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Author Topic:   Why is evolution so controversial?
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 875 of 969 (740524)
11-05-2014 2:56 PM
Reply to: Message 871 by Dr Adequate
11-05-2014 2:04 PM


Re: Any real evidence for evolution, point on point.
Good post....

This message is a reply to:
 Message 871 by Dr Adequate, posted 11-05-2014 2:04 PM Dr Adequate has not replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 884 of 969 (740573)
11-05-2014 10:17 PM
Reply to: Message 877 by Taq
11-05-2014 4:18 PM


Re: Any real evidence for evolution, point on point.
quote:
Let's look at the chimp genome paper:
"Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements."
Nature - Not Found
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.
quote:
For a 3 billion base haploid genome, 35 million substitutions would be 1.16%, consistent with other reports.
I agree for the gene segments analyzed.
quote:
If just 5 million indel events are added without reference to bases, this would be 40 million, or 1.33%. In order to get to the 5%, you need to transfer those 5 million indels into 90 million bases.
I 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.
In 5% of the chimpanzee genes, indels or substitutions caused premature stop codons that rendered the affected transcripts nonfunctional. Taken together, our findings demonstrate that indels comprise the majority of the genomic divergence. 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 | SpringerLink
quote:
The analysis of modest-sized insertions reveals ~32 Mb of human-specific sequence and ~35 Mb of chimpanzee-specific sequence, contained in ~5 million events in each species (Supplementary Information ‘Genome evolution’ and Supplementary Fig. S5)."
Nature - Not Found
Fine for the segments selected by the authors
Here is a link to the paper again that promotes 5% sequence divergence.
Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink
Here is a shameless repost of the calculation I did with only using indel variables from the proceeding paper and reduced mutation rate for indels.
2.37% -1.52% Gives ~.8% for human and chimp divergence concerning indels this seems low but it must be true.
Subbing in for indels gives:
t= number of generations since divergence (Generation =20 years)
k= percentage of autosomal sequence divergence Estimated at .8% (for indels)
Ne= effective size of population ~10^5
(u)=mutation rate 2 x 10^-9 (for indels)
t= .5(k/u-4Ne) from Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic
t = 1.8 million generations or 36 million years since divergence considering indels.
So the HCLCA was about 36 million years ago.
(u) for substations is ~70 per generation. 1/7 (u) makes (u’) = 10 mutation per generation in humans for indels only. (u’) is calculated by (10/6.4x10^9 ~ 2x 10^-9). (u’) for indels is ~ 2x10^-9. In using the empirical value of measured mutation rate and assuming 1/7(u) for indels.
As I have stated over and over indel and substitution rates are addable. They both reflect autosomal sequence divergence for the (k) in the calculation in question.

This message is a reply to:
 Message 877 by Taq, posted 11-05-2014 4:18 PM Taq has replied

Replies to this message:
 Message 887 by Taq, posted 11-06-2014 12:03 AM zaius137 has replied
 Message 889 by sfs, posted 11-06-2014 12:07 AM zaius137 has not replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 885 of 969 (740574)
11-05-2014 10:31 PM
Reply to: Message 880 by Taq
11-05-2014 5:11 PM


Re: Any real evidence for evolution, point on point.
quote:
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.
Just what I was looking for. thanks.

This message is a reply to:
 Message 880 by Taq, posted 11-05-2014 5:11 PM Taq has replied

Replies to this message:
 Message 892 by Taq, posted 11-06-2014 12:38 AM zaius137 has not replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 886 of 969 (740575)
11-05-2014 11:06 PM


The end of evolution
Just for one minute, step back and take a overall picture.
Do you see what is driving these large divergence times? 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.
This is that perfect storm I mentioned way back in the posts.
Regardless if you say I am misusing Nachman and Crowell’s paper. The trend is that Paleoanthropology and genetics are becoming more discordant with time. This is not supposed to happen with a healthy theory. It is evolution in decline.

