Wow.. that´s cool...
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    Quote Originally Posted by M_Gabriela View Post
    Quote Originally Posted by GTCethos View Post



    Interesting, I had a conversation with one of the authors of that paper…


    Wow.. that´s cool...
    Yes… but it yielded no satisfaction….
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    t= number of generations since divergence (Generation =20 years)
    k= percentage of sequence divergence Estimated at 5%
    Ne= effective size of population ~10^4
    (u)=mutation rate 1.1 x 10^-8


    t= .5(k/u-4Ne) from Estimate of the Mutation Rate per Nucleotide in Humans
    Common ancestor generation time could be lower than 20 years??

    Who or how is sequence divergence estimated?

    Ne (effective population size) what happens if that is varied down to 10^3 instead of 10^4?
    Is your formula written right? (It seems to be a correct rearrangement of the one in the paper. )

    t= .5(k/u-4Ne)
    Why did you use such a high k value, you're using 0.05 yet they are using 0.0133?
    Last edited by Robittybob1; October 1st, 2014 at 03:00 PM. Reason: clarity
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    Common ancestor generation time lower than 20 years


    This is a common estimate for average generation time of humans…

    Who or how is sequence divergence estimated?


    “Using data available from whole genome sequencing, the human genome mutation rate is similarly estimated to be ~1.1×10−8 per site per generation.[7]” https://en.wikipedia.org/wiki/Mutation_rate#Measurement

    Ne (effective population size) what happens if that is varied down to 10^3 instead of 10^4?


    The amazing thing here is “how come it is so small”? The answer stems from the relative similarity of all humanity.


    Is you formula written right? It seems to be a rearrangement of the one in the paper.



    a simple algebraic rearrangement…


    t= .5(k/u-4Ne)
    Why did you use such a high k value, you're using 0.05 yet they are using 0.0133?


    The 95% similarity or 5% difference comes from here:


    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129726/

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    Quick question…


    Can Paleoanthropology accommodate 45 million years since divergence?

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    What controversies in the genetics?

    And What are your calculations based on?
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    Quote Originally Posted by GTCethos View Post
    Common ancestor generation time lower than 20 years


    This is a common estimate for average generation time of humans…

    Who or how is sequence divergence estimated?


    “Using data available from whole genome sequencing, the human genome mutation rate is similarly estimated to be ~1.1×10−8 per site per generation.[7]” https://en.wikipedia.org/wiki/Mutation_rate#Measurement

    Ne (effective population size) what happens if that is varied down to 10^3 instead of 10^4?


    The amazing thing here is “how come it is so small”? The answer stems from the relative similarity of all humanity.


    Is you formula written right? It seems to be a rearrangement of the one in the paper.



    a simple algebraic rearrangement…


    t= .5(k/u-4Ne)
    Why did you use such a high k value, you're using 0.05 yet they are using 0.0133?


    The 95% similarity or 5% difference comes from here:


    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129726/

    Look if the common ancestor had a generation time of 10 years and if that generation only gradually increased over the millions of years will that make any difference? What is the generation time for chimps? Do you think the common ancestor generation time would reflect this.
    [IMO I think it is only in the last million years that human generation time has extended out to 20 years. Longer infant time slower development allows for brain growth.]
    "Effective population size" that isn't saying that was the "population size in total" is it?
    Can you explain why one estimate of divergence is 0.05 and the other 0.0133?
    Last edited by Robittybob1; October 1st, 2014 at 03:03 PM. Reason: clarity
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    Quote Originally Posted by GTCethos View Post
    Quick question…


    Can Paleoanthropology accommodate 45 million years since divergence?

    I would say so, the further you go back the more divergence. If you take a bigger divergence you need a longer time to get those changes.
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    OK I looked at the abstract of the next paper Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels
    Five chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best matching regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels. The gaps in alignment are present in about equal amounts in the chimp and human sequences. They occur equally in repeated and nonrepeated sequences, as detected by repeatmasker(http://ftp.genome.washington.edu/RM/RepeatMasker.html).
    So the difference between the two rates is explained by this statement if you know what "indels" means tell me for I don't.
    " the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels."
    Obviously "indels" has something to do with this clue "These groups did not compute the insertion/deletion contribution to divergence."

    and more
    This is an observation of the major way in which the genomes of closely related primates diverge—by insertion/deletion. More nucleotides are included in insertion/deletion events (3.4%) than base substitutions (1.4%) by much more than a factor of two. However, the number of events is small in comparison. About 1,000 indels listed in Tables Tables22 and and33 compared with about 10,000 base substitution events in this comparison of 779,142 nt between chimp and human. Little can be said about the effect of these indel events.
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    So I'd say you are not comparing apples with apples.
    You can't take a formula used to calculate time based on one type of divergence and apply it to the other type which includes the indels.
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    So the difference between the two rates is explained by this statement if you know what "indels" means tell me for I don't.
    " the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels."
    Obviously "indels" has something to do with this clue



    Indels are short for insertions and deletions. Most assuredly this is mutation. There are other mutations not counted by human and chimp differences in DNA. The majority of differences between the two genomes is in regions called regulatory or non-coding segments. If these segments were counted the genome comparison between humans and chimps could be as low as 70%.



    It is important to know that a human “scaffold” is first set up then the chimp genome is aligned to it. Alignment tools (like BLAST) are applied to identify sequences between gaps and non similar segments. It also might be noted here that about 700 million base pair of the chimp genome did not even align to the human scaffold. That would be about 21% of the genome. Who knows if these segments actually perform a function or not.

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    "Effective population size" isn't saying that was the "population in total" is it?
    Can you explain why one is 0.05 and the other 0.0133?



    Effective population size is a statistical evaluation. I could be wrong but I look at like this… say a population has an “effective population of 10,000’” in a global population of 7 billion. It means that 10,000 randomly chosen individuals would represent the total genetic diversity of the 7 billion individuals.




    Simply the .05 is 5% different and .0133 is 1.33% different between the two genomes….
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    Quote Originally Posted by GTCethos View Post
    So the difference between the two rates is explained by this statement if you know what "indels" means tell me for I don't.
    " the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels."
    Obviously "indels" has something to do with this clue



    Indels are short for insertions and deletions. Most assuredly this is mutation. There are other mutations not counted by human and chimp differences in DNA. The majority of differences between the two genomes is in regions called regulatory or non-coding segments. If these segments were counted the genome comparison between humans and chimps could be as low as 70%.



    It is important to know that a human “scaffold” is first set up then the chimp genome is aligned to it. Alignment tools (like BLAST) are applied to identify sequences between gaps and non similar segments. It also might be noted here that about 700 million base pair of the chimp genome did not even align to the human scaffold. That would be about 21% of the genome. Who knows if these segments actually perform a function or not.

    Obviously IMO this shows that when they are talking about mutation rates they are not talking about indels. Where did that "about 700 million base pair of the chimp genome did not even align to the human scaffold. That would be about 21% of the genome." come from?
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    Quote Originally Posted by GTCethos View Post
    "Effective population size" isn't saying that was the "population in total" is it?
    Can you explain why one is 0.05 and the other 0.0133?


