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Genetics and Human Brain Evolution

Author Topic:   Genetics and Human Brain Evolution
RAZD
Member (Idle past 34 days)
Posts: 20714
From: the other end of the sidewalk
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 Message 136 of 157 (361222) 11-03-2006 6:37 PM Reply to: Message 122 by eggasai11-02-2006 11:49 PM

comprehension/math/logic
 That's right, bp per generation.

{X} mut/bp/gen = {X} mut x 1/bp x 1/gen = {X} mut/(bp*gen)

32.2 ft/sec/sec = 32.2 ft/sec^2

To think that 32.2 ft/sec/sec = 32.2 feet would be an error of some incalculable gravity.

Enjoy.

Edited by RAZD, : for fun

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 This message is a reply to: Message 122 by eggasai, posted 11-02-2006 11:49 PM eggasai has responded

 Replies to this message: Message 139 by eggasai, posted 11-04-2006 9:17 PM RAZD has responded

RAZD
Member (Idle past 34 days)
Posts: 20714
From: the other end of the sidewalk
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 Message 137 of 157 (361425) 11-04-2006 9:24 AM Reply to: Message 110 by Hyroglyphx11-02-2006 6:40 PM

on the question of morality
 I don't why you were expecting honesty from a group that has no moral fiber to begin with and no real concept of morality apart from some relativistic, abstract concept.

My response to you is at Message 91 where this issue is more on topic than on this thread.

Enjoy.

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 This message is a reply to: Message 110 by Hyroglyphx, posted 11-02-2006 6:40 PM Hyroglyphx has not yet responded

eggasai
Inactive Member

 Message 138 of 157 (361666) 11-04-2006 9:03 PM Reply to: Message 132 by Wounded King11-03-2006 1:19 PM

You guys really don't have a clue do you, all I was saying is that bp in the formula meant base pair. You guys turn it over like a sizzling hamburger, dress it up with lettuce onions and tomato and smack your lips around it like it's lunch.

All this mellodrama for a simple straight forward statement, bp means base pair. 2 x 10^-8 means 2 per 100,000,000, bp means base pair, generation is estimated at 20 years. That's it, there is nothing left to explain. Then you want me to assume that bp does not mean base pair.

There are two clear line of deception with various tactics being imployed. One, pretend that 98% of the DNA is the same in chimpanzees and humans and if you lie about it most people will believe it. Two, if someone comes along and realizes that it is actually 95% immediatly act as it it made no difference that 100,000,000 base pairs doesn't change anything.

Viruses don't replicate as much as the human genome would have had to since the last common ancestor. Time magazine lied about the divergance, Nature lied about the divergance and you guys are twisting a very simple math problem into an incomprehesible gibberish.

There is only one conclusion I find remotely reasonable, the truth won't work so mainstream science lies.

 This message is a reply to: Message 132 by Wounded King, posted 11-03-2006 1:19 PM Wounded King has responded

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eggasai
Inactive Member

 Message 139 of 157 (361672) 11-04-2006 9:17 PM Reply to: Message 136 by RAZD11-03-2006 6:37 PM

Re: comprehension/math/logic
Try this:

Rate- 2 x 10^-8 = 2 per 100 Mb. 300 Mb in the human/chimpanzee genomes respectivly. That comes to 60 bp.

Time- Generation estimated at 20 years.

Distance- Measured in base pairs.

You plug 145 Mb into the bp, you plug 350,000 into generation, what is the rate?

I already know, if you are being honest you already know. What is the rate? I'll give you a big clue, 2 x 10^-8 comes to 16 million in the respective genomes which accounts for the 35 million single base substitutions that diverge. The indels are 3x that so we are looking at 6 x 10^-8 with the rearrangements it's roughly up one for 7 x 10^-8.

Let me guess...NO NO NO YOU DONT UNDERSTAND!!!...the trouble is I understand fine.