Replies to this message:
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 Message 891 by Dr Adequate, posted 11-06-2014 12:20 AM zaius137 has not replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 894 of 969 (740624)
11-06-2014 12:20 PM
Reply to: Message 887 by Taq
11-06-2014 12:03 AM


Re: Any real evidence for evolution, point on point.
quote:
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.
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).
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.
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. "
Nature - Not Found
Look at Table 1. They covered 2.7 billion bases.
Nature - Not Found
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.
So you will accept the initial sequencing interpretation over all subsequent papers? Sorry I do not
quote:
As I stated earlier, they can only be added if they have the same units.
And indels do the difference in mutations per site.
(divergence in) Mutaions per site (k)/ mutations per site per generation (u) = generations t=.5(k/u-4Ne) which gives t the units of generation.
Your argument is moot.

This message is a reply to:
 Message 887 by Taq, posted 11-06-2014 12:03 AM Taq has replied

Replies to this message:
 Message 895 by Dr Adequate, posted 11-06-2014 12:29 PM zaius137 has replied
 Message 897 by Taq, posted 11-06-2014 12:34 PM zaius137 has replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 896 of 969 (740627)
11-06-2014 12:32 PM
Reply to: Message 893 by Taq
11-06-2014 12:43 AM


Re: Any real evidence for evolution, point on point.
quote:
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.
Good count of mutations is (1) this gives (1) mutation per site. (k) = number of mutations different between species / number of sites
In this case:
Number of mutations = 1
Number of sites = 1
1/1 = 100% in this case.
Now given 2 sites...
Given 2 sites with 1 mutation.
Number of mutations = 1
number of sites =2
percent divergence = 1/2 or 50%.
Get it, Got it Mutations per site..

This message is a reply to:
 Message 893 by Taq, posted 11-06-2014 12:43 AM Taq has replied

Replies to this message:
 Message 899 by Taq, posted 11-06-2014 12:35 PM zaius137 has replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 898 of 969 (740630)
11-06-2014 12:35 PM
Reply to: Message 895 by Dr Adequate
11-06-2014 12:29 PM


Re: Any real evidence for evolution, point on point.
Good post... Too early for cheers.
Well maybe not in your case... Cheers!

This message is a reply to:
 Message 895 by Dr Adequate, posted 11-06-2014 12:29 PM Dr Adequate has replied

Replies to this message:
 Message 900 by Dr Adequate, posted 11-06-2014 12:42 PM zaius137 has not replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 901 of 969 (740637)
11-06-2014 1:01 PM
Reply to: Message 897 by Taq
11-06-2014 12:34 PM


Re: Any real evidence for evolution, point on point.
quote:
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.
Believe it or not sfs and I have hashed this out over a year ago. I never claimed 0% homology. By the same token sfs could not claim (100%) homology. It is as I have argued here, what are the important genes and how different are they?
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 897 by Taq, posted 11-06-2014 12:34 PM Taq has replied

Replies to this message:
 Message 903 by Taq, posted 11-06-2014 1:16 PM zaius137 has replied
 Message 905 by sfs, posted 11-06-2014 1:47 PM zaius137 has replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 902 of 969 (740638)
11-06-2014 1:04 PM
Reply to: Message 899 by Taq
11-06-2014 12:35 PM


Re: Any real evidence for evolution, point on point.
You are wearing a hole in the carpet my friend...
Site identified, site compared. Site unidentified site not compared.

This message is a reply to:
 Message 899 by Taq, posted 11-06-2014 12:35 PM Taq has replied

Replies to this message:
 Message 904 by Taq, posted 11-06-2014 1:17 PM zaius137 has replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 906 of 969 (740648)
11-06-2014 1:50 PM
Reply to: Message 903 by Taq
11-06-2014 1:16 PM


Re: Any real evidence for evolution, point on point.
quote:
Then where did you get the 70% from? How do you determine divergence when the DNA under question hasn't even been compared?
I was very carful to claim that it could be as high as 70%, not that it was.
quote:
I find that to be a strange statement since your main argument is based on a paper that compares pseudogenes.
Are pseudogenes important? My only complaint here it the ~1.5% divergence.

