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Author Topic:   Why is evolution so controversial?
zaius137
Member (Idle past 792 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:
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Replies to this message:
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zaius137
Member (Idle past 792 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 responded

  
zaius137
Member (Idle past 792 days)
Posts: 407
Joined: 05-08-2012


Message 948 of 969 (741074)
11-09-2014 1:08 PM


Crickets in a vacuum.
No more to say?
Replies to this message:
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 Message 953 by sfs, posted 11-09-2014 7:56 PM zaius137 has responded

  
NoNukes
Member
Posts: 9447
From: Central NC USA
Joined: 08-13-2010
Member Rating: 2.7


Message 949 of 969 (741080)
11-09-2014 1:23 PM
Reply to: Message 948 by zaius137
11-09-2014 1:08 PM


Re: Crickets in a vacuum.
You are welcome to have the last substantive post on the topic. Is that a problem for you?

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

I have never met a man so ignorant that I couldn't learn something from him. Galileo Galilei

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


This message is a reply to:
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RAZD
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Posts: 18257
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.2


Message 950 of 969 (741087)
11-09-2014 1:51 PM
Reply to: Message 949 by NoNukes
11-09-2014 1:23 PM


Re: Crickets in a vacuum.
You are welcome to have the last substantive post on the topic. Is that a problem for you?

Well that would be a good place to start now eh?


we are limited in our ability to understand
by our ability to understand
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Dr Adequate
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Posts: 15788
Joined: 07-20-2006
Member Rating: 3.1


Message 951 of 969 (741090)
11-09-2014 2:02 PM
Reply to: Message 946 by zaius137
11-08-2014 10:36 AM


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

This is halfwitted nonsense, for reasons that have been explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and 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Please find an argument that is not halfwitted nonsense.


This message is a reply to:
 Message 946 by zaius137, posted 11-08-2014 10:36 AM zaius137 has not yet responded

  
sfs
Member
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 952 of 969 (741119)
11-09-2014 7:48 PM
Reply to: Message 947 by zaius137
11-08-2014 11:28 AM


Re: A simpler calculation
quote:

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)


Simple is good. Let's use a cartoon organism. It has a mutation rate of 1x10^-9/bp/gen and a genome of 1 billion base pairs, so on average there is 1 mutation per generation. Half of its mutations are single-base substitutions, and half are large indels. Let's look at a copy of the genome from each branch just one generation after they split. In that 1 generation, one copy acquired one single-base substitution. The other copy acquired an insertion of 10 million base pairs. As a result, the genomes now differ by 10,000,001 base pairs, or just over 1%.

Using your formula, t = 0.5*(.01/1e-9) = 5,000,000 generations. That's wrong by a factor of 5 million. What do you think might be wrong with your formula?


This message is a reply to:
 Message 947 by zaius137, posted 11-08-2014 11:28 AM zaius137 has responded

Replies to this message:
 Message 954 by zaius137, posted 11-10-2014 1:51 AM sfs has not yet responded
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sfs
Member
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 953 of 969 (741120)
11-09-2014 7:56 PM
Reply to: Message 948 by zaius137
11-09-2014 1:08 PM


Re: Crickets in a vacuum.
Zaius asked why it was dumb to just add up the unique sequence from each species to get the total divergence. Here's why. Consider two sequences, each 20 bp long:

----------ACGGTTCCGATTTTTTTTTT
CCCCCCCCCCACGGTTCCGA----------

The dashes are sequence that doesn't exist in that copy. 10 out of the 20 bp in each sequence are identical and ten are different. 50% of the sequence in each is unique to that copy (e.g. represents an insertion in its lineage). If we add up the fraction of unique sequence in both, we conclude that they have 0% of their bases in common, even though they are 50% identical.

That is dumb.


This message is a reply to:
 Message 948 by zaius137, posted 11-09-2014 1:08 PM zaius137 has responded

Replies to this message:
 Message 956 by zaius137, posted 11-10-2014 2:00 AM sfs has not yet responded
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zaius137
Member (Idle past 792 days)
Posts: 407
Joined: 05-08-2012


Message 954 of 969 (741139)
11-10-2014 1:51 AM
Reply to: Message 952 by sfs
11-09-2014 7:48 PM


Re: A simpler calculation
quote:
Simple is good. Let's use a cartoon organism. It has a mutation rate of 1x10^-9/bp/gen and a genome of 1 billion base pairs, so on average there is 1 mutation per generation. Half of its mutations are single-base substitutions, and half are large indels. Let's look at a copy of the genome from each branch just one generation after they split. In that 1 generation, one copy acquired one single-base substitution. The other copy acquired an insertion of 10 million base pairs. As a result, the genomes now differ by 10,000,001 base pairs, or just over 1%.

Do you read any of my citations? Think average...

This would be a problem if mutation rates were as simple as you think they are. From my citation:

Mutation Rate = # of mutations observed [30] ÷ (# of experimental lines [198]) x (average # of generations [339]) x (average # of base pairs sequenced [~21,000])

The citation I showed you directly counted base pairs in the indel over an average of measurements. Mutation rates are considered in the citation as averages. One case won’t cut it.

