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Similarity of human and chimp DNA is down.

Discussion in 'Creation & Evolution' started by Zaius137, Sep 17, 2011.

  1. Loudmouth

    Loudmouth Contributor

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    Is math really this hard for you? You couldn't obviously, but no one is claiming that you could. Instead, the 98.74% number is from a comparison of 2.4 billion bases, not 100.

    The minimum number of bases that you would need to get 98.74% is 10,000 bases where 9,874 bases are identical and 126 are different.

    Where did the 90% come from in my example?

    What is bogus about this comparison?

    seq 1: AAAAAAAAAA
    seq 2: AAAAAAAAAT

    Similarity is 90%.

    Please explain why this percent similarity is bogus.
     
  2. Loudmouth

    Loudmouth Contributor

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    What does this have to do with the sequencing of the chimp genome and its comparison to the human genome?
     
  3. cupid dave

    cupid dave Guest




    Consider these links...
    http://kofh2u.tripod.com/id143.html


    The Last Human: A Guide to Twenty-Two Species of Extinct Humans
    by G.J. Sawyer, Viktor Deak
    Hardcover, 256 pages
    Published June 28th 2007 by Yale University Press
     

    Attached Files:

  4. cupid dave

    cupid dave Guest

    It has to do with the irrelevancy of even discussing the compariason if the matter is mute, assuming that Genesis is basically supported by the paleontology of today.
     
  5. Loudmouth

    Loudmouth Contributor

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    Why would it be moot? Even without evolution we can sequence the chimp genome and compare it to the human genome. Whether God created the differences between the genomes or if evolution did the differences are still real.

    Here are two 30 bp sequences:

    seq 1: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    seq 2: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAT

    As you can see, they are identical except for the last base which is different. I say that these two sequences are 96.67% similar. Zaius137, through the method used at Uncommon Descent, says that they are 0% similar. Which do you think is correct?
     
  6. cupid dave

    cupid dave Guest


    U R

    Since both the Bible and Science supports our evolution from Apes it seems supportive of what you say here, that these two seq were one of the points of further divergence.
     
  7. Loudmouth

    Loudmouth Contributor

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    Those two sequences are completely arbitrary. I just made them up. We are talking about the method used to compare sequences. Do you think it is correct to say that those two sequences are 96.67% identical or 0% identical?
     
  8. Zaius137

    Zaius137 Real science and faith are compatible.

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    By a simple ratio you come up with an answer here. But if you applied this method to the two genomes you would in fact get very bad results because of all the messaging for alignment. First off you would have to compare one for one each base pair (not possible) because of the length problem. I would love a one for one comparison that would clinch the deal for me.

    You know we finally have gotten to the crux of the matter. Does a match no match, (like Uncommon Decent method), actually produce a comparison after alignment. I think it is clear now why the Uncommon Decent method may be valid.

    At this point I would like the call attention to a possible explanation. The chimp genome that the uncommon Decent used for comparison was not raw data; it was in fact the aligned data published on the web. That indicates to me that the alignment was an artifact of various tools used to align it. The 2.4Gb that aligned was included in that genome. The .7Gb that did not align was not included. In essence the Uncommon Decent picked up the fact that the genomes as they stand are only 62% the same not 98.74% the same as concluded in the evolution fairytale. The truth is that real data was not used in the 98.74% conclusion. It is speculation that the missing .7Gb DNA will align to a human scaffold. In other words there is a forgone conclusion to data that might point out another possibility. Sorry that is just bad science and it will always be bad science to draw forgone conclusions to a bad theory. Science rests on experimental observation not prejudiced speculation.
     
  9. sfs

    sfs Senior Member

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    Frankly, it looks like lunacy. It's an exercise in ignoring what the Biblical text actually says in favor of projecting something completely foreign onto it. The text says that Cain tilled the ground, so that means he represents a species that was vegetarian. Why not have him be a species that lived in holes in the ground instead, or the first to descend from the trees to the ground? Tubalcain is presented as the origin of brass and iron working -- several million years before those skills were actually developed.

    Really, if you're going to ignore what the Bible says, just go ahead and ignore it. This way lies rump of skunk and madness.

    No one thinks all of those species were ancestors of modern humans -- cousins, yes, but not ancestors.
     
  10. sfs

    sfs Senior Member

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    There was no .7 Gb that did not align; that's something you made up in your head. 0.09 Gb did not align, and 0.24 Gb aligned to multiple regions in human.
     
  11. Loudmouth

    Loudmouth Contributor

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    How else are you supposed to align orthologous sequence while still detecting indels? How does the UD method detect indels (hint: it doesn't)?

    What length problem?

    The UD method can not detect indels. That makes it a bad method right from the start. Second, the UD method is asking a superfluous and irrelevant question. The UD method is asking how many randomly chosen 30 bp segments have an exact match in the other genome. As sfs mentioned earlier, the only reason I would do this is if I was designing specific primers for stringent PCR where a one base pair difference would not amplify. That is the only use I can see for the UD method.

    You have yet to show why these tools would produce false contigs.

    This is false, as sfs has already pointed out.

    You are once again claiming that 120 inches is different than 10 feet. The two results have different units.

    It is also speculation that the unsequenced DNA will not align as you have been claiming. We have yet to see a convincing argument that the divergence in the ambiguously aligned DNA will be strikingly different than the >70% of the genome that is quality sequence.

    You have not shown us any observations that puts the 98.74% (on a bp to bp comparison) in doubt. The UD method returns very comparable results when it is converted into the same units.
     
