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


Message 796 of 969 (740200)
11-02-2014 4:36 PM


A mutation is a mutation is a mutation.
New papers showing a drop in human chimp similarity abound. Regardless if the percentage number I used is right, the conclusion is still bad for evolution.
Here is representation of a SNP verses a indel event. Both are mutations and both decrease the sequence similarity (bp count is irrelevant).
Humans and chimps are far different than just 1.3% in their genomes. It seems like a perfect storm in new genetic discoveries all against common descent.
Outlining the individual problems from genetic studies:
There are not enough mutations available since divergence to accommodate a 95% similarity. 5.6 million years (the fossil nonsense) is below the needed time frame to produce enough beneficial mutations from divergence. Excessive junk DNA in the human and chimp genome is not real. Ancient bottlenecks in small human populations is unstable and can not explain observed linkage disequilibrium in humans. Epigenetic’s can not be explained by Darwinism. There is a mitochondrial Eve and a Y chromosome Adam.

Replies to this message:
 Message 797 by Coyote, posted 11-02-2014 4:45 PM zaius137 has replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 797 of 969 (740202)
11-02-2014 4:45 PM
Reply to: Message 796 by zaius137
11-02-2014 4:36 PM


Re: A mutation is a mutation is a mutation.
Nonsense!
Just to select one: Are you even aware of what the so-called mitochondrial Eve really represents?

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
How can I possibly put a new idea into your heads, if I do not first remove your delusions?--Robert A. Heinlein
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" does not include the American culture. That is what it is against.

This message is a reply to:
 Message 796 by zaius137, posted 11-02-2014 4:36 PM zaius137 has replied

Replies to this message:
 Message 800 by zaius137, posted 11-03-2014 1:18 AM Coyote has replied

  
sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 798 of 969 (740204)
11-02-2014 5:23 PM
Reply to: Message 789 by zaius137
11-01-2014 1:55 PM


Re: Any real evidence for evolution, point on point.
quote:
Even if you count each indel as a single mutation because those mutations affect coding (my citations) you get ~125 million mutation events (~45 million in chimp and ~45 million in humans the rest exist in both) regardless of bp lengths. This gives you a best similarity of .125/6.4 or ~2%.
I regress back to Nachman, Crowell.
t= number of generations since divergence (Generation =20 years)
k= percentage of sequence divergence Estimated at 2%
Ne= effective size of population ~10^5
(u)=mutation rate 1.1 x10^-8
t= .5(k/u-4Ne) from Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic
You still get a divergence time of ~14 million years.
The human and chimpanzee genomes differ in single-base substitutions at a rate of 1.23%. The single-base mutation rate is currently estimated to be roughly 1.1 x 10^-8/bp/gen. Using your other values, that gives t = 7.2 million years.
If you want to include indels, you have to increase the divergence by one-seventh. Unfortunately, we don't have a good independent estimate of the indel mutation rate, but a rate 1/7th that of substitutions is completely plausible.

This message is a reply to:
 Message 789 by zaius137, posted 11-01-2014 1:55 PM zaius137 has replied

Replies to this message:
 Message 799 by zaius137, posted 11-02-2014 11:27 PM sfs has replied

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


Message 799 of 969 (740212)
11-02-2014 11:27 PM
Reply to: Message 798 by sfs
11-02-2014 5:23 PM


Re: Any real evidence for evolution, point on point.
quote:
The human and chimpanzee genomes differ in single-base substitutions at a rate of 1.23%. The single-base mutation rate is currently estimated to be roughly 1.1 x 10^-8/bp/gen. Using your other values, that gives t = 7.2 million years.
As I understand the paper at Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic, (k) is estimate under a neutral model for total divergence between chimps and humans (their number 1.33%). Mutation rate by empirical measurement was found to be ~70 new mutations per generation (that is a mutation rate of 1.1 x 10^-8 mutations in the diploid genome per generation) that would be (u).
The calculation they preformed estimating mutation rate was based on effective ancestral population (Ne), specie divergence and time of divergence being 5.6 million years. This produced a calculated mutation rate of ~175 mutations per generation (u) or(2.5 x 10^-8) to time of divergence. This is about twice the measured mutation rate in humans.
You claim mutation rate of indels to be 1/7 that of substitutions, that would be ~ 10 per generation.
This would give a new mutation rate of (1.3 x 10^-8) per generation. This has nothing to do with the (k).
quote:
If you want to include indels, you have to increase the divergence by one-seventh. Unfortunately, we don't have a good independent estimate of the indel mutation rate, but a rate 1/7th that of substitutions is completely plausible.
That is fine, I accept 1/7 that of the empirical value for substitutions.
The actual value calculated for the generations from divergence did not change that much. Sorry.
Edited by zaius137, : No reason given.
Edited by zaius137, : correction...