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

I hope most who read this got over the indel being counted as one mutation a few posts back…

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

It is always important to read citations when continuing an argument.


This message is a reply to:
 Message 952 by sfs, posted 11-09-2014 7:48 PM sfs has not yet responded

  
zaius137
Member (Idle past 792 days)
Posts: 407
Joined: 05-08-2012


Message 955 of 969 (741140)
11-10-2014 1:56 AM
Reply to: Message 952 by sfs
11-09-2014 7:48 PM


The real world....
Where do you get “The other copy acquired an insertion of 10 million base pairs” (sfs)…
Most indels in coding regions are 10 million bp long???
This message is a reply to:
 Message 952 by sfs, posted 11-09-2014 7:48 PM sfs has not yet responded

  
zaius137
Member (Idle past 792 days)
Posts: 407
Joined: 05-08-2012


Message 956 of 969 (741141)
11-10-2014 2:00 AM
Reply to: Message 953 by sfs
11-09-2014 7:56 PM


Re: sfs in a vacuum.
quote:
Zaius asked why it was dumb to just add up the unique sequence from each species to get the total divergence. Here's why. Consider two sequences, each 20 bp long:

Ask the authors of the papers claiming that you can add indels to divergence. That is not going on anyway… read the paper.


This message is a reply to:
 Message 953 by sfs, posted 11-09-2014 7:56 PM sfs has not yet responded

Replies to this message:
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zaius137
Member (Idle past 792 days)
Posts: 407
Joined: 05-08-2012


Message 957 of 969 (741184)
11-10-2014 11:32 AM
Reply to: Message 953 by sfs
11-09-2014 7:56 PM


Re: Crickets in a vacuum.
Another look at your example….

Zaius asked why it was dumb to just add up the unique sequence from each species to get the total divergence. Here's why. Consider two sequences, each 20 bp long:

----------ACGGTTCCGATTTTTTTTTT
CCCCCCCCCCACGGTTCCGA----------

The dashes are sequence that doesn't exist in that copy. 10 out of the 20 bp in each sequence are identical and ten are different. 50% of the sequence in each is unique to that copy (e.g. represents an insertion in its lineage). If we add up the fraction of unique sequence in both, we conclude that they have 0% of their bases in common, even though they are 50% identical.

It looks to me as if you are comparing 30 bp with 2 indels. Your comparison is biased because you compare 20 bp on one side then 20 bp on the other. I would think that the comparison here would be 30 bp. The two outside indels are not in the same frame of your comparison.

Just trying to understand the reasoning here.


This message is a reply to:
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New Cat's Eye
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Posts: 11248
From: near St. Louis
Joined: 01-27-2005
Member Rating: 1.9


Message 958 of 969 (741317)
11-11-2014 12:25 PM
Reply to: Message 786 by zaius137
11-01-2014 12:03 AM


Re: Any real evidence for evolution, point on point.
quote:
Humans are apes.

"However, science tells us that animals can have cognitive faculties that are superior to human beings."

Read more at: http://phys.org/...2-humans-smarter-animals-experts.html#jCp

This could explain my frustration as it relates to evolutionists.

How easily can you keep up with this chimp?

http://youtu.be/JkNV0rSndJ0


This message is a reply to:
 Message 786 by zaius137, posted 11-01-2014 12:03 AM zaius137 has responded

Replies to this message:
 Message 959 by zaius137, posted 11-11-2014 8:34 PM New Cat's Eye has acknowledged this reply
 Message 960 by Percy, posted 11-12-2014 7:56 AM New Cat's Eye has responded

  
zaius137
Member (Idle past 792 days)
Posts: 407
Joined: 05-08-2012


Message 959 of 969 (741370)
11-11-2014 8:34 PM
Reply to: Message 958 by New Cat's Eye
11-11-2014 12:25 PM


Re: Any real evidence for evolution, point on point.
quote:
How easily can you keep up with this chimp?

That is simply amazing… And this was not speeded up… was it?


This message is a reply to:
 Message 958 by New Cat's Eye, posted 11-11-2014 12:25 PM New Cat's Eye has acknowledged this reply

  
Percy
Member
Posts: 15562
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.4


Message 960 of 969 (741399)
11-12-2014 7:56 AM
Reply to: Message 958 by New Cat's Eye
11-11-2014 12:25 PM


Re: Any real evidence for evolution, point on point.
I hope no one is missing what's most amazing, because it isn't the rapidity of the touches. It's that the chimp looks at the numbers for only a second before hitting the circle that replaces them with white boxes. The chimp not only knows the ordering of the digits 1-9, he can remember them positionally after just a glance.

People are occasionally born with amazing talents, and since we're just animals it shouldn't be surprising that the same is true of animals. This chimp's talents seem similar in nature to a human savant's.

--Percy


This message is a reply to:
 Message 958 by New Cat's Eye, posted 11-11-2014 12:25 PM New Cat's Eye has responded

Replies to this message:
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