  12. Zaius137

    Zaius137 Real science and faith are compatible.

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    Back to Loudmouth just for a moment.

    “Here are two 30 bp sequences:

    seq 1: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

    seq 2: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAT

    As you can see, they are identical except for the last base which is different. I say that these two sequences are 96.67% similar. Zaius137, through the method used at Uncommon Descent, says that they are 0% similar. Which do you think is correct?”




    Let’s look at this for a moment given the 30 bp interval.

    Remember I said a bp on bp comparison is hard on the numbers. If it can be done at all?

    First by (sfs)… (.9667)^30 = .36 or 36% Not a very good probability
    Second e^-m (poisson distribution) (occurrence per interval ~ .97) = (1-.38) = .62 or 62% of the time over this interval. Not good but better.

    So yes lets use your method and call the match 62% of the time for a 30bp interval.
     
  13. Zaius137

    Zaius137 Real science and faith are compatible.

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    (sfs) What does this mean?
    “Nucleotide divergence. 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.genome.gov/Pages/Research/DIR/Chimp_Analysis.pdf
     
  14. Loudmouth

    Loudmouth Contributor

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    What I posted before:

    seq 1: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    seq 2: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAT

    As you can see, they are identical except for the last base which is different. I say that these two sequences are 96.67% similar. Zaius137, through the method used at Uncommon Descent, says that they are 0% similar. Which do you think is correct?”


    I did exactly that in the above example. The bp to bp comparison gives a result of 96.67% (29/30) similarity. Using the method from the author at UD, the similarity is 0% because there is not a perfect match between the 30 bp segments. Which do you think accurately represents the comparison, and why?

    Probability of what?

    What is the distribution that you are looking for?

    How did you get 62% from the comparison of the two 30 bp segments that I created above? Please show your math, and justify each step.
     
  15. Zaius137

    Zaius137 Real science and faith are compatible.

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    What does a comparison of two strings of genes give us? It is just data, what the important information to have is average mutations per interval or overall mutations per data set from which to draw average mutations per interval. Once we have that number we can predict the average matches in a genome. When you say a genome is 99% similar to another genome you basically are saying that average similarity/ entire genome can generate a percentage. Now if you do a match no match scenario you can employ the binomial distribution which will approach the poisson distribution under the right conditions.
     
  16. sfs

    sfs Senior Member

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    It means that 2.4 Gb of sequence in the two genomes could be aligned to each other.

    As I have noted repeatedly, another 0.24 Gb of sequence could be aligned, but the chimpanzee assembly pieces in question aligned to multiple places in the human genome. This sort of thing is caused by 1) poor assembly of the chimpanzee genome (mostly the result of nearly identical duplicated sequence that is hard to assemble); 2) poor assembly of the human genome (same reason); and 3) sequence that is duplicated in humans but not in chimpanzees (i.e. the chimpanzee really should align to multiple places in human).

    An additional 0.09 Gb of chimpanzee sequence did not align at all to human. This can be caused by missing sequence in the human assembly, and by non-chimpanzee DNA in the chimp sequencing. (Little of this is likely to result from real differences, since for real insertions and deletions we should be able to find the edges of the indel, where the sequence does align).

    These together total a little over 2.7 Gb, which is the amount of chimpanzee genome that was sequenced. That means that a little over 0.1 Gb of the chimpanzee genome did not have enough sequencing coverage to be evaluated at all. All of this adds up to ~2.85 Gb, the length of the euchromatic genome in both humans and chimpanzees -- which is what we mean when we talk about sequencing a genome.
     
  17. Naraoia

    Naraoia Apprentice Biologist

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    Um... did it ever occur to you that the number of "species in our ascent to modern man" depends on where you start?

    Furthermore, no one even knows which (if any) of the known early hominin species were our direct ancestors. People can't even agree how many species some of our ancestors/cousins were (Homo erectus/ergaster for one). And that is just hominins. Pick a starting point further back in time, and even the vaguest illusion of an ability to actually count ancestral species vanishes.
     
  18. anabaptistfaith

    anabaptistfaith Newbie

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    Let's have a scientist himself comment on the similarity of chimps and humans. Specifically the similarity of the recently-sequenced Y chromosome. Here's the link: Chimp Y chromosome
     
  19. sfs

    sfs Senior Member

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    I don't know who it is you linked to, but he doesn't seem to know much about Y chromosome genetics. He seems to think it was a surprise that the Y controls sex determination in humans -- which is simply ridiculous from someone with a PhD in biology. He also claims that the evolution of the Y should slow down with loss of genes (why?) and is wrong on several other points (e.g. he thinks that large divergence between species on the Y is difficult to reconcile with low diversity within humans there, whereas in reality this is just what you would expect to see if positive selection acts frequently on the Y). On the other hand, his basic point is correct: the chimpanzee and human Y chromosomes are more different than anyone thought likely. Cool discovery, in fact. It does fit in with the general pattern of evolution, which is that sperm/testis-related proteins tend to evolve much faster than most proteins.
     
  20. cupid dave

    cupid dave Guest

    ?
    read more:


    The Last Human: A Guide to Twenty-Two Species of Extinct Humans
    by G.J. Sawyer, Viktor Deak
    Hardcover, 256 pages
    Published June 28th 2007 by Yale University Press

    Compare these 22 extinct species to the 22 names from Adam through Noah's three sons, Caucasian, Negroid, and mongoloid.


    see this link:
    http://kofh2u.tripod.com/id143.html
     

    Attached Files:

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