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Thread: Humans diverged from chimps, when and how?

  1. #101  
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    [QUOTE=GTCethos;598280]
    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
    Incorrect, multiple members have now asked fro you to provide the source of your numbers that results in the lower figure you keep referencing, please do so in your next post.
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    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.


    I like John Hawks by the way. Some of his blogs are very good read.


    I know what you are talking about in some of these molecular studies for the argument of common descent. Most of these molecular studies while being exhaustive about mutation rates or similarity (humans and chimps) do not step back and take both into account on the same page. I have not seen a recent article about either mutation or similarity improving for the argument of common descent and can only assume that might be a reason.


    I can blitz you with many recent articles about the importance of counting indels in similarity between species. I do not think that is necessary here.


    The broader point I am trying to make is that when all considerations are accounted for common descent is in trouble.


    For a bit of relief. Can you provide a hominid linage for 12 million years?
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    [QUOTE=Paleoichneum;598880]
    Quote Originally Posted by GTCethos View Post
    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
    Incorrect, multiple members have now asked fro you to provide the source of your numbers that results in the lower figure you keep referencing, please do so in your next post.
    I think my citation is good enough for the 2.4 gigabase assertion.




    “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.


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    Quote Originally Posted by GTCethos
    The broader point I am trying to make is that when all considerations are accounted for common descent is in trouble.
    I think all that we can safely conclude from the this thread, so far, is that estimates of the time of human-chimpanzee divergence are what they claim to be. That is, estimates. What has been discussed has not dented the concept of common descent - your argument actually depends upon the reality of common descent.

    Quote Originally Posted by GTCethos
    Can you provide a hominid linage for 12 million years?
    I'm not sure what you are asking here. Do you mean a phylogenetic tree?
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  5. #105  
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    [QUOTE=GTCethos;598973]
    Quote Originally Posted by Paleoichneum View Post
    Quote Originally Posted by GTCethos View Post
    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
    Incorrect, multiple members have now asked fro you to provide the source of your numbers that results in the lower figure you keep referencing, please do so in your next post.
    I think my citation is good enough for the 2.4 gigabase assertion.




    “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.


    That is not the citation that has been asked for a number of times now. We are asking for the one you are relying in that you assert would not meet our liking.

    What is the citation and why do you rely on it?

    Also common decent is not in trouble as you maths have been shown to be doubious at best in this thread.
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    I have been more than patient with your requests. Frankly, I am having trouble with you incoherent questions. What on earth….


    That is not the citation that has been asked for a number of times now. We are asking for the one you are relying in that you assert would not meet our liking.
    ???


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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by GTCethos
    The broader point I am trying to make is that when all considerations are accounted for common descent is in trouble.
    I think all that we can safely conclude from the this thread, so far, is that estimates of the time of human-chimpanzee divergence are what they claim to be. That is, estimates. What has been discussed has not dented the concept of common descent - your argument actually depends upon the reality of common descent.

    Quote Originally Posted by GTCethos
    Can you provide a hominid linage for 12 million years?
    I'm not sure what you are asking here. Do you mean a phylogenetic tree?
    Why not...
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    I think all that we can safely conclude from the this thread, so far, is that estimates of the time of human-chimpanzee divergence are what they claim to be. That is, estimates.



    About the same thing can be said of all evolution… a estimate. On closer examination a bad one at that.
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    [QUOTE=GTCethos;599099]
    I think all that we can safely conclude from the this thread, so far, is that estimates of the time of human-chimpanzee divergence are what they claim to be. That is, estimates.


    What difference does that make?
    Tree to me:
    CHLCA => Orrorin tugenensis => Homo habilis => Homo erectus => homo sapiens => us all over about 8 million years.
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    Quote Originally Posted by GTCethos View Post
    I have been more than patient with your requests. Frankly, I am having trouble with you incoherent questions. What on earth….


    That is not the citation that has been asked for a number of times now. We are asking for the one you are relying in that you assert would not meet our liking.
    ???


    Your assertion of you having a preferred reference for the lower Homo-Pan DNA profile matches, which you assert the forum members would not approve of, and so, even though you rely on it, you will not tell what it is. See post #85 and provide asserted reference.
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    [QUOTE=Robittybob1;599117]
    Quote Originally Posted by GTCethos View Post
    I think all that we can safely conclude from the this thread, so far, is that estimates of the time of human-chimpanzee divergence are what they claim to be. That is, estimates.


    What difference does that make?
    Tree to me:
    CHLCA => Orrorin tugenensis => Homo habilis => Homo erectus => homo sapiens => us all over about 8 million years.
    Why do you exclude the Austaliopithicenes and Ardipithicenes?
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    [QUOTE=Paleoichneum;599123]
    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    I think all that we can safely conclude from the this thread, so far, is that estimates of the time of human-chimpanzee divergence are what they claim to be. That is, estimates.


    What difference does that make?
    Tree to me:
    CHLCA => Orrorin tugenensis => Homo habilis => Homo erectus => homo sapiens => us all over about 8 million years.
    Why do you exclude the Austaliopithicenes and Ardipithicenes?
    I'm no expert on this, but I have allowed those others to be side branches in the tree, not direct line descendants.

    So you would like them included, is that what you are implying? I'll look into it again, but please discuss your thoughts with us, so I have something to judge what I'll be reading against.
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    Your assertion of you having a preferred reference for the lower Homo-Pan DNA profile matches, which you assert the forum members would not approve of, and so, even though you rely on it, you will not tell what it is. See post #85 and provide asserted reference.



    I did not need to upset the participants here because if you look at post #88 I provided the superior peer reviewed citation. All is right with the world.
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    So you would like them included, is that what you are implying? I'll look into it again, but please discuss your thoughts with us, so I have something to judge what I'll be reading against.



    I hope your efforts go back at least 12 to 14 million years… as per Zirko’s accepted human chimp similarity of 2%.
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    Quote Originally Posted by GTCethos View Post
    So you would like them included, is that what you are implying? I'll look into it again, but please discuss your thoughts with us, so I have something to judge what I'll be reading against.



    I hope your efforts go back at least 12 to 14 million years… as per Zirko’s accepted human chimp similarity of 2%.
    You seem to be becoming agitated Ethos. Stay civil and helpful please. The CHLCA could have been around for another 4-5 million years slowly differentiating into 2 lines before the Orrorin, one can't really tell. No DNA exists and the fossil record is virtually non existent for that species that long ago.
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    So you would like them included, is that what you are implying? I'll look into it again, but please discuss your thoughts with us, so I have something to judge what I'll be reading against.