    Effective population size is a statistical evaluation. I could be wrong but I look at like this… say a population has an “effective population of 10,000’” in a global population of 7 billion. It means that 10,000 randomly chosen individuals would represent the total genetic diversity of the 7 billion individuals.




    Simply the .05 is 5% different and .0133 is 1.33% different between the two genomes….
    It would be even better for both of us try and find the actual definition of "effective population".
    Quote Originally Posted by wikipedia
    In population genetics, the concept of effective population sizeNe was introduced by the AmericangeneticistSewall Wright.[1][2] He defined it as "the number of breeding individuals in an idealised population that would show the same amount of dispersion of allele frequencies under random genetic drift or the same amount of inbreeding as the population under consideration". More generally, an effective population size may be defined as the number of individuals in an idealised population that has a value of any given population genetic quantity that is equal to the value of that quantity in the population of interest. The two population genetic quantities identified by Wright were the one-generation increase in variance across replicate populations (variance effective population size) and the one-generation change in the inbreeding coefficient (inbreeding effective population size). These two are closely linked, and derived from F-statistics, but they are not identical.[3]Today, the effective population size is usually estimated empirically with respect to the sojourn or coalescence time, estimated as the within-species genetic diversitydivided by the mutation rate.[4] Another important effective population size is the selection effective population size 1/scritical, where scritical is the critical value of theselection coefficient at which selection becomes more important than genetic drift.[5]
    However defined, the effective population size is usually less than the census population size (N).
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    GTCethos, are you Zaius137 on Christianforums.com? If not, I think it a little disingenuous to recycle and pass off that users posts as your own.
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    I never plagiarize anyones posts. Where you posting on that forum?
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    So you are Zaius137 then?
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    "Effective population size" isn't saying that was the "population in total" is it?
    Can you explain why one is 0.05 and the other 0.0133?


    Effective population size is a statistical evaluation. I could be wrong but I look at like this… say a population has an “effective population of 10,000’” in a global population of 7 billion. It means that 10,000 randomly chosen individuals would represent the total genetic diversity of the 7 billion individuals.




    Simply the .05 is 5% different and .0133 is 1.33% different between the two genomes….
    It would be even better for both of us try and find the actual definition of "effective population".
    Quote Originally Posted by wikipedia
    In population genetics, the concept of effective population sizeNe was introduced by the AmericangeneticistSewall Wright.[1][2] He defined it as "the number of breeding individuals in an idealised population that would show the same amount of dispersion of allele frequencies under random genetic drift or the same amount of inbreeding as the population under consideration". More generally, an effective population size may be defined as the number of individuals in an idealised population that has a value of any given population genetic quantity that is equal to the value of that quantity in the population of interest. The two population genetic quantities identified by Wright were the one-generation increase in variance across replicate populations (variance effective population size) and the one-generation change in the inbreeding coefficient (inbreeding effective population size). These two are closely linked, and derived from F-statistics, but they are not identical.[3]Today, the effective population size is usually estimated empirically with respect to the sojourn or coalescence time, estimated as the within-species genetic diversitydivided by the mutation rate.[4] Another important effective population size is the selection effective population size 1/scritical, where scritical is the critical value of theselection coefficient at which selection becomes more important than genetic drift.[5]
    However defined, the effective population size is usually less than the census population size (N).
    You see why I was unsure about “effective population” can you decipher that definition…
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    Quote Originally Posted by Zwirko View Post
    So you are Zaius137 then?
    You answer my question and I will answer yours. By the way what avatar did you post under? That is a precious frog by the way.
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    Quick question…


    Can Paleoanthropology accommodate 45 million years since divergence?

    I would say so, the further you go back the more divergence. If you take a bigger divergence you need a longer time to get those changes.
    What ancestor of man has definitively been identified 45 million years ago. Simply show me the proposed ancestor…

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    Quote Originally Posted by GTCethos View Post
    You see why I was unsure about “effective population” can you decipher that definition…
    No; not without a lot of thought.
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    Quote Originally Posted by GTCethos View Post
    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    Quick question…


    Can Paleoanthropology accommodate 45 million years since divergence?

    I would say so, the further you go back the more divergence. If you take a bigger divergence you need a longer time to get those changes.
    What ancestor of man has definitively been identified 45 million years ago. Simply show me the proposed ancestor…

    There wasn't that much divergence in the first place. Your calculations were based on a different analysis. No one can be sure what our ancestor was. They would certainly put up suggestions. But you can't get DNA to check it out.
    So you want a definite ancestor but also one that is proposed, so make up your mind, what do you want?
    There are definitely no human fossils that are 45 million years ago but there were other primate type fossils weren't there.
    So it will be from one of them, or else what do you propose?
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    Quick question…


    Can Paleoanthropology accommodate 45 million years since divergence?

    I would say so, the further you go back the more divergence. If you take a bigger divergence you need a longer time to get those changes.
    What ancestor of man has definitively been identified 45 million years ago. Simply show me the proposed ancestor…

    There wasn't that much divergence in the first place. Your calculations were based on a different analysis. No one can be sure what our ancestor was. They would certainly put up suggestions. But you can't get DNA to check it out.
    So you want a definite ancestor but also one that is proposed, so make up your mind, what do you want?
    There are definitely no human fossils that are 45 million years ago but there were other primate type fossils weren't there.
    So it will be from one of them, or else what do you propose?
    They would certainly put up suggestions. But you can't get DNA to check it out.



    We have the DNA… remember this ancestor had the same DNA as we do, albeit modified in accordance with the evolution paradigm.


    As for my suggestion about the validity of the calculation, that is for you to discredit. You can simply tell me you do not accept it and I will honor your opinion…
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    Quote Originally Posted by GTCethos View Post


    We have the DNA… remember this ancestor had the same DNA as we do, albeit modified in accordance with the evolution paradigm.

    As for my suggestion about the validity of the calculation, that is for you to discredit. You can simply tell me you do not accept it and I will honor your opinion…
    Of course it has NOT got the same DNA as we do. How you be so unscientific for if we had the same DNA as them we would look like them or they would look like us.
    Well there animals that look something like us, so we can be certain they are probable ancestors.
    Well make it known you are confusing the situation by using two methods of calculating divergence, but using only to formula based on one type of divergence.
    Your arguments seem to be mischievous.
    Last edited by Robittybob1; October 1st, 2014 at 11:59 AM.
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post


    We have the DNA… remember this ancestor had the same DNA as we do, albeit modified in accordance with the evolution paradigm.

    As for my suggestion about the validity of the calculation, that is for you to discredit. You can simply tell me you do not accept it and I will honor your opinion…
    Of course it has got the same DNA as we do. How you be so unscientific for if we had the same DNA as them we would look like them or they would look like us.
    Well there animals that look something like us, so we can be certain they are probable ancestors.
    Well make it known you are confusing the situation by using two methods of calculating divergence, but using only to formula based on one type of divergence.
    Your arguments seem to be mischievous.
    Your arguments seem to be mischievous.



