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


Message 919 of 969 (740696)
11-06-2014 8:45 PM
Reply to: Message 917 by Taq
11-06-2014 3:40 PM


Re: Any real evidence for evolution, point on point.
quote:
I am claiming that your interpretation of the papers is wrong.
One thing is certain you do not want to count indel divergence as autosomal segment divergence. It is clear now that secular scientists have caught up to the fact that a human chimp divergence of 1.5% is nonsense. At this point I do not even know what you point is. Is it because you think there is not enough indels to count? If that is your point, it is in direct contradiction to my citations (I have at this point provided 6) that implicitly added them to substitution rates. I have tried and failed to correct your perspective of what constitutes a site as it relates to mutation.
You have repeatedly mixed up (u) and (k) in the calculation I was using. That is rate and percentage divergence.
I used .8% autosomal divergence in one calculation (even though I suspect it is more) and you still don’t buy it, that was a concession to the evolutionist perspective.
I will, at this point, let you name the additional divergence you think is acceptable. If you claim it is zero, argue with the secular scientists who say that it is more than zero.
Indel inclusion does not violate the neutral model as provided by Kimura’s neutral theory of evolution. It is his calculation for neutral mutation that is the basis of the calculation I used.
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 917 by Taq, posted 11-06-2014 3:40 PM Taq has replied

Replies to this message:
 Message 920 by Coyote, posted 11-06-2014 9:57 PM zaius137 has replied
 Message 925 by Taq, posted 11-06-2014 11:44 PM zaius137 has replied
 Message 931 by Dr Adequate, posted 11-07-2014 10:55 AM zaius137 has replied

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


Message 921 of 969 (740709)
11-06-2014 10:03 PM
Reply to: Message 918 by sfs
11-06-2014 3:55 PM


Re: Any real evidence for evolution, point on point.
quote:
(*)No, you really shouldn't measure divergence this way.
Specifically.. Why?

This message is a reply to:
 Message 918 by sfs, posted 11-06-2014 3:55 PM sfs has not replied

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


Message 922 of 969 (740712)
11-06-2014 10:06 PM
Reply to: Message 920 by Coyote
11-06-2014 9:57 PM


Re: Secular scientists????????
quote:
You keep mentioning "secular scientists."
Is there any other kind?
In the spirit of defining the other white meat, yes.

This message is a reply to:
 Message 920 by Coyote, posted 11-06-2014 9:57 PM Coyote has replied

Replies to this message:
 Message 923 by Coyote, posted 11-06-2014 10:11 PM zaius137 has replied

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


Message 924 of 969 (740714)
11-06-2014 10:24 PM
Reply to: Message 923 by Coyote
11-06-2014 10:11 PM


Re: Secular scientists????????
You mean To be termed scientific, a method of inquiry must be based on empirical and measurable evidence subject to specific principles of reasoning (wiki)
I guess that leaves out the evolutionist by definition.

This message is a reply to:
 Message 923 by Coyote, posted 11-06-2014 10:11 PM Coyote has replied

Replies to this message:
 Message 926 by Coyote, posted 11-07-2014 12:37 AM zaius137 has replied
 Message 932 by Dr Adequate, posted 11-07-2014 10:58 AM zaius137 has not replied

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


Message 927 of 969 (740723)
11-07-2014 3:40 AM
Reply to: Message 925 by Taq
11-06-2014 11:44 PM


Re: Any real evidence for evolution, point on point.
quote:
It is the way that you add them together that is wrong. The authors of the peer reviewed papers do it correctly.
If they are added correctly, then I can use them as autosomal divergence, right.
quote:
I have already discussed the mutation rate with you multiple times. If you are going to use the 5% divergence as measured by differences in bases then you need to use a mutation rate that incorporates the number of bases changed per generation. You aren't doing that. The mutation rate needs to be about 250 bases changed per generation. You are using 70.
I am using 70 because the current measurement is a average of 70 new mutations per generation (mutation rate of 1.1 x 10^-8), a base number change of 250 bases per generation is not reasonable. As I suggested earlier a mutation rate of 250 mutations per site per generation yields a deleterious rate of U = (250 x .017) = 4.25. A U of 4.25 is unacceptable. Genome load would exceed 99%.
I do not know how you calculated 250 new mutations per generation without specifying time since divergence (t x 20). You must use the formula I used to derive a mutation rate then calculate the number of mutations needed per generation.
t= number of generations since divergence (Generation =20 years) = 300,000 and 6 million years since divergence.
k= percentage of autosomal sequence divergence Estimated at 5%
Ne= effective size of population ~10^5
(u)=mutation rate to be calculated
u = k/(2t + 4Ne) from Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic
With a 5% autosomal sequence divergence between a human and chimp you need a mutation rate of ~5 x 10^-8 for 6 million years. That would be 320 new mutations per generation. Impossible. Even 250 new mutations per generation is impossible.