    I hope your efforts go back at least 12 to 14 million years… as per Zirko’s accepted human chimp similarity of 2%.
    You seem to be becoming agitated Ethos. Stay civil and helpful please. The CHLCA could have been around for another 4-5 million years slowly differentiating into 2 lines before the Orrorin, one can't really tell. No DNA exists and the fossil record is virtually non existent for that species that long ago.
    You have the chimp and human DNA. The Chimp DNA would represent twice the divergence of the DNA to the LCA. So the LCA would only be half the total divergence between humans and chimps. It would look even more like human DNA than the chimps.


    Let us see… Zirko says he accepts 2% divergence. Why you are looking at DNA difference between 1 and 2%. You have that DNA in your own body. Not to say you look like an ape, I never saw you.
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    IMO What would the features of the CHLCA be?

    1. Opposable big toes
    2. Longer toes
    3. Knuckle walking generally walking on all four feet.
    4. Hairy
    5. Small brained. (Maybe even smaller than a chimpanzee today.)
    6. Smaller than man
    7. Strong muscular jaws
    8 Lived in the trees

    We can't say that chimps haven't evolved smarter too in those 10 million odd years.
    So the base pairs will mutate but I won't agree that the CHLCA will be half way between chimp and man because I accept that man changed his environment/habitat and way of life so evolved faster than the chimpanzee.
    Last edited by Robittybob1; October 6th, 2014 at 12:10 AM. Reason: base pairs NOT base points
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    GTCethos,

    I didn't actually say I accepted 98%. I said I accepted 98-99, as in 98 point something. It's perhaps a little uncharitable to take this as meaning 98.0.

    A point worth noting (mentioning it again actually) is that just because there is some divergence at a particular date doesn't necessarily mean there is a speciation event at that same date. The divergence date tells us when the separation of two gene pools took place. Older dates of divergence are not incompatible with younger dates of species splitting.
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    Interestingly, a comparable evolution may have taken place in the deep ocean, a very special environment, requiring sophistication in the biophysics of the organism. My favorite "smart animal" is the cuttlefish, a highly evolved (but equally vulnerable) succesful species.

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    To Zwirko

    I didn't actually say I accepted 98%. I said I accepted 98-99, as in 98 point something. It's perhaps a little uncharitable to take this as meaning 98.0.
    I have been overly charitable about your number…

    So you do not accept 98% similarity? Even though It is a unrealistic estimation in the first place.

    “Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.


    You know I could easily show that many evolutionists are in agreement about a lower figure for similarity (most claims are in their books). I have at least 5 more citations about indels in my notes that are from peer review.

    “Thus the total divergence was estimated as 6.58%”



    In addition, we will provide some examples of indels that may affect protein function as well as alternative splicing. http://www.els.net/WileyCDA/ElsArticle/refId-a0020851.html


    A point worth noting (mentioning it again actually) is that just because there is some divergence at a particular date doesn't necessarily mean there is a speciation event at that same date. The divergence date tells us when the separation of two gene pools took place. Older dates of divergence are not incompatible with younger dates of species splitting.So you do not accept 98% similarity.


    I am suspicious that any divergence in the genome specifies a “speciation event” at all. On the contrary, the null hypothesis can not exclude other suggestions.

    If the HCLCA is not a separation of two pools of hominids… What is it? (my opinion is the paradigm is lacking) So what is that statement that “older dates of divergence are not incompatible with younger dates of species splitting”? You are trying to wedge out any basis of genomic comparison that evaluates a HCLCA.
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    GTCethos,

    I'm not prepared to pay $40 to read the reference. If you read the next line of the abstract you'll notice that their 6.58% drops to 2.37%. I hope you are not going to resort to quote mining? In addition, note that this study is looking only at human chromosome 21 and chimpanzee chromosome 22. You are extrapolating from one chromosome to the entire genome.This is not the best way to determine similarity when one considers that almost the entire sequences are available.

    If you want me to round down to 98% then fine, it makes no difference.


    Indels are not the problem you imagine them to be. We can count how many there are, estimate their average size etc. You end up with a fairly small number - a fraction of a percent.


    I don't understand your last paragraph. All I'm saying is that genomes can diverge long before we'd notice anything in the fossil record.
    Last edited by Zwirko; October 6th, 2014 at 12:52 PM. Reason: extra info
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    I’m not prepared to pay $40 to read the reference. If you read the next line of the abstract you'll notice that their 6.58% drops to 2.37%. I hope you are not going to resort to quote mining? In addition, note that this study is looking only at human chromosome 21 and chimpanzee chromosome 22. You are extrapolating from one chromosome to the entire genome.This is not the best way to determine similarity when one considers that almost the entire sequences are available.



    About the quote mining you just did. We could do this all day because the truth is that indels are essential to divergence and you can not maintain a contrary argument.


    A myriad of papers have been produced arguing for indel significance. I have have found exactly zero recent papers affirming that SNP’s are the only relevant divergence between the two genomes.


    “This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species. http://www.mobilednajournal.com/content/2/1/13”






    While the results confirmed that single nucleotide substitutions did account for roughly 1.4 percent of the differences, in accordance with previous estimates, Britten also found that indels account for a further 3.9 percent of divergence. This gives a rough estimate of five percent difference, he said. Humans, Chimps Not as Closely Related as Thought?



    Your position is unsupportable…
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    Again you post that Britten (2002) paper. We've been there.


    Please be aware that I'm not arguing that indels have little evolutionary significance. I'm arguing that they comprise a small fraction of the base-for-base difference between the two genomes.


    In the other paper, the authors studied a little over 26,500 indels, the majority of which were found to be insertions in the human lineage. Of these, most were determined to be retrotransposons, the rest largely being comprised of SINEs, LINEs, and ERVs etc. The sizes of the indels studied ranged from 80 to 12,000 bp. An average length was not given.


    As far as I'm aware there may in fact be a million or more indels. Their average size is very small.
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    Quote Originally Posted by Zwirko View Post
    Again you post that Britten (2002) paper. We've been there.


    Please be aware that I'm not arguing that indels have little evolutionary significance. I'm arguing that they comprise a small fraction of the base-for-base difference between the two genomes.