    Not at all. I am only using peer reviewed material to bring up inconsistencies in accepted evolution paradigm. Now if my dissent to common descent is irrational, by all means give me a scientific rebuke.
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    Quote Originally Posted by GTCethos View Post
    ... Not at all. I am only using peer reviewed material to bring up inconsistencies in accepted evolution paradigm. Now if my dissent to common descent is irrational, by all means give me a scientific rebuke.
    You were using peer reviewed material but confusing the estimates of divergence.
    The formula was based on divergence of base pairs not indels, yet you used the indels containing divergence to get the 45 million year figure, so your method was mischievous.
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    You were using peer reviewed material but confusing the estimates of divergence.
    The formula was based on divergence of base pairs not indels, yet you used the indels containing divergence to get the 45 million year figure, so your method was mischievous.


    I did not produce the paper questioning the percentage of similarity between humans and chimps. These are simply new findings from the original sequencing of the human and chimp genome.


    My only contribution here is to apply a calculation from a peer reviewed paper to produce a controversial result. There is other objections to the accepted span of common descent. These can be found on the web from authorities in the field.


    You seem like a inquisitive person, do not accept my argument or any one else’s. Do the foot work yourself.
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    GTCethos,

    plug the numbers you used back into the original equation that "you" rearranged. Let me know if you notice anything odd.
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    Quote Originally Posted by GTCethos View Post
    ...You seem like a inquisitive person, do not accept my argument or any one else’s. Do the foot work yourself.
    I am showing the forum that you are trying to confuse them.
    Do you accept that you used a formula designed to calculate time using base pair changes but plug in a figure for divergence based on base pair changes and (plus) endels?
    Last edited by Robittybob1; October 1st, 2014 at 01:33 PM.
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    Quote Originally Posted by Zwirko View Post
    GTCethos,

    plug the numbers you used back into the original equation that "you" rearranged. Let me know if you notice anything odd.
    Define the values you are using please?
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    I think I lost in the first 4 posts... hahaha
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    Quote Originally Posted by Robittybob1 View Post
    Define the values you are using please?
    I think he takes this formula: and rearranges to this: . If not, then I've no idea. I'm not too hot at maths, but I don't get that equation when making the subject. Maybe it is?

    Values he used were:

    = number of generations since divergence (Generation =20 years)
    = percentage of sequence divergence Estimated at 5%
    = effective size of population ~10^4
    =mutation rate 1.1 x 10^-8
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    GTCethos, all available evidence from the fossil record and genetic analysis points to a divergence between man and chimp from 5 to 10 million years ago
    you edit an equation and fill it with estimates of your own and come up with a vastly different value of 45 million years

    now tell me, just on the basis of probabilities : that the whole anthropology / geology / genetics fields have conjured to come up with the same wrong answer, or that it is you who made a mistake

    until i get stronger evidence that you have a real case to make, i'll have to assume that on the basis of probabilities it's you who's wrong and not a large portion of the scientific community

    remember, extraordinary claims must be backed up by extraordinarily strong evidence - a back-of-the fag-packet calculation does imo not make the grade
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    ok, here's your answer : you've decided to use a value for k of 0.05 instead of 0.013 as set out in the paper
    also you set the value for µ as 1.1 10^-8 whereas the graph in the paper (see below) clearly shows that for a population size Ne of 10,000 your value for µ should be 2.5 10^-8



    now if i pop your values in your equation then i get 45,054,545 years, whereas if i use the values from article i get 4,800,000 years

    QED
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    you edit an equation and fill it with estimates of your own and come up with a vastly different value of 45 million years



    I hope you can appreciate the vast problem that a downgrade in human chimp similarity has had on evolution. That is just half the issue, there is empirical evidence that only about half the needed mutations are measured between generations in humans. That issue is to fulfill the predictions of evolutionists (actually from the equation I rearranged).

    I acknowledge the unusual usage of that paper, but I have still not received any credible argument about it. I have objections myself but have not been able to verify them, your help in this area would be welcome. No I am not going to help you out with an argument....
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    ok, here's your answer : you've decided to use a value for k of 0.05 instead of 0.013 as set out in the paper
    also you set the value for µ as 1.1 10^-8 whereas the graph in the paper (see below) clearly shows that for a population size Ne of 10,000 your value for µ should be 2.5 10^-8



    The entire point is that chimp human similarity is downgraded to 95% and that average mutation rate in humans per generation is half the value used by the authors.
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    Quote Originally Posted by GTCethos View Post
    The entire point is that chimp human similarity is downgraded to 95% and that average mutation rate in humans per generation is half the value used by the authors.
    says who ?
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    Quote Originally Posted by marnixR View Post
    ok, here's your answer : you've decided to use a value for k of 0.05 instead of 0.013 as set out in the paper
    also you set the value for µ as 1.1 10^-8 whereas the graph in the paper (see below) clearly shows that for a population size Ne of 10,000 your value for µ should be 2.5 10^-8



    now if i pop your values in your equation then i get 45,054,545 years, whereas if i use the values from article i get 4,800,000 years

    QED
    Neither of those figures match the current concept or do they ? Read wikipedia on the Chimpanzee–human last common ancestor (CHLC) the figure jump around a lot, 4.8 - 13 mya so it is not an exact science.
    We are comparing the difference between two closely species. Would we assume the divergence is happening along both lines equally?
    I tend to the view that the Chimpanzee is more like the CHLC rather than is the human.
    So how does the Chimpanzee genes stay the same in the face of mutation? Maybe they didn't.
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    Quote Originally Posted by Robittybob1 View Post
    I tend to the view that the Chimpanzee is more like the CHLC rather than is the human.
    chimps may or may not look more like the common ancestor, we just don't have enough evidence to decide either way
    however, when it comes to genetics, the divergence would have been more or less equal along both the human and the chimp lineage since the split - that's just the nature of mutations in the vast majority of the genome, which is not expressed in the phenotype
    mutation is essentially a random walk unless directed by natural selection, and a large portion of the genome is essentially invisible to natural selection
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    Quote Originally Posted by marnixR View Post
    Quote Originally Posted by Robittybob1 View Post
    I tend to the view that the Chimpanzee is more like the CHLC rather than is the human.
    chimps may or may not look more like the common ancestor, we just don't have enough evidence to decide either way
    however, when it comes to genetics, the divergence would have been more or less equal along both the human and the chimp lineage since the split - that's just the nature of mutations in the vast majority of the genome, which is not expressed in the phenotype
    mutation is essentially a random walk unless directed by natural selection, and a large portion of the genome is essentially invisible to natural selection
    OK if the divergence is equal over the two branches and these base changes are not expressed in the phenotype, basically you end up with two groups of animals that haven't changed in appearance at all.
    The phenotypical changes are expressed in the larger divergence (the indels) pointed out by ethos. We are just looking at the base changes to estimate the time of split from the CHLCA.
    "Generation time" and "effective population" are two variables I still feel are questionable and could be different to the values we have used.
    How did they get a handle on those figures?
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    Quote Originally Posted by marnixR View Post
    Quote Originally Posted by GTCethos View Post
    The entire point is that chimp human similarity is downgraded to 95% and that average mutation rate in humans per generation is half the value used by the authors.
    says who ?
    I am sure you do not want me to give a 70% similarity number (which has been quoted). That would be overkill…