 This message is a reply to: Message 136 by RAZD, posted 11-03-2006 6:37 PM RAZD has responded

 Replies to this message: Message 142 by RAZD, posted 11-05-2006 10:11 PM eggasai has not yet responded Message 143 by sfs, posted 11-05-2006 10:54 PM eggasai has responded

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 Message 140 of 157 (361693) 11-04-2006 10:27 PM Reply to: Message 122 by eggasai11-02-2006 11:49 PM

 For starters, we should be able to predict how different the genomes should be. The seven million years of evolution in each lineage represents about 350,000 generations in each (assuming 20 years per generation). How many mutations happen per generation? Estimating mutation rates is not easy (at least without assuming common descent): it is hard to find a few changed nucleotides out of 3 billion that have not changed. By studying new cases of genetic diseases, individuals whose parents' do not have the disease, however, it is possible to identify and count new mutations, at least in a small number of genes. Using this technique, it has been estimated[1] that the single-base substitution rate for humans is approximately 1.7 x 10^-8 substitutions/nucleotide/generation, that is, 17 changes per billion nucleotides. That translates into ~100 new mutations for every human birth. (17 x 3, for the 3 billion nucleotides in the genome, x 2 for the two genome copies we each carry). At that rate, in 350,000 generations a copy of the human genome should have accumulated about 18 million mutations, while the chimpanzee genome should have accumulated a similar number.The evolutionary prediction, then, is that there should be roughly 36 million single-base differences between humans and chimpanzees. The actual number could be determined when both the chimpanzee and human genomes had been completely sequenced. When the two genomes were compared[2], thirty-five million substitutions were found, in remarkably good agreement with the evolutionary expectation. Fortuitously good agreement, in fact: the uncertainty on most of the numbers used in the estimate is large enough that it took luck to come that close.

Despite the fact that it has been clearly demonstrated that divergence is 100 Mb greater then previous estimates, only the single substitutions are accounted for. No one was predicting that the indels would dwarf the single nucleotide substitutions.

You have, once again, entirely misunderstood what you read.

No-one was predicting anything about the number of indels. Their methods allowed them to predict the number of single nucleotide substitutions, which they did accurately. They were not estimating the number of mutations of all kinds, just the number of single nucleotide substitions. And they were right.

Edited by Dr Adequate, : No reason given.

 This message is a reply to: Message 122 by eggasai, posted 11-02-2006 11:49 PM eggasai has not yet responded

Wounded King
Member (Idle past 2723 days)
Posts: 4149
From: Edinburgh, Scotland
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 Message 141 of 157 (361789) 11-05-2006 6:13 AM Reply to: Message 138 by eggasai11-04-2006 9:03 PM

 I was saying is that bp in the formula meant base pair.

Bull! No one has ever denied that. What you have repeatedly said in multiple posts is that SFS was denying that this was what bp menat, which he has never done!!

 msg 90 writes:quote:2x10^-8/bp/generation,is the number of mutation events, not the number of base pairsThen what does bp stand for in your formula if not base pairs?

This seems to be thefirst instance of your issue and Sfs has already answered it, the bp is base pairs but the mutation rate isn't measured in base pairs. If he had said 'bp is the number of mutation events not the number of base pairs', then you might have a leg to stand on, but he never did and neither did anyone else.

It is you that wishes to make a meal out of these piddling little things. I'd much rather get back to your complete misunderstanding of fundamental molecular biology or to your non-existent references for seminal papers from Watson and Crick.

Better still we could get back to discussing Har1 and the evolution of the human brain or to the paper I referenced on non-coding mRNAs with a possible role in neural development due to expression differences between chimp and human brains.

 Then you want me to assume that bp does not mean base pair.

Give us any example of anyone saying any such thing!!

The only person who has ever said anything suggesting anyone believes this is you!

You keep saying that mutations should be measured in bps but this only make sense in terms of measuring the length of a mutation not its frequency. If someone derived a reliable average for the number of bases affected per mutation then you could use the number of bps of difference as a metric for the frequency of mutation, but the 2x10^-8 figure was not derived in any such way and conseqently can't be used in that way. So, no matter how often you claim it, in the absence of such an average length value for all mutations bps are not a suitable measure for the number of mutational events.

If you think the mutation rate we are discussing does include such an averaging of the length of mutations then please provide a source reference that we can use to verify it. I have referenced at least 2 papers producing similar estimates neither of which account for any indels over 4bp in length.