    In the other paper, the authors studied a little over 26,500 indels, the majority of which were found to be insertions in the human lineage. Of these, most were determined to be retrotransposons, the rest largely being comprised of SINEs, LINEs, and ERVs etc. The sizes of the indels studied ranged from 80 to 12,000 bp. An average length was not given.


    As far as I'm aware there may in fact be a million or more indels. Their average size is very small.
    Why are you so hung up on recent dates of peer reviewed papers? And the indel location of study? Peer review accepts significant “new” findings and a paper not presenting any does not make it to the publishing process. Also you do realize that the percent deviation is never taken genome wide. If it were, you are looking at a value of similarity of 70% or less (I covered this before).


    An estimate from this paper marked 2008 (for your satisfaction):


    estimated to 3–5% indel divergence… http://www.els.net/WileyCDA/ElsArticle/refId-a0020851.html


    I am not concerned about the total base pair evaluation. The only thing that matters about indels is the affect on proteins and phylogeny (many coding changes).


    By the way I did read the talkorigins.com article supporting a 98 to 99% similarity. If you want we can take this apart one piece at a time.

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    Your latest link is a tiny one paragraph abstract that requires me to cough up good money for a measly 24 hrs access. There's nothing I can do with it, sorry.


    You should be concerned about "total base pair evaluations" because you are using their presence to support the divergence values that you plug in to that equation of yours, are you not? If not, then you're divergence values are sunk. If you are just pointing out that these sequences have possibly played important roles in human evolution, then you'll get no counter-argument from me, for I agree.
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    What we know: Sequence divergence is about 1.23% - see the paper referenced previously (Nature 2005).

    re your "genome wide" comment:

    Quote Originally Posted by Nature (2005)
    Genome-wide rates. We calculate the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%, confirming recent results from more limited studies.
    This is for coding and non-coding DNA. Indels are not included.
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    Quote Originally Posted by Zwirko View Post
    What we know: Sequence divergence is about 1.23% - see the paper referenced previously (Nature 2005).

    re your "genome wide" comment:

    Quote Originally Posted by Nature (2005)
    Genome-wide rates. We calculate the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%, confirming recent results from more limited studies.
    This is for coding and non-coding DNA. Indels are not included.
    THAT IS CLOSE TO THE PREVIOUS FIGURE OF 1.33% previously put into the spreadsheet, Gives good results with Ne of 100,000 and gen of 22 years. =7.9 million ya. Shorter time if the Ne goes up. 120,000 => 7.2 mya.
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    Quote Originally Posted by Robittybob1 View Post

    THAT IS CLOSE TO THE PREVIOUS FIGURE OF 1.33% previously put into the spreadsheet, Gives good results with Ne of 100,000 and gen of 22 years. =7.9 million ya. Shorter time if the Ne goes up. 120,000 => 7.2 mya.
    Indeed, an Ne 100,000 gives very good results, even with a 20 year generation time. 100,000 is not unreasonable,
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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Robittybob1 View Post

    THAT IS CLOSE TO THE PREVIOUS FIGURE OF 1.33% previously put into the spreadsheet, Gives good results with Ne of 100,000 and gen of 22 years. =7.9 million ya. Shorter time if the Ne goes up. 120,000 => 7.2 mya.
    Indeed, an Ne 100,000 gives very good results, even with a 20 year generation time. 100,000 is not unreasonable,
    True. There are too many variables to be really certain, but those figures fit well with Orrorin tugenensis being part of the picture.
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    Quote Originally Posted by Zwirko View Post
    Your latest link is a tiny one paragraph abstract that requires me to cough up good money for a measly 24 hrs access. There's nothing I can do with it, sorry.


    You should be concerned about "total base pair evaluations" because you are using their presence to support the divergence values that you plug in to that equation of yours, are you not? If not, then you're divergence values are sunk. If you are just pointing out that these sequences have possibly played important roles in human evolution, then you'll get no counter-argument from me, for I agree.
    Simply if mutations per generation over the diploid genome gives you a accepted mutation rate then the “genome wide definition” is correct.


    Diploid genome = 2(3.2gb) ~ 6.4Gb


    Mutations per generation = ~75


    75/6.4Gb = 1.17 X 10 ^-8….


    Oops this looks just like the mutation rate stated in the wiki…. I never imagined it is that simple...
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    Wait I am looking at the wrong value… SNP’s and indels… OK sorry I misread your post. I will maintain that the similarity figure of 95% is a good one with current values.
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    The following is not mine but seems reasonable from the paper I used this thread (The chimp genome sequencing).

    "However, based on the numbers given in the chimp genome paper, one can determine a rough overall genome similarity between humans and chimp by including published concurrent information from the human genome project. In regards to the overall alignment, the authors state, “Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover ~2.4 gigabases (Gb) of high-quality sequence”. At this time, the human euchromatic assembly was estimated to be 99% complete at 2.85 Gb and had an error rate of 1 in 100,000 bases. The chimp genome authors state, “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.”

    In summary, only 2.3 Gb of chimp sequence aligned onto the highly accurate and complete human genome (2.85 Gb) an operation that included the masking of low complexity sequences. For the chimp sequence that aligned, the data for substitutions and indels indicates 95.8% similarity, a biased figure which excludes the masked regions. Using these numbers, an overall estimate of chimp compared to human DNA produces a conservative estimate of genome-wide similarity at 80.6%."
    http://releasingthetruth.wordpress.com/2013/04/27/dna-sim/
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    I have been asking for a hominid time line… What do you think of this page? It seems to fit our current calculation with the new mutation rate.


    It would certainly seem like humans and chimps started to diverge ~14 million years ago, and all the other divergence dates should be doubled too. This is the biggest revolution in human origins research for many years. Humans and chimps diverged earlier than previously thought | EvoAnth
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    Quote Originally Posted by GTCethos View Post
    I have been asking for a hominid time line… What do you think of this page? It seems to fit our current calculation with the new mutation rate.


    It would certainly seem like humans and chimps started to diverge ~14 million years ago, and all the other divergence dates should be doubled too. This is the biggest revolution in human origins research for many years. Humans and chimps diverged earlier than previously thought | EvoAnth
    Well wasn't that basically what we've been telling you!