    Here is a citation for 96%… “A comparison of Clint's genetic blueprints with that of the human genome shows that our closest living relatives share 96 percent of our DNA” Chimps, Humans 96 Percent the Same, Gene Study Finds


    Also the 95% number: Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels


    Here is the figure for the 1.1 x 10^-8 mutation rate: “Using data available from whole genome sequencing, the human genome mutation rate is similarly estimated to be ~1.1×10−8 per site per generation.[7]” https://en.wikipedia.org/wiki/Mutation_rate#Measurement




    “Indels are short for insertions and deletions. Most assuredly this is mutation. There are other mutations not counted by human and chimp differences in DNA. The majority of differences between the two genomes is in regions called regulatory or non-coding segments. If these segments were counted the genome comparison between humans and chimps could be as low as 70%.




    It is important to know that a human “scaffold” is first set up then the chimp genome is aligned to it. Alignment tools (like BLAST) are applied to identify sequences between gaps and non similar segments. It also might be noted here that about 700 million base pair of the chimp genome did not even align to the human scaffold. That would be about 21% of the genome. Who knows if these segments actually perform a function or not.”



    This last part was from a previous post…
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    ”Generation time" and "effective population" are two variables I still feel are questionable and could be different to the values we have used.
    How did they get a handle on those figures?”


    If you look at the formula you notice… (-4Ne) is relatively insignificant given Ne = 10,000 or even 100k.


    I did chose the 20 year generation time because it is the smaller estimation. Humans are relatively slow reproducers.


    The authors of the article in question at one point used the 25 year generation time. That usage only gives a larger divergence year.


    By far the most affect is given by divergence percentage and mutation rate. Hence the very large divergence time with small changes in both figures.
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    Can you explain where your formula comes from? Is it a rearrangement of the formula I mentioned in #36?
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    Quote Originally Posted by GTCethos View Post
    ”Generation time" and "effective population" are two variables I still feel are questionable and could be different to the values we have used.
    How did they get a handle on those figures?”


    If you look at the formula you notice… (-4Ne) is relatively insignificant given Ne = 10,000 or even 100k.


    I did chose the 20 year generation time because it is the smaller estimation. Humans are relatively slow reproducers.


    The authors of the article in question at one point used the 25 year generation time. That usage only gives a larger divergence year.


    By far the most affect is given by divergence percentage and mutation rate. Hence the very large divergence time with small changes in both figures.
    I have set up a formulated spreadsheet so I can follow how the resulting time back to the CHLCA varies when I vary the input variables.
    Effective population is quite significant at the lower divergence rate.

    If the Orrorin are the start of the divergence and we go with their dating of around 6 million year and say the CHLCA was a million before that we need an average generation time of 12 years with an effective population of 10^4.
    What is the generation time for chimpanzees?
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    Quote Originally Posted by Robittybob1 View Post
    What is the generation time for chimpanzees?
    ~14 years.
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    Quote Originally Posted by Robittybob1 View Post
    What is the generation time for chimpanzees?
    This paper suggest 22-29 years.
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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Robittybob1 View Post
    What is the generation time for chimpanzees?
    This paper suggest 22-29 years.
    Maybe I have misunderstood how a generation is measured, but I thought it was the time between the birth of a parent to the birth of their child.

    That paper you linked takes into account "female age of first reproduction, interbirth interval, age of last reproduction, and survivorship".
    Does that make for a more accurate number?
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    I don't really understand the concept of generation time either. The wikipedia page Generation time - Wikipedia, the free encyclopedia has all sorts of nasty formulae in it.
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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Robittybob1 View Post
    What is the generation time for chimpanzees?
    This paper suggest 22-29 years.
    Is that the generation time they are really meaning?
    Chimpanzees reach puberty at an age of between eight and 10 years and rarely live past age 40 in the wild, but some have lived longer than 60 years in captivity.
    In the time period we are considering, the pressure to mate early and to have a relatively short life is a real possibility too.
    There is a difference between average age of the adults to generation isn't there?

    If the Generation time was say 14 years, as Red Panda suggested, the split would be 7 million years ago if the Effective population was 40,000 rather than 10,000.
    There are so many variables I wonder if it really can be fixed! You can certainly select variables and make it fit. In fact as Ethos does you can chose whatever figures you want and get outlandish answers.

    As the generation time increases you need to increase the size of the effective population to keep the output "years since split" the same. It makes sense to me to have a larger effective population, doesn't it?
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Robittybob1 View Post
    What is the generation time for chimpanzees?
    This paper suggest 22-29 years.
    Is that the generation time they are really meaning?
    Chimpanzees reach puberty at an age of between eight and 10 years and rarely live past age 40 in the wild, but some have lived longer than 60 years in captivity.
    In the time period we are considering, the pressure to mate early and to have a relatively short life is a real possibility too.
    There is a difference between average age of the adults to generation isn't there?

    If the Generation time was say 14 years, as Red Panda suggested, the split would be 7 million years ago if the Effective population was 40,000 rather than 10,000.
    There are so many variables I wonder if it really can be fixed! You can certainly select variables and make it fit. In fact as Ethos does you can chose whatever figures you want and get outlandish answers.

    As the generation time increases you need to increase the size of the effective population to keep the output "years since split" the same. It makes sense to me to have a larger effective population, doesn't it?
    Effective population is not really a variable parameter in current human population. It is a empirical finding, measurable and testable.

    “This was somewhat surprising since the present day effective population size of humans is estimated to be only ~10,000.” https://en.wikipedia.org/wiki/Human_evolutionary_genetics


    You can not vary it to produce a desired outcome.

    Mutation rate per generation in humans is also a measured value these days (worked out over and over again to improve accuracy).

    Human chimp similarity is continuously refined with new technology and understanding of the DNA.

    Wiggle room is not implied here.

    A fly in the ointment…

    One thing that everyone here has overlooked. Most of the mutations are deleterious to an organism. There must be a cleansing of the population by mortality to maintain population fitness given a value of “U”.

    The estimated “U” in the paper I cited was ~3. That gives a mandatory birth rate of at least 40 offspring per mating couple or else the genome load becomes critical over time (under hard selection the population could collapse). That “U” is ridiculous.

    With lower mutation rate a lower “U” is predicted but evolution time is extended. A “U” of say 1.2 is more reasonable.

    Birthrate (sexual reproduction) = 2e^U (to escape deleterious effects on fitness).

    Birthrate = 2e^1.2 = 6.6 offspring.

