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Author | Topic: Why is evolution so controversial? | |||||||||||||||||||||||||||||||||||||||
Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
Here is my attempt at using Zaius math to show that it is impossible to drive to a store just 5 km away.
We will be using a car. In order for a car to be a viable mode of transportation, it will need to be able to reach the store within the lifetime of an individual (80 years) at the speed it was designed to go (100 kph). I will show that a car is not a viable means of getting to the store. First, we need to know the distance to the store. According to my calculations from the first paragraph, that would be 5 x 10^15 picometers. As I discussed above, a car is designed to go 100. Therefore, it would take 5 x 10^13 hours to reach the store. By my calculations, that is 5703979438 years. Therefore, it is impossible to get to the store 5 km away using a car.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
I assume the same holds true with how indels were counted alongside substation sequences, presented in the paper I cited. Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink
How many indels were there? What was the average size of the indels?
Looking forward to your finding. Also I am curious how insertions in multiples of 3 are counted (those that change open reading frames). Indels of 1 base or more are counted as single indels. A 3 base indel is one indel. An 18 base indel is 1 indel. A 5 base indel is 1 indel.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
Another is that it's much harder to accurately detect indels, especially ones that are more than a few base pairs. Is this due to the difficulty of aligning gappy sequence and distinguishing indels from DNA that wasn't sequenced? Could these problems by solved by using slower, but more accurate sequencing methods on BAC clones? Edited by Taq, : No reason given. Edited by Taq, : No reason given.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
I am sure this is accurate for what genes this paper looked at. These numbers do vary from paper to paper according to the focus of the researchers. They looked at over 90% of the chimp genome, including the non-coding DNA. Their sequencing covered about 95% of the genome, if memory serves. Genes only make up about 3% of the genome. The chimp genome paper is the definitive paper for comparing the chimp genome to the human genome. Any subsequent papers will only be covering the 10% that they were not able to align with the human genome, or haplotypes within the chimp genome.
would say you can not get to 5% from 1.33% in these results. Like I say, different findings for different genes investigated. Here is a paper comparing different genes ( it covered exclusively chromosome 21 in humans and chromosome 22 in chimps) high-quality BAC clone sequences of the homologous chimpanzee chromosome 22 quote. I don't think you have a grasp of how much the chimp genome paper covered. "The draft genome assemblygenerated from ~3.6-fold sequence redundancy of the autosomes and ~1.8-fold redundancy of both sex chromosomescovers ~94% of the chimpanzee genome with >98% of the sequence in high-quality bases. "Initial sequence of the chimpanzee genome and comparison with the human genome | Nature Look at Table 1. They covered 2.7 billion bases. Initial sequence of the chimpanzee genome and comparison with the human genome | Nature They didn't look at a handful of genes or just a couple chromosomes. They sequenced nearly the entire genome and then compared it to the draft human genome which is even more complete than the chimp genome.
As I have stated over and over indel and substitution rates are addable/ As I stated earlier, they can only be added if they have the same units. Edited by Taq, : No reason given.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
The big deal is the rate of mutation Indels rate of occurrence is slower than that of substitutions. Also the relevance of indels to human chimp divergence is only growing with new research. The rate of mutation is not the same as the rate of bases changed. That's what you keep forgetting. Scientists have understood the relevance of indels for the entire time. No one is ignoring them, and no one has been ignoring them.
The trend is that Paleoanthropology and genetics are becoming more discordant with time. References?
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Taq Member Posts: 10084 Joined: Member Rating: 5.1
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Just what I was looking for. thanks. With that in mind, let's see if this example sticks this time. Here are two sequences that differ by 1 indel.
seq A: AGTGTCT_____ACTATCCT seq B: AGTGTCTCCCCCACTATCCT The sequences differ by 5 bases. That is a 25% nucleotide difference out of the 20 bases in seq B. However, there is only 1 mutation, so the difference by number of mutations is 5% (if we count 1 mutation in 20 bases). Although sfs will probably correct me and point out that 5% is not technically correct, it should give you a feel for the difference between number of bases and number of mutations.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1
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In particular, the coding sequence of genes makes up less than 2% of the genome. I would even be wiling to add in RNA genes, upstream regulatory elements, and splicing sites. I could even be talked into 5% or even 10% of the genome that is under negative selection if we consider genes to be heritable units that factor into fitness. However, to come away with the impression that the chimp genome paper only covered a few genes . . . well, that's a bird of a different color. Luckily, zaius is here to clear up any misunderstandings you have about genetics. Edited by Taq, : No reason given.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
Look my friend not all the differences they found ended up in the percentage of autosomal variance. If they counted all divergence, humans and chimps would have a similarity less than 70%. About 700 million base pair did not even align at that time (that is .7/6.2 or about 11% of the two genomes). sfs can explain it much better than I can, but "not aligning" is not a synonym for "0% homology". If you don't know where the sequence fits in the chimp genome then you can't even compare it to the human genome to begin with. Therefore, you have no evidence that the unaligned sequence would have 0% homology. Even random sequence will have 25% homology.
I have no problems with the findings except the same old 1.5% divergence (that is an interpretation). Face the fact that interpretive comparisons are a bit more than a cherry pick (especially this one). Let us talk about papers written after the initial sequencing back in 2005 for further new and hopefully more objective interpretation. Any paper after 2005 will also be interpretations. Unless you can show us how the reported sequence in the 2005 paper is wrong, I don't see what objection you really have. They sequenced 94% of the genome. Do you really think the other 6% is going to be strikingly different?
And indels do the difference in mutations per site. The 5% number you keep using is in "bases changed". Therfore, they are not in the same units.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
In this case: Number of mutations = 1 Number of sites = 1
In seq B there are 20 sites. Perhaps you want to try that again?
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
I never claimed 0% homology. Then where did you get the 70% from? How do you determine divergence when the DNA under question hasn't even been compared?
It is as I have argued here, what are the important genes and how different are they? I find that to be a strange statement since your main argument is based on a paper that compares pseudogenes.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
You are wearing a hole in the carpet my friend... Site identified, site compared. Site unidentified site not compared. There are 20 identified sites in seq B. Perhaps you want to try again?
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
I was very carful to claim that it could be as high as 70%, not that it was. Why would you expect the 10% of the genome that wasn't compared between humans and chimps to be different than the 90% that was compared?
Are pseudogenes important? My only complaint here it the ~1.5% divergence. Are pseudogenes important for what? Why do you continue to complain about statistics you don't understand?
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
If you identified 20 sites then it is bp per bp on each segment. You have sites 7-11 100% divergent. Divergence per site is: Number of mutations = 5 Number of sites = 20
There is only 1 mutation. Want to try that again?
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
Then I can use the 1/7(u) again? If (u) is 1.3%, then an additional indel rate of (u)/7 would be a total of 1.49%. That would work for me. Edited by Taq, : No reason given.
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Taq Member Posts: 10084 Joined: Member Rating: 5.1 |
Again (u) is not a percentage. It is rate of mutation per generation. Then we are looking at 10 indels per generation (70 subsitutions per generation). Each indel is 20 bases, on average. 10 indels at 20 bases each would be 200 bases changed plus the 70 from substitutions.
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