    I wonder if the homo sapiens came via ardipithecus. If this Wikipedia is the current viewpoint.
    Ardipithecus is a genus of an extinct hominine which lived during Late Miocene and Early Pliocene in Afar Depression, Ethiopia. Originally described as one of the earliest ancestors of humans after they diverged from the main ape lineage, it is now a matter of debate what was the relation of this genus to human ancestors, that is whether it is a hominin, or not.[1] Two fossil species are described in the literature: A. ramidus, which lived about 4.4 million years ago[2] during the early Pliocene, and A. kadabba, dated to approximately 5.6 million years ago (late Miocene).[3] Behavioral analysis showed that Ardipithecus could be very similar to those of chimpanzees, indicating that the early human ancestors were very much like chimpanzees in behaviour.[4]
    That makes them more of a side branch.
    Also Australopithecus, was it a side branch that found the going too tough?
    Some of the species of Australopithecines were not in our lineage but one of them did (current accepted knowledge).
    Archaeologists and palaeontologists widely hold that the australopiths played a significant part in human evolution, being the first of the hominids to show presence of a gene that causes increased length and ability of neurons in the brain, the duplicated SRGAP2 gene.[1] One of the australopith species eventually evolved into the Homo genus in Africa around two million years ago, which contained within it species like Homo habilis, H. ergaster, and eventually the modern human species, H. sapiens sapiens.[2]
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    I have been asking for a hominid time line… What do you think of this page? It seems to fit our current calculation with the new mutation rate.


    It would certainly seem like humans and chimps started to diverge ~14 million years ago, and all the other divergence dates should be doubled too. This is the biggest revolution in human origins research for many years. Humans and chimps diverged earlier than previously thought | EvoAnth
    Well wasn't that basically what we've been telling you!

    I wonder if the homo sapiens came via ardipithecus. If this Wikipedia is the current viewpoint.
    Ardipithecus is a genus of an extinct hominine which lived during Late Miocene and Early Pliocene in Afar Depression, Ethiopia. Originally described as one of the earliest ancestors of humans after they diverged from the main ape lineage, it is now a matter of debate what was the relation of this genus to human ancestors, that is whether it is a hominin, or not.[1] Two fossil species are described in the literature: A. ramidus, which lived about 4.4 million years ago[2] during the early Pliocene, and A. kadabba, dated to approximately 5.6 million years ago (late Miocene).[3] Behavioral analysis showed that Ardipithecus could be very similar to those of chimpanzees, indicating that the early human ancestors were very much like chimpanzees in behaviour.[4]
    That makes them more of a side branch.
    Also Australopithecus, was it a side branch that found the going too tough?
    Some of the species of Australopithecines were not in our lineage but one of them did (current accepted knowledge).
    Archaeologists and palaeontologists widely hold that the australopiths played a significant part in human evolution, being the first of the hominids to show presence of a gene that causes increased length and ability of neurons in the brain, the duplicated SRGAP2 gene.[1] One of the australopith species eventually evolved into the Homo genus in Africa around two million years ago, which contained within it species like Homo habilis, H. ergaster, and eventually the modern human species, H. sapiens sapiens.[2]
    I know that would make you happy my friend.

    Now add in the new divergence percentage... Happiness is fleeting.
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    Quote Originally Posted by GTCethos View Post
    ....I know that would make you happy my friend.

    Now add in the new divergence percentage... Happiness is fleeting.
    You can't use the same formula with the new divergence percentage, the formula was specifically designed for that one type of mutation to Base Pairs only I believe.
    remember the k/u factor? You can't use the value for u = 1.1*10^-8 if you do use the higher divergence rate..
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    ....I know that would make you happy my friend.

    Now add in the new divergence percentage... Happiness is fleeting.
    You can't use the same formula with the new divergence percentage, the formula was specifically designed for that one type of mutation to Base Pairs only I believe.
    remember the k/u factor? You can't use the value for u = 1.1*10^-8 if you do use the higher divergence rate..
    Now you can give me a reason why... not just a gut feeling but technical reasons.
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    Quote Originally Posted by GTCethos View Post
    Now you can give me a reason why... not just a gut feeling but technical reasons.
    my main reason for doubting your conclusions is that an organism's genome (and the difference with another organism) can't be assessed from a small portion of DNA unless you have some indication that it is representative for the whole
    failing that you have to get as close as possible to assessing all of the genome, either by trying to take representative sample in various parts of the genome, or (something that nowadays is more practical than it used to be even 5 years ago) by doing a like for like comparison of its individual components
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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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
    ....I know that would make you happy my friend.

    Now add in the new divergence percentage... Happiness is fleeting.
    You can't use the same formula with the new divergence percentage, the formula was specifically designed for that one type of mutation to Base Pairs only I believe.
    remember the k/u factor? You can't use the value for u = 1.1*10^-8 if you do use the higher divergence rate..
    Now you can give me a reason why... not just a gut feeling but technical reasons.
    Have you read this article?
    What is the human mutation rate?


    What is the human mutation rate? – john hawks weblog

    I would need to double check his figures against the divergence spreadsheet to see how it compares to what we've discussed before. (the spreadsheet is on another computer so it will have to wait)
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    GTCethos,

    There is a major problem with the way your are treating indels. Dropping them into your equation the way you are doing will give misleading results. The dominant term in the equation is k over mu (sequence divergence over mutation rate). Implicit in the treatment of k is the assumption that we are dealing with single mutations. We divide the total number of mutations by the rate of mutation to derive a time.


    For each 5,000 bp retroviral insertion, you will treat this as 5,000 separate mutations. That is, each bp of the insertion contributes to the value of t. In reality, such an insertion is a just a single mutational event. Adding up all the indels, calculating their size as a percentage of the total genome length and adding this to k is not a sensible approach.
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    Quote Originally Posted by Zwirko View Post
    GTCethos,

    There is a major problem with the way your are treating indels. Dropping them into your equation the way you are doing will give misleading results. The dominant term in the equation is k over mu (sequence divergence over mutation rate). Implicit in the treatment of k is the assumption that we are dealing with single mutations. We divide the total number of mutations by the rate of mutation to derive a time.


    For each 5,000 bp retroviral insertion, you will treat this as 5,000 separate mutations. That is, each bp of the insertion contributes to the value of t. In reality, such an insertion is a just a single mutational event. Adding up all the indels, calculating their size as a percentage of the total genome length and adding this to k is not a sensible approach.
    Thanks - well put and I think that is the heart of the problem
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    For each 5,000 bp retroviral insertion, you will treat this as 5,000 separate mutations. That is, each bp of the insertion contributes to the value of t. In reality, such an insertion is a just a single mutational event. Adding up all the indels, calculating their size as a percentage of the total genome length and adding this to k is not a sensible approach.