    Result… shorten evolution time and birthrate is unreasonable.
    Lengthen evolution time and birthrate becomes more reasonable.

    There is an implied long divergence time

    By the way this effect lengthens generation time.
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    Quote Originally Posted by GTCethos View Post
    ...Effective population is not really a variable parameter in current human population. It is a empirical finding, measurable and testable.

    “This was somewhat surprising since the present day effective population size of humans is estimated to be only ~10,000.” https://en.wikipedia.org/wiki/Human_evolutionary_genetics


    You can not vary it to produce a desired outcome.
    [I might just pick off little bits from what you say at a time.]
    Firstly you seem to have had this bit really wrong too!
    That Wikipedia link says this about effective population:
    Additionally they estimated the effective population size of the common ancestor of humans and chimpanzees to be ~100,000. This was somewhat surprising since the present day effective population size of humans is estimated to be only ~10,000.
    So does that mean you can't have the same "effective population right throughout? It starts off at 100,000 and when does it drop to 10,000?
    If true that means that the human lineage would have experienced an immense decrease of its effective population size (and thus genetic diversity) in its evolution. (see Toba catastrophe theory)
    When did the Toba catastrophe occur?
    The Toba supereruption was a supervolcaniceruption that occurred some time between 69,000 and 77,000 years ago at the site of present-day Lake Toba(Sumatra, Indonesia). It is one of the Earth's largest known eruptions.
    So for the greater part of human evolution does that mean you have to run with the 100,000 effective population?
    Right I believe it does. I'll put that in the spreadsheet and see what effect it has.

    Using various combinations an interesting combination would be Ne = 130,000 Generation time (Generation time = 22 years) * number of generations (t) =7.58 mya.
    If you want a smaller Ne you have to shorten the generation time.
    If you went to the Ne = 100,000 the generation time has to be between 18 -19 years (generation time as the average age of giving birth, or fathering offspring)
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    I've asked twice now but CTCethos does not want to answer the question: where does the equation he uses comes from?


    As far as I can tell he starts with this:
    And derives this:


    If I change the subject of the first equation to t, I get this:


    If anyone has more competence with basic algebra than I do, it'd be cool if you could let me know if I have done this correctly or wrongly.


    Secondly, are you plugging in 5% or 0.05?


    I think the whole mathematical soundness of what you are doing is messed up.
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    I don't think the calculations can be accurate because they are measuring the wrong thing. The problem is not the rate of mutation, but the frequency and severity of "survival challenging events". Evolution is driven by death not by mutation. Mutations just keep happening at a steady rate. One estimate is approximately 200 per individual. But disasters that severely challenge a population to avoid extinction, tend to be random.
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    Quote Originally Posted by Zwirko View Post
    I've asked twice now but CTCethos does not want to answer the question: where does the equation he uses comes from?


    As far as I can tell he starts with this:
    And derives this:


    If I change the subject of the first equation to t, I get this:


    If anyone has more competence with basic algebra than I do, it'd be cool if you could let me know if I have done this correctly or wrongly.
    no, the equation µ = k / (2t + 4 Ne) does convert into

    t = ˝ (k/µ - 4 Ne)

    it's just that changing the values of some of the parameters such as µ has a massive influence on the value of t
    for all intents and purposes you can ignore relatively small values of Ne such as 10,000 since k/µ is a couple of orders of magnitude larger than Ne
    however, i take issue with cherry-picking other values of mutation rate for different parts of the genome since for that part of the genome the correlation between t, µ and Ne may be different from that in the article

    what GTCethos has done is essentially a reductio ad absurdum : coming up with an impossibly large value means you've broken the assumptions underlying the equation, and hence your deductions you try and draw from them are null and void
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    I think the two equations are equivalent; just different ways of saying the same thing? (my maths skills are truly shocking btw, so I may be way off in this claim).


    Anyway, the authors of the linked paper use at one point a value of 0.0133 for k. GTCethos's number here is about 400 times larger. What happens when we express his 5% as a decimal (0.05)?




    I feel that a thourough understanding of population genetics is essential to understanding modern evolutionary theory. It saddens me no end that my knowledge in this areas is so weak; without it an uunderstanding of evolution is greatly impoverished. Must rectify this one day.
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    Quote Originally Posted by Zwirko View Post
    I've asked twice now but CTCethos does not want to answer the question: where does the equation he uses comes from?


    As far as I can tell he starts with this:
    And derives this:


    If I change the subject of the first equation to t, I get this:


    If anyone has more competence with basic algebra than I do, it'd be cool if you could let me know if I have done this correctly or wrongly.


    Secondly, are you plugging in 5% or 0.05?


    I think the whole mathematical soundness of what you are doing is messed up.
    I’ve asked twice now but CTCethos does not want to answer the question: where does the equation he uses comes from?



    If you read my intro. That equation comes from a peer reviewed paper here:


    http://www.genetics.org/content/156/1/297.full


    If you read the paper. The scientists go threw a step by step explanation of the reasoning for there proposed equation (citations and all).


    Secondly, are you plugging in 5% or 0.05?


    I think the whole mathematical soundness of what you are doing is messed up.
    The authors of the article assumed a 98.7% similarity between humans and chimps. This figure is unrealistic given new evaluations. Even in the best light, scientists now agree that the similarity is about 96% and that by some scientists estimation is still too low.


    If you read my post explaining the procedure of scaffolding the human genome to evaluate the chimp genome you would understand the issue that some scientists have with the “similarity” finding.
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    “coming up with an impossibly large value means you've broken the assumptions underlying the equation, and hence your deductions you try and draw from them are null and void”



    This was my first impulse when I ran the updated finding in similarity and mutation rate. Since then I have tried to verify an issue with what you claim is “broken assumptions”. I have not found a sound argument yet.


    I know this is probably beyond the realm of this forum… but I would like to locate some of these “broken assumptions”.
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    GTCethos,

    Yes the authors assumed 98.7%. That is where the value of 0.0133 for k comes from.

    When you assumed 5% (a value I have no major issues with) did you use "5" or "0.05" in your calculation?
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    Quote Originally Posted by Zwirko View Post
    GTCethos,

    Yes the authors assumed 98.7%. That is where the value of 0.0133 for k comes from.

    When you assumed 5% (a value I have no major issues with) did you use "5" or "0.05" in your calculation?

    .05
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    Using various combinations an interesting combination would be Ne = 130,000 Generation time (Generation time = 22 years) * number of generations (t) =7.58 mya.


    Looking at your results in running the numbers you may be missing something…



    Remember: (t) is the number of generations found. You must multiply (t) times the years per generation…


    (t) x (generation time) = years since human chimp split.
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    OK, now we need to know where you got this figure of 5% from.
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    Quote Originally Posted by Zwirko View Post
    OK, now we need to know where you got this figure of 5% from.
    A shameless re-post....