This message is a reply to:
 Message 903 by Taq, posted 11-06-2014 1:16 PM Taq has replied

Replies to this message:
 Message 909 by Taq, posted 11-06-2014 2:31 PM zaius137 has replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 907 of 969 (740651)
11-06-2014 2:03 PM
Reply to: Message 905 by sfs
11-06-2014 1:47 PM


Re: Any real evidence for evolution, point on point.
quote:
If by "hashed out", you mean that you made rambling, inaccurate claims, I corrected you, and you ignored me, then yes, we hashed it out.
I remember I maintained a point on several issues.
If I remember correctly, your little program you wrote was using asexual reproduction rates contrary to our sexual reproduction discussion, your similarity in protein coding segments was not using the poisson distribution like you should have. etc.
The past is the past, I always say....Ohh... by the way I did prevail in the discussion on alignment.

This message is a reply to:
 Message 905 by sfs, posted 11-06-2014 1:47 PM sfs has replied

Replies to this message:
 Message 908 by sfs, posted 11-06-2014 2:21 PM zaius137 has replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 910 of 969 (740659)
11-06-2014 2:38 PM
Reply to: Message 904 by Taq
11-06-2014 1:17 PM


Re: Any real evidence for evolution, point on point.
quote:
There are 20 identified sites in seq B.
Perhaps you want to try again?
How many mutations over those 20 sites? And the resulting percentage?
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
Number of divergent sites is 5/20 or 25% divergent (75% similar). As per the definition... "compared" Mutation per site.
If the site is 20 bp then you have 1 mutation per site.
number of sites = 1
number of mutations = 1
divergence is 100%..
But you only compared 1 site.
Would you like to use the bp per bp comparison for the entire genome?
I thought you claimed that a single insertion is counted as one mutation?
Are you retracting that statement?
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 904 by Taq, posted 11-06-2014 1:17 PM Taq has replied

Replies to this message:
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zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 911 of 969 (740663)
11-06-2014 2:47 PM
Reply to: Message 908 by sfs
11-06-2014 2:21 PM


Re: Any real evidence for evolution, point on point.
quote:
Of course you think you prevailed. That's because, as is obvious from this thread, that you understand so little of what you're talking about that you can have no way of telling when you're wrong.
Then I can use the 1/7(u) again?

This message is a reply to:
 Message 908 by sfs, posted 11-06-2014 2:21 PM sfs has not replied

Replies to this message:
 Message 913 by Taq, posted 11-06-2014 2:49 PM zaius137 has replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 914 of 969 (740667)
11-06-2014 2:55 PM
Reply to: Message 909 by Taq
11-06-2014 2:31 PM


Re: Any real evidence for evolution, point on point.
quote:
Why do you continue to complain about statistics you don't understand?
I understand the papers I cited claim more than 1.5% divergence counting indels. So far no argument you have made causes me to doubt The authors conclusions, since they are recognized authorities in the field.
Are you still claiming they are wrong?

This message is a reply to:
 Message 909 by Taq, posted 11-06-2014 2:31 PM Taq has replied

Replies to this message:
 Message 917 by Taq, posted 11-06-2014 3:40 PM zaius137 has replied

  
zaius137
Member (Idle past 3409 days)
Posts: 407
Joined: 05-08-2012


Message 915 of 969 (740668)
11-06-2014 2:57 PM
Reply to: Message 913 by Taq
11-06-2014 2:49 PM


Re: Any real evidence for evolution, point on point.
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.
Again (u) is not a percentage. It is rate of mutation per generation.
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 913 by Taq, posted 11-06-2014 2:49 PM Taq has replied

Replies to this message:
 Message 916 by Taq, posted 11-06-2014 3:35 PM zaius137 has not replied

  
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