    Actually aligning these individual base pairs in indels is handled by the alignment “tools” used. For this reason not all bp is counted. The indel itself is noted as a single mutation event. That is how I understand it….


    As far as the retroviral insertion, most of those have been relegated to the (non-coding) bit bucket and thus ignored.
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    Quote Originally Posted by GTCethos View Post
    For each 5,000 bp retroviral insertion, you will treat this as 5,000 separate mutations. That is, each bp of the insertion contributes to the value of t. In reality, such an insertion is a just a single mutational event. Adding up all the indels, calculating their size as a percentage of the total genome length and adding this to k is not a sensible approach.



    Actually aligning these individual base pairs in indels is handled by the alignment “tools” used. For this reason not all bp is counted. The indel itself is noted as a single mutation event. That is how I understand it….


    As far as the retroviral insertion, most of those have been relegated to the (non-coding) bit bucket and thus ignored.
    Can you back both of those statements with words from the studies you prefer?
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post
    For each 5,000 bp retroviral insertion, you will treat this as 5,000 separate mutations. That is, each bp of the insertion contributes to the value of t. In reality, such an insertion is a just a single mutational event. Adding up all the indels, calculating their size as a percentage of the total genome length and adding this to k is not a sensible approach.



    Actually aligning these individual base pairs in indels is handled by the alignment “tools” used. For this reason not all bp is counted. The indel itself is noted as a single mutation event. That is how I understand it….


    As far as the retroviral insertion, most of those have been relegated to the (non-coding) bit bucket and thus ignored.
    Can you back both of those statements with words from the studies you prefer?
    I believe the details of these observations is what separates us from the authorities in the field. I am not a scientist…


    Not likely to show up in such papers as we are dealing with here.
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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
    For each 5,000 bp retroviral insertion, you will treat this as 5,000 separate mutations. That is, each bp of the insertion contributes to the value of t. In reality, such an insertion is a just a single mutational event. Adding up all the indels, calculating their size as a percentage of the total genome length and adding this to k is not a sensible approach.



    Actually aligning these individual base pairs in indels is handled by the alignment “tools” used. For this reason not all bp is counted. The indel itself is noted as a single mutation event. That is how I understand it….


    As far as the retroviral insertion, most of those have been relegated to the (non-coding) bit bucket and thus ignored.
    Can you back both of those statements with words from the studies you prefer?
    I believe the details of these observations is what separates us from the authorities in the field. I am not a scientist…


    Not likely to show up in such papers as we are dealing with here.
    You implied you understood it to be so, where did that view come from?
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    Quote Originally Posted by GTCethos View Post
    Actually aligning these individual base pairs in indels is handled by the alignment “tools” used. For this reason not all bp is counted. The indel itself is noted as a single mutation event. That is how I understand it….
    YOU - right here on this thread - are counting the indels as a percentage of the total genome. You repeatedly added them to the 1.x% divergence value. That's one of the ways you arrived at 95% as well as your other value of 86 point something from Britten (2002).

    Quote Originally Posted by GTCethos View Post
    As far as the retroviral insertion, most of those have been relegated to the (non-coding) bit bucket and thus ignored.
    The vast majority of these indels (which include erv's) are in the non-coding component, see the Polavarapu (2011) paper you linked to previously. If you are now ignoring non-coding DNA then you are going to have to swallow a bitter pill and deal with the fact that the human and chimp genomes are almost identical. The 1.23% value is for coding and non-coding. If you ignore non-coding you are dealing with two genomes that differ by a fraction of a percent. Is that what you want to now claim?
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    The vast majority of these indels (which include erv's) are in the non-coding component, see the Polavarapu (2011) paper you linked to previously. If you are now ignoring non-coding DNA then you are going to have to swallow a bitter pill and deal with the fact that the human and chimp genomes are almost identical. The 1.23% value is for coding and non-coding. If you ignore non-coding you are dealing with two genomes that differ by a fraction of a percent. Is that what you want to now claim?



    I restricted my statement to the ERV’s… Although some ERV’s are now accepted to code. (as far as I know still not included)


    The new evidence I am accepting is indels directly influencing protein coding and phyloginy. The thought here is that since SNP’s in the protein coding are accepted so must the indels.


    “Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.”Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution - Springer


    We might also now include segmental duplication as being counted also.. Implicitly ignored in some current similarity counts.


    “It has recently become clear that segmental duplications (SDs) have had a very significant impact on genome plasticity during primate evolution.”
    http://link.springer.com/article/10.1007/s10577-007-1207-1
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    You don't seem to understand: the 1.23% figure includes the coding and non-coding.

    The snippets of brown text you include don't address any of the points I made in the post you are replying to. You are effectively arguing for a divergence value of less than 1% without realising it. All because you refuse to admit an error.
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    You don't seem to understand: the 1.23% figure includes the coding and non-coding.



    So SNP’s plus indels = 1.23%… Nonsence.
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    I have no problem proving SNP's plus indels > 1.23% and exceeds 3%.

    Let me give you my opinion. All the statistical evaluation of the HCLCA completely swings on similarity percentage.



    As humans we still do not know much about how DNA really works (we know some peripheral mechanisms in detail). In other words we know some of the how but little of the why. We know sites where proteins are coded for and how messenger RNA transcribes information in the genome… ect. But what about the regulatory long strings and epigenetic expression triggers and open reading frames? As of yet there is no adequate explanation of “molecular evolution”.


    All that we are doing here is playing some games with a simple relationship between numbers of mutations between a species, mutation rate and time to the LCA. By the formulation in this paper we have been examining, the largest value swing is clearly dependent on the number of mutations between a species (similarity percentage).


    In my humble opinion we have passed any hope of there being a common ancestor between humans and chimps when we hit a 97% similarity between the two species. To date this number is only getting worse for the evolutionist. If your hope is just to throw in some more mutations between generations (somewhere down the two lines) then you are going against the deleterious mutation rate (namely “U”). We see empirically what happens to humans when “U” gets too high (Hiroshima is proof).