    I am sure you do not want me to give a 70% similarity number (which has been quoted). That would be overkill…


    Here is a citation for 96%… “A comparison of Clint's genetic blueprints with that of the human genome shows that our closest living relatives share 96 percent of our DNA” Chimps, Humans 96 Percent the Same, Gene Study Finds


    Also the 95% number: Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels


    Here is the figure for the 1.1 x 10^-8 mutation rate: “Using data available from whole genome sequencing, the human genome mutation rate is similarly estimated to be ~1.1×10−8 per site per generation.[7]” https://en.wikipedia.org/wiki/Mutation_rate#Measurement





    “Indels are short for insertions and deletions. Most assuredly this is mutation. There are other mutations not counted by human and chimp differences in DNA. The majority of differences between the two genomes is in regions called regulatory or non-coding segments. If these segments were counted the genome comparison between humans and chimps could be as low as 70%.








    It is important to know that a human “scaffold” is first set up then the chimp genome is aligned to it. Alignment tools (like BLAST) are applied to identify sequences between gaps and non similar segments. It also might be noted here that about 700 million base pair of the chimp genome did not even align to the human scaffold. That would be about 21% of the genome. Who knows if these segments actually perform a function or not.”






    This last part was from a previous post…
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    Only one acceptable reference, dating from 2002. The chimpanzee genome was not even complete then. Early sequences of both human and chimpanzee genomes were riddled with sequence errors.

    If you try a more up to date analysis you will find that the supposed problems with insertions/deletions are pretty much resolved. It appears that the Britten (2002) paper is a very popular piece to see referenced on creation/ID sites.
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    Quote Originally Posted by Zwirko View Post
    Only one acceptable reference, dating from 2002. The chimpanzee genome was not even complete then. Early sequences of both human and chimpanzee genomes were riddled with sequence errors.

    If you try a more up to date analysis you will find that the supposed problems with insertions/deletions are pretty much resolved. It appears that the Britten (2002) paper is a very popular piece to see referenced on creation/ID sites.

    What similarity do you suggest?
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    Quote Originally Posted by Sealeaf View Post
    I don't think the calculations can be accurate because they are measuring the wrong thing. The problem is not the rate of mutation, but the frequency and severity of "survival challenging events". Evolution is driven by death not by mutation. Mutations just keep happening at a steady rate. One estimate is approximately 200 per individual. But disasters that severely challenge a population to avoid extinction, tend to be random.
    I think you have missed what is being measured here. It is not selectable traits no it just the background DNA base changes that don't affect the function of proteins
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    Quote Originally Posted by GTCethos View Post
    Using various combinations an interesting combination would be Ne = 130,000 Generation time (Generation time = 22 years) * number of generations (t) =7.58 mya.


    Looking at your results in running the numbers you may be missing something…



    Remember: (t) is the number of generations found. You must multiply (t) times the years per generation…


    (t) x (generation time) = years since human chimp split.
    I have not missed anything. That is exactly how I am calculating the time back to the split. Note: I am using the lower value of divergence not the one you want us to use. My results seem to match the fossil record better than your figures at this stage.
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    A citation on percentage similarity needed here.... Yours please, you have mine.
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    Quote Originally Posted by GTCethos View Post
    A citation on percentage similarity needed here.... Yours please, you have mine.
    I read it in one of your posts at the beginning of the thread 0.0133 divergence in base pairs. This figure is not including the endels.
    Estimate of the Mutation Rate per Nucleotide in Humans ??
    Results section:
    The average level of divergence for autosomal pseudogenes was 1.33 ± 0.11% and ranged from a low of 0.4% to a high of 2.56% (Table 1). The average level of divergence for X-linked pseudogenes was 1.08 ± 0.14% and ranged from a low of 0.65% to a high of 1.47% (Table 2). While the average level of divergence was lower on the X chromosome than on autosomes, this difference was not significant (Mann-Whitney U = 29.5, P > 0.5). Substitution rates among loci varied by a factor of six and there was a slight trend toward higher rates in pseudogenes with intermediate GC content (WOLFEet al. 1989; Tables 1 and2),
    Last edited by Robittybob1; October 2nd, 2014 at 05:36 PM.
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    You know that human and chimp similarities are only 86.7%...

    Key finding:


    However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region.
    Finally, if generalized, these data suggest that evolution may have used the mechanistically more drastic indels instead of the more subtle single-nucleotide substitutions for shaping the recently emerged primate species.http://www.pnas.org/content/100/13/7708.abstract
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    Quote Originally Posted by GTCethos View Post
    You know that human and chimp similarities are only 86.7%...

    Key finding:


    However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region.
    Finally, if generalized, these data suggest that evolution may have used the mechanistically more drastic indels instead of the more subtle single-nucleotide substitutions for shaping the recently emerged primate species.http://www.pnas.org/content/100/13/7708.abstract
    Yes that could well be true but you can't get a time factor out of the larger mix-up. Indels are activity within the DNA and not due to external random mutations causing the "subtle single-nucleotide substitutions". I've forgotten what they are called but they are like residual endogenised viruses that move chunks of the genome around, so not random. Is it transposons? Things like that.
    What you say is true but it is not the time-able portion.
    It would be like looking at a tree and saying "the biggest tree is obviously the oldest", but it is not till you count the growth rings that you find out how old it really is.
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    GTCethos,

    Again you are providing information from extrapolative studies carried out before the P. troglodytes draft genome was published in 2005. The key paper here is:

    Nature 437, 69-87 (1 September 2005) | doi:10.1038/nature04072;
    Initial sequence of the chimpanzee genome and comparison with the human genome
    The Chimpanzee Sequencing and Analysis Consortium

    If there are studies that support values such as 70-90 % published after this date I'd be interested to see them.
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    Quote Originally Posted by Zwirko View Post
    GTCethos,

    Again you are providing information from extrapolative studies carried out before the P. troglodytes draft genome was published in 2005. The key paper here is:

    Nature 437, 69-87 (1 September 2005) | doi:10.1038/nature04072;
    Initial sequence of the chimpanzee genome and comparison with the human genome
    The Chimpanzee Sequencing and Analysis Consortium

    If there are studies that support values such as 70-90 % published after this date I'd be interested to see them.
    @Zirko - Can you understand the entire paper?

    @GTCethos - Can you understand the entire paper?
    It was too hard for me.
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    Not in its entirety, no. It's quite technical.
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    Yes that could well be true but you can't get a time factor out of the larger mix-up. Indels are activity within the DNA and not due to external random mutations causing the "subtle single-nucleotide substitutions”.



    I do not think you could say that indel mutation is outside the realm of “genetic drift”. That as you know may be random but is essential to the evolution principle… It is mutation and statistically significant.


    ERV’s are another issue all together and must be dealt with a closer examination.
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by Zwirko View Post
    GTCethos,

    Again you are providing information from extrapolative studies carried out before the P. troglodytes draft genome was published in 2005. The key paper here is:

    Nature 437, 69-87 (1 September 2005) | doi:10.1038/nature04072;
    Initial sequence of the chimpanzee genome and comparison with the human genome
    The Chimpanzee Sequencing and Analysis Consortium

    If there are studies that support values such as 70-90 % published after this date I'd be interested to see them.
    @Zirko - Can you understand the entire paper?