This message is a reply to:
 Message 798 by sfs, posted 11-02-2014 5:23 PM sfs has replied

Replies to this message:
 Message 801 by sfs, posted 11-03-2014 7:18 AM zaius137 has replied

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


Message 800 of 969 (740213)
11-03-2014 1:18 AM
Reply to: Message 797 by Coyote
11-02-2014 4:45 PM


Re: A mutation is a mutation is a mutation.
quote:
Just to select one: Are you even aware of what the so-called mitochondrial Eve really represents?
Perfect time to present your understanding. I am familiar with the evo perspective but my personal view differs somewhat.

This message is a reply to:
 Message 797 by Coyote, posted 11-02-2014 4:45 PM Coyote has replied

Replies to this message:
 Message 802 by Dr Jack, posted 11-03-2014 9:09 AM zaius137 has replied
 Message 803 by Coyote, posted 11-03-2014 9:43 AM zaius137 has replied
 Message 805 by Taq, posted 11-03-2014 1:24 PM zaius137 has replied

  
sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 801 of 969 (740221)
11-03-2014 7:18 AM
Reply to: Message 799 by zaius137
11-02-2014 11:27 PM


Re: Any real evidence for evolution, point on point.
I don't know what point you're trying to make in your response. Using your (correct) formula from Nachman and Crowell, and the values you specified for ancestral population size, generation time and mutation rate, and using the best estimate for human/chimpanzee divergence, the estimated divergence time is 7.2 million years. If you use different numbers, you'll get a different result.

This message is a reply to:
 Message 799 by zaius137, posted 11-02-2014 11:27 PM zaius137 has replied

Replies to this message:
 Message 806 by zaius137, posted 11-03-2014 3:07 PM sfs has replied

  
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


(1)
Message 802 of 969 (740225)
11-03-2014 9:09 AM
Reply to: Message 800 by zaius137
11-03-2014 1:18 AM


Re: A mutation is a mutation is a mutation.
I am familiar with the evo perspective but my personal view differs somewhat.
That doesn't make any sense. Mitochondrial Eve is only a meaningful concept under the evolutionary perspective. The very calculations are, like everything else in biology, saturated in evolutionary theory.

This message is a reply to:
 Message 800 by zaius137, posted 11-03-2014 1:18 AM zaius137 has replied

Replies to this message:
 Message 807 by zaius137, posted 11-03-2014 3:14 PM Dr Jack has replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


(2)
Message 803 of 969 (740235)
11-03-2014 9:43 AM
Reply to: Message 800 by zaius137
11-03-2014 1:18 AM


Re: A mutation is a mutation is a mutation.
quote:
Just to select one: Are you even aware of what the so-called mitochondrial Eve really represents?
Perfect time to present your understanding. I am familiar with the evo perspective but my personal view differs somewhat.
I don't really care what your personal view is. When we discuss science personal views don't mean anything--it is the evidence that counts.
And the personal views you have been sharing with us, as pointed out by several posters, are contradicted by the evidence.

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
How can I possibly put a new idea into your heads, if I do not first remove your delusions?--Robert A. Heinlein
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" does not include the American culture. That is what it is against.

This message is a reply to:
 Message 800 by zaius137, posted 11-03-2014 1:18 AM zaius137 has replied

Replies to this message:
 Message 808 by zaius137, posted 11-03-2014 3:17 PM Coyote has replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 804 of 969 (740271)
11-03-2014 1:13 PM
Reply to: Message 783 by zaius137
10-31-2014 11:15 PM


Re: Any real evidence for evolution, point on point.
Yes, I used indel count of 95%, here are half a dozen papers promoting just that issue, similarity between 93% and 95%:
That number is the number of bases that differ between. That is not the indel count. A single indel can cause two genomes to vary by more than 1 base. That is what you keep getting wrong. Here is yet another example using two random sequences.
Seq A: ggcaataa_____tgctcgt
Seq B: ggcaataaccggatgctcgt
Those sequences differ by 25% at the level of the DNA bases. They differ by 1 indel, by one mutation. If you use the base difference, your estimate of the number of indels would be 25 times too high.
As sfs states, the good estimate for the indel rate is 1/7th of the substitution rate. Therefore, the number of mutations is (1.23)+(1.23/7)=1.4%. Not 5%.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 783 by zaius137, posted 10-31-2014 11:15 PM zaius137 has replied

Replies to this message:
 Message 810 by zaius137, posted 11-03-2014 3:27 PM Taq has replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 805 of 969 (740272)
11-03-2014 1:24 PM
Reply to: Message 800 by zaius137
11-03-2014 1:18 AM