    The problem is past the point of being intractable… Common descent is dead…

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    Quote Originally Posted by GTCethos View Post
    The vast majority of these indels (which include erv's) are in the non-coding component, see the Polavarapu (2011) paper you linked to previously. If you are now ignoring non-coding DNA then you are going to have to swallow a bitter pill and deal with the fact that the human and chimp genomes are almost identical. The 1.23% value is for coding and non-coding. If you ignore non-coding you are dealing with two genomes that differ by a fraction of a percent. Is that what you want to now claim?



    I restricted my statement to the ERV’s… Although some ERV’s are now accepted to code. (as far as I know still not included)


    The new evidence I am accepting is indels directly influencing protein coding and phyloginy. The thought here is that since SNP’s in the protein coding are accepted so must the indels.


    “Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.”Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution - Springer


    We might also now include segmental duplication as being counted also.. Implicitly ignored in some current similarity counts.


    “It has recently become clear that segmental duplications (SDs) have had a very significant impact on genome plasticity during primate evolution.”
    http://link.springer.com/article/10.1007/s10577-007-1207-1
    Those quotes only show what we already know, but don't go any way to support your counting method. So will you back down from the first of the two statements? It is possible #2 could still be a fact ("ignored" from the divergence count).
    Actually aligning these individual base pairs in indels is handled by the alignment “tools” used. For this reason not all bp is counted. The indel itself is noted as a single mutation event. That is how I understand it….


    As far as the retroviral insertion, most of those have been relegated to the (non-coding) bit bucket and thus ignored.
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    No. You dismissed a valid point I made by saying that non-coding DNA can be ignored. Thus, most of your beloved indels are gone and with it most of your divergence.

    You then said each was treated as a single mutation. Assume there are a million of them then. Add this to your value of k.
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    Quote Originally Posted by GTCethos
    In my humble opinion we have passed any hope of there being a common ancestor between humans and chimps when we hit a 97% similarity between the two species.
    What?
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    Quote Originally Posted by GTCethos View Post
    I have no problem proving SNP's plus indels > 1.23% and exceeds 3%.

    Let me give you my opinion. All the statistical evaluation of the HCLCA completely swings on similarity percentage.



    As humans we still do not know much about how DNA really works (we know some peripheral mechanisms in detail). In other words we know some of the how but little of the why. We know sites where proteins are coded for and how messenger RNA transcribes information in the genome… ect. But what about the regulatory long strings and epigenetic expression triggers and open reading frames? As of yet there is no adequate explanation of “molecular evolution”.


    All that we are doing here is playing some games with a simple relationship between numbers of mutations between a species, mutation rate and time to the LCA. By the formulation in this paper we have been examining, the largest value swing is clearly dependent on the number of mutations between a species (similarity percentage).


    In my humble opinion we have passed any hope of there being a common ancestor between humans and chimps when we hit a 97% similarity between the two species. To date this number is only getting worse for the evolutionist. If your hope is just to throw in some more mutations between generations (somewhere down the two lines) then you are going against the deleterious mutation rate (namely “U”). We see empirically what happens to humans when “U” gets too high (Hiroshima is proof).


    The problem is past the point of being intractable… Common descent is dead…

    When you talk of "we hit a 97% similarity between the two species" and make that sound bad, what is going on? That seems bad logic to me. If two organisms are 97% similar I'd say that is proof of common descent, but are you saying it isn't now?
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    I wonder what he'd think if he calculated divergence times for human-gorilla, chimp-gorilla, orang-human, gorilla-orang, chimp-bonobo etc?
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    Quote Originally Posted by GTCethos View Post
    In my humble opinion we have passed any hope of there being a common ancestor between humans and chimps when we hit a 97% similarity between the two species.
    a good thing Zwirko highlighted this piece of nonsense - why should a difference of a mere 3% prevent a common ancestor when closely related birds differ by that much ?
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Quote Originally Posted by marnixR View Post
    Quote Originally Posted by GTCethos View Post
    In my humble opinion we have passed any hope of there being a common ancestor between humans and chimps when we hit a 97% similarity between the two species.
    a good thing Zwirko highlighted this piece of nonsense - why should a difference of a mere 3% prevent a common ancestor when closely related birds differ by that much ?
    a good thing Zwirko highlighted this piece of nonsense - why should a difference of a mere 3% prevent a common ancestor when closely related birds differ by that much ?



    What birds of the same species differ by 3%? Closely related already assumes common descent. (not supported)
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    Quote Originally Posted by GTCethos View Post
    Quote Originally Posted by marnixR View Post
    Quote Originally Posted by GTCethos View Post
    In my humble opinion we have passed any hope of there being a common ancestor between humans and chimps when we hit a 97% similarity between the two species.
    a good thing Zwirko highlighted this piece of nonsense - why should a difference of a mere 3% prevent a common ancestor when closely related birds differ by that much ?
    a good thing Zwirko highlighted this piece of nonsense - why should a difference of a mere 3% prevent a common ancestor when closely related birds differ by that much ?



    What birds of the same species differ by 3%? Closely related already assumes common descent. (not supported)
    It is logical to assume a common descent when species "share" 90+% of genes. Under what circumstance would it be possible for species to share the same "fundamental" DNA and "not" be related? Is there any counter indication which places the evolutionary process from simple organism to greater adaption to the environment in doubt?

    Provide an example and justification, please.
    "Art is the creation of that which evokes an emotional response, leading to thoughts of the noblest kind" (W4U)
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    Evolution not only makes zero sense by mutation rates and similarity percentage but the logic is missing.


    The LCA of chimps and humans did not start to walk upright or develop a larger brain size or change it diet preferences. That same split that led to humans also led to chimps who are arboreal. So all that development that made us human took place in our line only. But with only half the noted divergence between humans and chimps. Do you see we are related more to the HCLCA than to chimps. So all this radical change from hominid to human took place with very little change in the genome, if we are indeed 98% similar to chimps. That has to be between 1% and 2% divergent from the HCLCA. But it can’t be close to 1% because that is how much variation there is between human races.


    Your 2% difference is nonsense by measurement and just logic.
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    Quote Originally Posted by GTCethos View Post
    Evolution not only makes zero sense by mutation rates and similarity percentage but the logic is missing.