    @GTCethos - Can you understand the entire paper?
    It was too hard for me.
    “Nature 437, 69-87 (1 September 2005) | doi:10.1038/nature04072;
    Initial sequence of the chimpanzee genome and comparison with the human genome
    The Chimpanzee Sequencing and Analysis Consortium”



    I have spent a great deal of time on the conclusions and findings of this paper. I have seen the actual data sets produced. By “brut force count” this is where I found 700gbp missing from the alignment of the chimp genome to the human scaffold. Talking directly with some one supposedly involved (I can not verify that credential) that person told me all the alinement technique and tools fail to aline these missing segments, so they were assumed to just agree with similarity of the two genomes. I rejected that notion and the conversation ended shortly after.
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    Quote Originally Posted by GTCethos View Post
    Yes that could well be true but you can't get a time factor out of the larger mix-up. Indels are activity within the DNA and not due to external random mutations causing the "subtle single-nucleotide substitutions”.



    I do not think you could say that indel mutation is outside the realm of “genetic drift”. That as you know may be random but is essential to the evolution principle… It is mutation and statistically significant.


    ERV’s are another issue all together and must be dealt with a closer examination.
    I'm not saying it isn't significant, but that is not what I was getting at. I thought we were looking at divergence as a way of estimating when the CHLCA was around.
    I took it that they were measuring changes that don't show up in the offspring for they are so minor they have no expression, just a base pair change on a very long length of DNA. The base pair change change but the codon still selects for the same amino acid in the resulting protein. A mutation of a base pair may not have any effect. Can you agree with that?
    So all that other divergence caused by those indels, transposable elements, chromosomes splitting and rejoining, retroviruses repeating themselves etc. they are the things that drive the phenotype change, the thing that gives an organism a selection advantage and hence we see evolution of that species.
    But this is not what the geneticist can time the split time from.
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    Quote Originally Posted by GTCethos View Post


    I have spent a great deal of time on the conclusions and findings of this paper. I have seen the actual data sets produced. By “brut force count” this is where I found 700gbp missing from the alignment of the chimp genome to the human scaffold. Talking directly with some one supposedly involved (I can not verify that credential) that person told me all the alinement technique and tools fail to aline these missing segments, so they were assumed to just agree with similarity of the two genomes. I rejected that notion and the conversation ended shortly after.
    700gbp? As in 7x1011 ? Do you know the size of the human and chimp genomes?

    The rest of your story I think I'll dismiss as BS if you don't mind.
    Last edited by Zwirko; October 3rd, 2014 at 01:01 PM.
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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by GTCethos View Post


    I have spent a great deal of time on the conclusions and findings of this paper. I have seen the actual data sets produced. By “brut force count” this is where I found 700gbp missing from the alignment of the chimp genome to the human scaffold. Talking directly with some one supposedly involved (I can not verify that credential) that person told me all the alinement technique and tools fail to aline these missing segments, so they were assumed to just agree with similarity of the two genomes. I rejected that notion and the conversation ended shortly after.
    700gbp? As in 7x1011 ? Do you know the size of the human and chimp genomes?

    The rest of your story I think I'll dismiss as BS if you don't mind.
    Please Zwirko don't leave us in suspenders! What was your killer blow, what is the size of the human and chimp genomes? bp = base pairs 700 gbp = seven hundred giga base pairs.
    Genome size 3,234.83 Mb (Mega-basepairs)
    Mega base pairs means millions of base pairs 3,234.83 million base pairs so it doesn't go over 10^10 bps - Ethos you are in error!
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    700gbp? As in 7x1011 ? Do you know the size of the human and chimp genomes?



    The rest of your story I think I'll dismiss as BS if you don't mind.



    No, sorry… my mistake. that is 7 x 10^5 or .7gbp. I missed the decimal.


    700 million base pair or about 21% of the human genome.

    Rough crowd...
    Last edited by GTCethos; October 3rd, 2014 at 01:56 PM.
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    "No, sorry… my mistake. that is 7 x 10^5 or .7gbp. I missed the decimal." that doesn't seem right either!
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    Quote Originally Posted by Robittybob1 View Post
    "No, sorry… my mistake. that is 7 x 10^5 or .7gbp. I missed the decimal." that doesn't seem right either!
    You can look at it yourself.... I will give you a citation but it violates my commitment of only providing secular papers and articles.

    2.4/3.2 ~.8
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    Quote Originally Posted by GTCethos View Post
    Quote Originally Posted by Robittybob1 View Post
    "No, sorry… my mistake. that is 7 x 10^5 or .7gbp. I missed the decimal." that doesn't seem right either!
    You can look at it yourself.... I will give you a citation but it violates my commitment of only providing secular papers and articles.

    2.4/3.2 ~.8
    7 x 10^5 = 700,000 and that is 0.7 million not 0.7 billion.

    Citation please and too bad about your self imposed restrictions!
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    There is likely about 3 million base pairs of difference between Robittybob1 and GTCethos. So I'm not convinced there is anything to fret about over this 700K claim, regardless of its dubious origins and lack of reference.
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    7 x 10^5 = 700,000 and that is 0.7 million not 0.7 billion.


    Citation please and too bad about your self imposed restrictions!


    Well actually I don’t need to reference another paper right now it is in this one we are talking about…

    “Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover
    ~2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y.”

    http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

    Same paper you referenced…. and from my hint 2.4/3.2 ~ .8 gigabases. I said about .7gbp just to be on the safe side.


    ”One study reports that the
    chimp genome contains 3.8 billion base pairs compared to close to 3.2 billion for humans.” Pellicciari, C., Formenti, D., Redi, C.A. and Manfredi Romanini, M.G., DNA Content variability in primates, Journal of Human Evolution 1:131–141, 1982.


    Given only 2.4 gig abases sequenced (aligned) in 2005 you are left with about 1.4 gigabases unaccounted for in the comparison of human and chimp DNA.
    Look the chimp genome is .6 gigabases larger than the human genome…
    So total divergence is grater than .8gbp + .6gbp = 1.4gbp


    That means unless thos extra DNA gets placed humans and chimps can not agree more than 56%… Remarkable isn’t it.




    I have some work right now so please wait for any further responses until tonight.
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    You used a 1982 reference to get the size of the chimpanzee genome.

    The actual size of the chimpanzee genome is about 3323.27 MB (Pan troglodytes (ID 202) - Genome - NCBI).
    Human is 3251.72 MB (Homo sapiens (ID 51) - Genome - NCBI).

    At least 2.99 GB of the chimpanzee genome has been sequenced so far.
    Ensembl genome browser 77: Pan troglodytes -

    Neither the human or chimpanzee genome sequences are complete due to the difficulty of sequencing highly repetitive regions. This doesn't mean we have to drastically reduce the sequence similarity.
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    Quote Originally Posted by Zwirko View Post
    You used a 1982 reference to get the size of the chimpanzee genome.