This message is a reply to:
 Message 925 by Taq, posted 11-06-2014 11:44 PM Taq has replied

Replies to this message:
 Message 929 by sfs, posted 11-07-2014 7:48 AM zaius137 has not replied
 Message 937 by Taq, posted 11-07-2014 4:23 PM zaius137 has replied

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


Message 928 of 969 (740724)
11-07-2014 3:42 AM
Reply to: Message 926 by Coyote
11-07-2014 12:37 AM


Re: Secular scientists????????
You can believe in magic, superstition, wishful thinking, old wives tales, folklore, what the stars foretell and what the neighbors think, omens, public opinion, astromancy, spells, Ouija boards, anecdotes, Da Vinci codes, tarot cards, sorcery, seances, sore bunions, black cats, divine revelation, table tipping, witch doctors, crystals and crystal balls, numerology, divination, faith healing, miracles, palm reading, the unguessable verdict of history, magic tea leaves, new age mumbo-jumbo, hoodoo, voodoo and all that other weird stuff.
You missed one EVOLUTION

This message is a reply to:
 Message 926 by Coyote, posted 11-07-2014 12:37 AM Coyote has not replied

Replies to this message:
 Message 930 by New Cat's Eye, posted 11-07-2014 9:45 AM zaius137 has not replied

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


Message 934 of 969 (740755)
11-07-2014 12:10 PM
Reply to: Message 933 by sfs
11-07-2014 11:36 AM


Re: Any real evidence for evolution, point on point.
That is just funny...

This message is a reply to:
 Message 933 by sfs, posted 11-07-2014 11:36 AM sfs has not replied

Replies to this message:
 Message 940 by Taq, posted 11-07-2014 4:33 PM zaius137 has replied

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


Message 935 of 969 (740766)
11-07-2014 12:50 PM
Reply to: Message 933 by sfs
11-07-2014 11:36 AM


Re: Any real evidence for evolution, point on point.
Please do not let the following chase you away from the conversation it has just started.
Examining the DNA sequences from their experimental animals (a total of over 4 million base pairs!), and comparing them with the controls, turned up a total of 30 mutations.
17 of these were insertions or deletions ("indels')
◦ 7 in exons all but 2 of which produced frameshifts and a premature STOP codon.
◦ 10 in introns or between genes
13 of these were single base substitutions ("point" mutations)
◦ 3 in exons : one "silent" producing a synonymous codon; two that changed the encoded amino acid.
◦ 10 in introns or between genes
Calculating Mutation Rate
From these results I have pooled their data to calculate an approximate rate at which spontaneous mutations occur throughout the genome.
Mutation Rate = # of mutations observed [30] (# of experimental lines [198]) x (average # of generations [339]) x (average # of base pairs sequenced [~21,000])
yielding a rate of 2.1 x 10-8 mutations per base pair per generation.
The total C. elegans genome contains some 108 base pairs so this tells us that two new germline mutations occur somewhere in each of C. elegans's two haploid genomes in each generation.
http://users.rcn.com/...Mutations.html#MeasuringMutationRate
That is how you calculate mutation rate using indels and SNPs.

This message is a reply to:
 Message 933 by sfs, posted 11-07-2014 11:36 AM sfs has not replied

Replies to this message:
 Message 938 by Taq, posted 11-07-2014 4:27 PM zaius137 has not replied

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


Message 936 of 969 (740769)
11-07-2014 12:56 PM


A real (k)
Now knowing the combined (u) (1.1 x10^-8) we can calculate the combined (k) for humans or what it should be.