    The LCA of chimps and humans did not start to walk upright or develop a larger brain size or change it diet preferences. That same split that led to humans also led to chimps who are arboreal. So all that development that made us human took place in our line only. But with only half the noted divergence between humans and chimps. Do you see we are related more to the HCLCA than to chimps. So all this radical change from hominid to human took place with very little change in the genome, if we are indeed 98% similar to chimps. That has to be between 1% and 2% divergent from the HCLCA. But it can’t be close to 1% because that is how much variation there is between human races.


    Your 2% difference is nonsense by measurement and just logic.
    You seem to be terribly confused (it is confusing with all the different ways of measuring divergence). There definitely isn't 1% difference between the races. I don't know the figure but it might be 1/100th of that.
    Do you see we are related more to the HCLCA than to chimps.
    That is true. Did someone say that is not true?
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    To W4U…

    It is logical to assume a common descent when species "share" 90+% of genes.


    Why? Is the null hypothesis so strong for this point of view to declare it fact?

    Under what circumstance would it be possible for species to share the same "fundamental" DNA and "not" be related?


    That is not a goal of this thread, to determine alternate hypothesis.

    Is there any counter indication which places the evolutionary process from simple organism to greater adaption to the environment in doubt?


    In the case of humans, yes, it is the genome mutation rate and similarity percentage between humans and chimps.

    Provide an example and justification, please.


    OK, There are simply not enough mutations available to explain morphing of a hominid genome into a human genome.
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    Are you ignoring me Ethos?
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    You seem to be terribly confused (it is confusing with all the different ways of measuring divergence). There definitely isn't 1% difference between the races. I don't know the figure but it might be 1/100th of that.



    It seems I have seen .1% or below somewhere…
    Last edited by GTCethos; October 8th, 2014 at 12:08 AM. Reason: forgot the decimal
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    Quote Originally Posted by GTCethos View Post
    You seem to be terribly confused (it is confusing with all the different ways of measuring divergence). There definitely isn't 1% difference between the races. I don't know the figure but it might be 1/100th of that.



    It seems I have seen 1% or below somewhere…
    It was more like 1% of the difference between chimps and humans. I read it recently and was surprised at the smallness of it. It would be rather difficult to Google it.
    What words would you use? Human genetic variation

    Human genetic variation - Wikipedia, the free encyclopedia
    Human genetic variation is the genetic differences both within and among populations. There may be multiple variants of any given gene in the human population (genes), leading to polymorphism. Many genes are not polymorphic, meaning that only a single allele is present in the population: the gene is then said to be fixed.[1] On average, biochemically all humans are 99.9% similar to any other humans.[2]
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  65. #165  
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    I did fix my error... thanks.
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  66. #166  
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    Quick question:


    Which genome would logically be closer to the HCLCA? The human genome or the chimp genome?


    Did the common ancestor of humans and chimps resemble Humans?


    The logical answer is No, so logic and paleoanthropology say the chimp.


    So where is the major change happening? Answer: in the human genome.


    But mutation rate is basically the same for humans and chimps.


    Human mutation rate should be much higher… Right… Wrong.
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  67. #167  
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    Quote Originally Posted by GTCethos View Post
    Quick question:


    Which genome would logically be closer to the HCLCA? The human genome or the chimp genome?


    Did the common ancestor of humans and chimps resemble Humans?


    The logical answer is No, so logic and paleoanthropology say the chimp.


    So where is the major change happening? Answer: in the human genome.


    But mutation rate is basically the same for humans and chimps.


    Human mutation rate should be much higher… Right… Wrong.
    How many questions? I think the Chimp would be closer to the CHLCA.
    The CHLCA did resemble both the chimp and humans (What does resemble mean? We are similar to the chimpanzee even as it is today.)
    I agree that since the hominid line adopted a different niche we ended up evolving more.
    The base pair change is not what reflects the major difference in phenotype AFAIK.
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  68. #168  
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    Quote Originally Posted by GTCethos View Post
    Evolution not only makes zero sense by mutation rates and similarity percentage but the logic is missing.


    The LCA of chimps and humans did not start to walk upright or develop a larger brain size or change it diet preferences. That same split that led to humans also led to chimps who are arboreal. So all that development that made us human took place in our line only. But with only half the noted divergence between humans and chimps. Do you see we are related more to the HCLCA than to chimps. So all this radical change from hominid to human took place with very little change in the genome, if we are indeed 98% similar to chimps. That has to be between 1% and 2% divergent from the HCLCA. But it can’t be close to 1% because that is how much variation there is between human races.


    Your 2% difference is nonsense by measurement and just logic.
    When an organism finds a comfortable niche in its environment, there is no need for further "natural selection", except perhaps refinement of already existing skills in coping with the environment. A tree dweller (apes) uses different skills than a ground dweller (humans).
    Why should we expect the same rate of change and variety in any organism when the result does not improve its survivability in a stable suitable environment, such as a rain forest?
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  69. #169  
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    Quote Originally Posted by GTCethos View Post
    What birds of the same species differ by 3%? Closely related already assumes common descent. (not supported)
    have a look at this paper, in particular the following section :

    Setting aside these polytypic species, the average intraspecific distance was very low, 0.27%, and the maximum average intraspecific difference was only 1.24%. Most congeneric species pairs showed divergences well above this value, but 13 species in four genera had interspecific distances that were below 1.25%. They included Larus argentatus, L. canus, L. delawarensis, L. glaucoides, L. hyperboreus, L. marinus, and L. thayeri (Herring Gull, Mew Gull, Ring-billed Gull, Iceland Gull, Glaucous Gull, Great Black-Backed Gull, and Thayer's Gull); Haematopus bachmani and H. palliatus (Black Oystercatcher and American Oystercatcher); Corvus brachyrhynchos and C. caurinus (American Crow and Northwestern Crow); and Anas platyrhynchos and A. rubripes (Mallard and American Black Duck)
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    GTCethos,

    In answer your quick questions and answers in #166: the lineage that led to chimpanzees, by some estimates, is actually considered to have undergone more evolution than the lineage that led to humans (don't confuse this with the silly term "more evolved"). More selection in a larger population. This result was achieved by comparing both the human and chimpanzee genomes to the macaque genome.
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    In answer your quick questions and answers in #166: the lineage that led to chimpanzees, by some estimates, is actually considered to have undergone more evolution than the lineage that led to humans (don't confuse this with the silly term "more evolved"). More selection in a larger population. This result was achieved by comparing both the human and chimpanzee genomes to the macaque genome.