    The actual size of the chimpanzee genome is about 3323.27 MB (Pan troglodytes (ID 202) - Genome - NCBI).
    Human is 3251.72 MB (Homo sapiens (ID 51) - Genome - NCBI).

    At least 2.99 GB of the chimpanzee genome has been sequenced so far.
    Ensembl genome browser 77: Pan troglodytes -

    Neither the human or chimpanzee genome sequences are complete due to the difficulty of sequencing highly repetitive regions. This doesn't mean we have to drastically reduce the sequence similarity.
    It is certainly is amazing what scientists can do.
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    The actual size of the chimpanzee genome is about 3323.27 MB (Pan troglodytes (ID 202) - Genome - NCBI).
    Human is 3251.72 MB (Homo sapiens (ID 51) - Genome - NCBI).


    This seems to be another scaffold assembly and you may have to do a bit of addition to get the total genome length… It shows the total sequence length but I am not sure this is direct bp.

    adding line 1 to line 2 you get: 3,744,165,594 this number appears to be close to the bp length of 3.8 gigabases.
    From page: Pan_troglodytes-2.1.4 - Assembly - NCBI

    At least 2.99 GB of the chimpanzee genome has been sequenced so far.
    Ensembl genome browser 77: Pan troglodytes -

    Neither the human or chimpanzee genome sequences are complete due to the difficulty of sequencing highly repetitive regions. This doesn't mean we have to drastically reduce the sequence similarity.


    Your second article has nothing to do with chimp DNA alignment to the human scafold…

    By the way these highly repetitive regions can not be simply rejected out of hand because we do not know there function at this time.

    If you want to form a opinion out of technical ignorance that is good for opinion but bad for science.

    So what similarity would you accept?
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    Quote Originally Posted by GTCethos View Post
    Quote Originally Posted by Robittybob1 View Post
    "No, sorry… my mistake. that is 7 x 10^5 or .7gbp. I missed the decimal." that doesn't seem right either!
    You can look at it yourself.... I will give you a citation but it violates my commitment of only providing secular papers and articles.

    2.4/3.2 ~.8
    If the source doesnt meet peer-reviewed standards, why are you utilizing it for information?
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    GTCethos,

    "Total Sequence Length" (in the table) is an estimate of the number of bases sequenced plus the estimate of the gap lengths. In other words, it's an estimate of the size of the genome. P. troglodytes has a genome of 3.3 GB, not 3.8 GB. You can't just add these numbers together in the hope that they come out somewhere near 3.8. The other link I provided showed the actual sequenced length (2.9 GB) as of a particular date.


    Highly repetitive regions are not rejected because their function is not known. You don't need to know function to determine sequence or sequence similarity. Besides, many of their functions are known: they include centromere sequences, telomere sequences. ribosomal RNA sequences and so on. Large gaps tend to be found in regions where these sorts of sequences occur. Improved sequencing technologies and bioinformatic techniques are overcoming the problems these regions have presented.


    The number I accept is 98%-99%. That's what the data shows, That's what the primary literature shows. If it's revised, then I will revise my opinion. This figure is little different from older estimates arrived at from hybridisation studies.
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    The number I accept is 98%-99%. That's what the data shows, That's what the primary literature shows. If it's revised, then I will revise my opinion. This figure is little different from older estimates arrived at from hybridisation studies.



    I do not see 99% similarity in any peer reviews anymore (Dawkins even gave that one up)… I will take your lower number of 98% (even though it is not supportable).


    so with the following:


    u= 1.1 x 10^-8 (well established)
    k= 2% (not supported by new findings)
    Ne= 100,000


    I calculate about 14 million years since divergence mostly by the lower measured mutation rate.


    This figure although unrealistic for too high a similarity between humans and chimps destroys the 6.6 million year divergence time in paleoanthropology.


    By the way here is a paper establishing the importance of counting indels in the similarity figures.


    ”However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region. “
    “Finally, if generalized, these data suggest that evolution may have used the mechanistically more drastic indels instead of the more subtle single-nucleotide substitutions for shaping the recently emerged primate species.”http://www.pnas.org/content/100/13/7708.abstract


    I still think your wrong about the total bp count for the chimp….
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    P.S. I did a calculation using the assumed mutation rate of 2.5 x 10^-8 , 2% divergence and produced about 4 million years since divergence.
    It seems the formula I am using is in the ball park.
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    Quote Originally Posted by GTCethos View Post
    P.S. I did a calculation using the assumed mutation rate of 2.5 x 10^-8 , 2% divergence and produced about 4 million years since divergence.
    It seems the formula I am using is in the ball park.
    The second post above you say "u= 1.1 x 10^-8 (well established)" So why have you upped it to 2.5 x 10^-8? Make up your mind!
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    P.S. I did a calculation using the assumed mutation rate of 2.5 x 10^-8 , 2% divergence and produced about 4 million years since divergence.
    It seems the formula I am using is in the ball park.
    The second post above you say "u= 1.1 x 10^-8 (well established)" So why have you upped it to 2.5 x 10^-8? Make up your mind!
    I always allow the other participants the choice of how I prove my point… I was simply back calculating an expected result by evolutionists. The 2.5 x 10^-8 is the exact value touted in the paper and that I had made the subject of this thread. It was a critical mutation rate that must have existed to make a man out of a monkey.


    Of course reality set in when the empirical evidence finally demonstrated that not all the mutations were there to produce the man….


    Any other questions?
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    You cannot make a man out of a monkey but you can make a monkey out of a man…
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    GTCethos,


    98%-99% means 98.xx %. That is supported by the data. That is what the primary literature shows.


    A good summary article (just a blog post) by anthropologist John Hawks explains some of the history of mutation rate calculation and it's spotty history: What is the human mutation rate? You might find it surprisingly in agreement with some of your observations about the accuracy of studies in this area.


    You can play around with mutation rates, effective population sizes and generation times all day if you want. It's all estimation with many factors that can influence how fast or slow or changeable our molecular clock of choice is. The variables simply can't be pinned down at this point in time. Chimpanzee-human divergence dates are all over the place in the scientific literature. Your figure is not too different from some of the larger estimates I've seen. I've actually seen larger. Despite what you appear to claim, a divergence time of 12 million years woiuld not destroy the field of paleoanthropology. I don't think it'd even contradicts the fossil evidence.
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    Quote Originally Posted by GTCethos View Post
    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    Quick question…


    Can Paleoanthropology accommodate 45 million years since divergence?

    I would say so, the further you go back the more divergence. If you take a bigger divergence you need a longer time to get those changes.
    What ancestor of man has definitively been identified 45 million years ago. Simply show me the proposed ancestor…

    Or else we should conclude that man and chimp did not evolve from a common ancestor? What is your point?

    Timeline of evolutionary history of life - Wikipedia, the free encyclopedia
    Timeline of human evolution - Wikipedia, the free encyclopedia
    Last edited by Write4U; October 5th, 2014 at 06:35 PM.
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