Re: A mutation is a mutation is a mutation.
Perfect time to present your understanding. I am familiar with the evo perspective but my personal view differs somewhat.
All you have to do is go back a few generations in your own family. Your paternal grandfather's mother (your great grandmother) contributed just as much DNA to your autosomal genome as any other great grandparent (as averaged across all births), and yet she did not give you your mitochondrial DNA. Your mothers', mother's, mother did that. So you carry a lot of DNA from other women that were not your great-grandmother responsible for your mitochondrial DNA.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 800 by zaius137, posted 11-03-2014 1:18 AM zaius137 has replied

Replies to this message:
 Message 813 by zaius137, posted 11-03-2014 4:10 PM Taq has replied

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


Message 806 of 969 (740283)
11-03-2014 3:07 PM
Reply to: Message 801 by sfs
11-03-2014 7:18 AM


Re: Any real evidence for evolution, point on point.
quote:
If you use different numbers, you'll get a different result.
You have pointed out an inconsistency in the way I was using the Nachman and Crowell paper. You are correct about mutation rates and Percent divergence.
As you have suggested mutation rate of indels is less than that for substitutions. you say about 1/7 (u).
Also I have been using the wrong (k). It must only consider indels.
Following is my corrections:
(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
A new number for (k) must be arrived at from the following:
quote:
The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%. When excluding repeats and low-complexity DNA the total divergence decreased to 2.37%. The chromosomal distribution of nucleotide substitutions and indel events was significantly correlated. Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink
With repeats and low complexity DNA is excluded
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 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.
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 801 by sfs, posted 11-03-2014 7:18 AM sfs has replied

Replies to this message:
 Message 811 by sfs, posted 11-03-2014 3:42 PM zaius137 has replied

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


Message 807 of 969 (740285)
11-03-2014 3:14 PM
Reply to: Message 802 by Dr Jack
11-03-2014 9:09 AM


Re: A mutation is a mutation is a mutation.
quote:
That doesn't make any sense. Mitochondrial Eve is only a meaningful concept under the evolutionary perspective. The very calculations are, like everything else in biology, saturated in evolutionary theory.
Yes I can accept the consensus on this:
Using this much faster mutation rate from the two studies as a basis for a new mitochondrial clock speed, Eve can be calculated to have lived a mere 6500 or 6000 years ago, rather than 200,000 years ago.
http://www.mhrc.net/mitochondrial.htm

This message is a reply to:
 Message 802 by Dr Jack, posted 11-03-2014 9:09 AM Dr Jack has replied

Replies to this message:
 Message 831 by Dr Jack, posted 11-04-2014 9:59 AM zaius137 has replied

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


Message 808 of 969 (740286)
11-03-2014 3:17 PM
Reply to: Message 803 by Coyote
11-03-2014 9:43 AM


Re: A mutation is a mutation is a mutation.
quote:
And the personal views you have been sharing with us, as pointed out by several posters, are contradicted by the evidence.
Your presented evidence so far = 0

This message is a reply to:
 Message 803 by Coyote, posted 11-03-2014 9:43 AM Coyote has replied

Replies to this message:
 Message 809 by Coyote, posted 11-03-2014 3:27 PM zaius137 has not replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 809 of 969 (740289)
11-03-2014 3:27 PM
Reply to: Message 808 by zaius137
11-03-2014 3:17 PM


Re: A mutation is a mutation is a mutation.
quote:
And the personal views you have been sharing with us, as pointed out by several posters, are contradicted by the evidence.
Your [sic] presented evidence so far = 0
Correct, on this subject I have presented no evidence so far. This is not my field. But, as I said, other posters have presented evidence that you are wrong.
And the link you had above on Mitochondrial Eve was to a creationist's website. That kind of website has no credibility in a scientific discussion as creationists are inherently anti-science.
Care to try again?

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
How can I possibly put a new idea into your heads, if I do not first remove your delusions?--Robert A. Heinlein
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" does not include the American culture. That is what it is against.

This message is a reply to:
 Message 808 by zaius137, posted 11-03-2014 3:17 PM zaius137 has not replied

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


Message 810 of 969 (740290)
11-03-2014 3:27 PM
Reply to: Message 804 by Taq
11-03-2014 1:13 PM


Re: Any real evidence for evolution, point on point.
quote:
That number is the number of bases that differ between. That is not the iindel count. A single indel can cause two genomes to vary by more than 1 base. That is what you keep getting wrong. Here is yet another example using two random sequences.
Not knowing anything about the location or nature of the indel, you can not come to that conclusion.
quote:
As sfs states, the good estimate for the indel rate is 1/7th of the substitution rate. Therefore, the number of mutations is (1.23)+(1.23/7)=1.4%. Not 5%.
sfs has confused the (k) with the (u), sfs can correct me if I am wrong.

This message is a reply to:
 Message 804 by Taq, posted 11-03-2014 1:13 PM Taq has replied

Replies to this message:
 Message 812 by sfs, posted 11-03-2014 3:44 PM zaius137 has not replied
 Message 815 by Taq, posted 11-03-2014 4:26 PM zaius137 has not replied

  
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