    I am not saying I disagree with you here. But on the surface and just looking at morphology, who has changed more?


    A larger earlier population would solve some of a supposed time disparity since human chimp divergence, if the chromosome #2 fusion were not the cause of the split (at that point population drops to two in the human line). Also where is just one fossil from that population? Not a single one has been identified from a supposed large population.


    The macaque genome having 21 pairs of chromosomes split at what time from the chimp line? At that split, that population drops to two. I guess occum’s razor is on hold for now.
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  72. #172  
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    Quote Originally Posted by marnixR View Post
    Quote Originally Posted by GTCethos View Post
    What birds of the same species differ by 3%? Closely related already assumes common descent. (not supported)
    have a look at this paper, in particular the following section :

    Setting aside these polytypic species, the average intraspecific distance was very low, 0.27%, and the maximum average intraspecific difference was only 1.24%. Most congeneric species pairs showed divergences well above this value, but 13 species in four genera had interspecific distances that were below 1.25%. They included Larus argentatus, L. canus, L. delawarensis, L. glaucoides, L. hyperboreus, L. marinus, and L. thayeri (Herring Gull, Mew Gull, Ring-billed Gull, Iceland Gull, Glaucous Gull, Great Black-Backed Gull, and Thayer's Gull); Haematopus bachmani and H. palliatus (Black Oystercatcher and American Oystercatcher); Corvus brachyrhynchos and C. caurinus (American Crow and Northwestern Crow); and Anas platyrhynchos and A. rubripes (Mallard and American Black Duck)
    Thank you for the article… I read most of it. Thanks…


    Somethings you may have picked up that I did not:


    Is cytochrome-c barcoding passed on from classic recombination? Or strictly mitochondria transfer (mother to offspring)? I assume since it acts in the membrane of the mitochondria it is by mother to offspring.


    One thing here is the lack of any suggestion that it is any kind of molecular clock. Plants and animals posses this same compound and it is highly conserved in all. So the difference between suggested bird species could be 100 years or 1 million years or 100 million years… Or 20 years.
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  73. #173  
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    Quote Originally Posted by Zwirko View Post
    GTCethos,

    In answer your quick questions and answers in #166: the lineage that led to chimpanzees, by some estimates, is actually considered to have undergone more evolution than the lineage that led to humans (don't confuse this with the silly term "more evolved"). More selection in a larger population. This result was achieved by comparing both the human and chimpanzee genomes to the macaque genome.
    Where was this study please?
    Reference please?
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    What about some genes in humans and chimps that are present in one species and not the other? Are they de novo creations of nucleotides or are they composed of rearrangements of existing genes?



    It turns out that the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans. If there are 22,000 genes in the genome, then this total of 1,418 differences represents 6.4% of the genes.


    It's important to note that this does not mean that entirely new genes are created or destroyed. What it means is that there have been duplication events such that a gene has been duplicated in one of the lineages. For example, let's say that the region of the chromosome containing the α-globin genes was duplicated in the chimpanzee lineage. This would count as a gain in chimps relative to humans.


    http://sandwalk.blogspot.com/2006/12/mammalian-gene-families-humans-and.html
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  75. #175  
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    Quote Originally Posted by GTCethos View Post


    What about some genes in humans and chimps that are present in one species and not the other? Are they de novo creations of nucleotides or are they composed of rearrangements of existing genes?



    It turns out that the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans. If there are 22,000 genes in the genome, then this total of 1,418 differences represents 6.4% of the genes.


    It's important to note that this does not mean that entirely new genes are created or destroyed. What it means is that there have been duplication events such that a gene has been duplicated in one of the lineages. For example, let's say that the region of the chromosome containing the α-globin genes was duplicated in the chimpanzee lineage. This would count as a gain in chimps relative to humans.


    http://sandwalk.blogspot.com/2006/12/mammalian-gene-families-humans-and.html
    Those figures seem rather high. Does anyone have confirmation of those numbers?
    the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans.
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  76. #176  
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by GTCethos View Post


    What about some genes in humans and chimps that are present in one species and not the other? Are they de novo creations of nucleotides or are they composed of rearrangements of existing genes?



    It turns out that the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans. If there are 22,000 genes in the genome, then this total of 1,418 differences represents 6.4% of the genes.


    It's important to note that this does not mean that entirely new genes are created or destroyed. What it means is that there have been duplication events such that a gene has been duplicated in one of the lineages. For example, let's say that the region of the chromosome containing the α-globin genes was duplicated in the chimpanzee lineage. This would count as a gain in chimps relative to humans.


    http://sandwalk.blogspot.com/2006/12/mammalian-gene-families-humans-and.html
    Those figures seem rather high. Does anyone have confirmation of those numbers?
    the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans.
    There are plenty of references to this aspect but which ones can be trusted??
    I found this article a good easy to read starting point.
    Human-chimp Difference May Be Bigger -- ScienceDaily
    Human-chimp Difference May Be Bigger

    That finding complements reports by University of Colorado and University of Michigan researchers in the journals Science and PLoS Biology earlier this year, in which researchers showed that both gains and losses of individual genes have contributed to human divergence from chimpanzees and other primates.Hahn and his research partners examined 110,000 genes in 9,990 gene families that are shared by humans, common chimpanzees (Pan troglodytes), mice, rats and dogs. The scientists found that 5,622, or 56 percent, of the gene families they studied from these five species have grown or shrunk in the number of genes per gene family, suggesting changes in gene number have been so common as to constitute an evolutionary "revolving door."
    The researchers paid special attention to gene number changes between humans and chimps. Using a statistical method they devised, the scientists inferred humans have gained 689 genes (through the duplication of existing genes) and lost 86 genes since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence, the total gene differences between humans and chimps was estimated to be about 6 percent.
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  77. #177  
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    Human-chimp Difference May Be Bigger -- ScienceDaily

    I have had the numbers for some time but not the origin. Thanks…
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    Quote Originally Posted by GTCethos View Post
    Human-chimp Difference May Be Bigger -- ScienceDaily

    I have had the numbers for some time but not the origin. Thanks…
    Was it saying the same thing you were saying? Some of the numbers were the same but the categories were expressed differently weren't they?
    you said "the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans.

    But they said: "humans have gained 689 genes (through the duplication of existing genes) and lost 86 genes since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence,"

    Are those two statements saying the same thing?
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