Replies to this message:
 Message 939 by Taq, posted 11-07-2014 4:28 PM zaius137 has replied

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


Message 942 of 969 (740893)
11-08-2014 1:09 AM
Reply to: Message 937 by Taq
11-07-2014 4:23 PM


Re: Any real evidence for evolution, point on point.
quote:
I have given you this calculation several times now.
Thanks for your patients.
quote:
There are 70 new substitutions each generation. If the indel rate is 1/7th of that as sfs indicated, then that is 10 indels.
The point that I am highlighting, at this time, is that the 70 new mutations include the indels and substitutions. See the break down for the mutations above the calculation of mutation rate.
quote:
Indels can be more than one base. In fact, the average indel is ~20 bases.
Most indels (for average of papers) in the examined segments were 1 to 4 bp in length (that is dependent on the segments examined).
quote:
So we have 70 bases changed from substitutions and 200 bases changed from indels. 200 +70 is 270 bases changed per generation.
Not at all. The 70 is the total number used in the mutation rate figure. Look at the break down for that particular example above.
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 937 by Taq, posted 11-07-2014 4:23 PM Taq has not replied

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


Message 943 of 969 (740894)
11-08-2014 1:15 AM
Reply to: Message 941 by sfs
11-07-2014 8:29 PM


Re: Any real evidence for evolution, point on point.
quote:
Note that all I did was take the 5 million indels from the chimpanzee genome paper and divide by the 35 million substitutions.
Which does not have anything to do with mutation rate scratch the 1/7u again.
(Also, I suspect the reason he's tried to denigrate the chimp genome paper and suggest it's been superseded is that he knows I'm one of the authors.)
Sincerely, I have the utmost respect for you and your work.
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 941 by sfs, posted 11-07-2014 8:29 PM sfs has not replied

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


Message 944 of 969 (740896)
11-08-2014 1:19 AM
Reply to: Message 939 by Taq
11-07-2014 4:28 PM


Re: A real (k)
quote:
What are the units? Number of bases, or number of mutations?
Settling this once and for all a rate of 1.1 x 10-8 mutations per base pair per generation.
http://users.rcn.com/...Mutations.html#MeasuringMutationRate
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 939 by Taq, posted 11-07-2014 4:28 PM Taq has replied

Replies to this message:
 Message 967 by Taq, posted 11-17-2014 5:46 PM zaius137 has not replied

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


Message 945 of 969 (740898)
11-08-2014 1:22 AM
Reply to: Message 931 by Dr Adequate
11-07-2014 10:55 AM


Re: Any real evidence for evolution, point on point.
Good post... and it is that time of the evening.
CHEERS!

This message is a reply to:
 Message 931 by Dr Adequate, posted 11-07-2014 10:55 AM Dr Adequate has not replied

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


Message 946 of 969 (740919)
11-08-2014 10:36 AM
Reply to: Message 940 by Taq
11-07-2014 4:33 PM


Re: Any real evidence for evolution, point on point.
Now do you see that mutation rate (u) and autosomal divergence (k) both have the same units and they include (indels). At least where they were counted (the paper I cited).
So you can not only use indels in the divergence calculation, you must use indels when you use the empirical value for mutation rate in humans, that of (1.1 x 10^-8 mutations per base pair per generation).
Remember the ratio of k/u must yield units of generation.
If I apply both the autosomal divergence percentage of (5%) and observed mutation rate (70 new mutations per generation) the time of human chimp common ancestor is beyond 40 million years...
You accept that?
Edited by zaius137, : No reason given.
Edited by zaius137, : add units to mutation rate.
Edited by zaius137, : No reason given.
Edited by zaius137, : No reason given.

This message is a reply to:
 Message 940 by Taq, posted 11-07-2014 4:33 PM Taq has not replied

Replies to this message:
 Message 951 by Dr Adequate, posted 11-09-2014 2:02 PM zaius137 has not replied

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


Message 947 of 969 (740930)
11-08-2014 11:28 AM


A simpler calculation
Here is the simple version of divergence time used in calculating difference between species Without Ne. A simple approximation. I like simple.
d = 2*r*t or t = .5(d/r)
where
d = DNA differences between two individuals
r = the measured mutation rate in the species or lineage
t = time of origin derived from each origins model (in generations)
Time in years equals (t x years per generation).

Replies to this message:
 Message 952 by sfs, posted 11-09-2014 7:48 PM zaius137 has replied

  
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