 Time magazine lied about the divergance, Nature lied about the divergance and you guys are twisting a very simple math problem into an incomprehesible gibberish.

Get over it already. Time and the people who produce the press releases at Nature are not exactly the cutting edge of evolutionary research. If you want to show that people are still frequently misquoting the divergence in science then why not refer us to some scientific papers? If you want to argue that science is poorly understood in the media and much of science reporting is badly done I doubt you will get much argument.

 Two, if someone comes along and realizes that it is actually 95% immediatly act as it it made no difference that 100,000,000 base pairs doesn't change anything.

Of coure it changed things but it didn't change estimates of single nucleotide substitution rates and it didn't change historical estimates of the overall divergence derived using less accurate techniques. Did it make it impossible for chimps and humans to have a common ancestor 7 million years ago? No.

TTFN,

WK

 This message is a reply to: Message 138 by eggasai, posted 11-04-2006 9:03 PM eggasai has not yet responded

RAZD
Member (Idle past 34 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004

 Message 142 of 157 (362038) 11-05-2006 10:11 PM Reply to: Message 139 by eggasai11-04-2006 9:17 PM

Re: comprehension/math/logic
 Try this:Rate- 2 x 10^-8 = 2 per 100 Mb. 300 Mb in the human/chimpanzee genomes respectivly. That comes to 60 bp.Time- Generation estimated at 20 years.Distance- Measured in base pairs.

From australopithicus to homo sap = ~3 million years, at an average of ~25 years per generation is ~3,000,000/~25 = ~120,000 generations.

Using your number of 145 million base pairs for the genetic sequence in question (for the sake of argument) and applying the formula:

0.00000002 mutations/bp/gen x 145 million bp x 120,000 gen = 348,000 mutations. Accumulated in that section of the human genome since Lucy walked the earth.

And that is all it says.

Notice that the units cancel:

{X}(bp) x {Y}(gen) x {Z}(mutations)/(bp)/(gen)
= {X}{Y}{Z} (bp)(gen)(mutations)/(bpxgen)
= {X}{Y}{Z} (bpxgen)(mutations)/(bpxgen)
= {X}{Y}{Z} mutations.

 You plug 145 Mb into the bp, you plug 350,000 into generation, what is the rate?

And "bp" and "gen" are not variables that you plug {values} into to get results. They don't have {values} that CHANGE the rate of mutation, they are PART of the rate of mutation. The RATE is already given. It is just an average rate of the number of mutations per (base pair) per (generation).

-----

And you still haven't answered the question about the fossil skulls that show a gradual progression in size from australopithicus to homo sap, thus validating that there has been a rather constant change in the volume of the brain,

NOR have you dealt with the issue of sexual selection that can cause an accellerated degree of selection towards a "desired" feature,

NOR how the size of the brain being at the maximum end of the range for survival of mother and fetus shows it is likely a result of runaway sexual selection.

With this information the number of mutations given is not a surprise, nor a quandry.

Enjoy.

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 This message is a reply to: Message 139 by eggasai, posted 11-04-2006 9:17 PM eggasai has not yet responded

sfs
Member (Idle past 1162 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003

 Message 143 of 157 (362046) 11-05-2006 10:54 PM Reply to: Message 139 by eggasai11-04-2006 9:17 PM

Re: comprehension/math/logic
quote:
Let me guess...NO NO NO YOU DONT UNDERSTAND!!!...the trouble is I understand fine.

No, Mark, you don't understand fine. I see no point to further discussion with you, since no communication is taking place here. You've invented the idea that mutation rates are measured in base pairs out of whole cloth, invented me saying that "bp" doesn't mean base pairs, and ignored all attempts to point out your mistakes. What's the point? You're talking about your own fantasies, not science.

 This message is a reply to: Message 139 by eggasai, posted 11-04-2006 9:17 PM eggasai has responded

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eggasai
Inactive Member

 Message 144 of 157 (362496) 11-07-2006 7:21 PM Reply to: Message 143 by sfs11-05-2006 10:54 PM

bp does not mean base pair no matter what
quote:
No, Mark, you don't understand fine. I see no point to further discussion with you, since no communication is taking place here. You've invented the idea that mutation rates are measured in base pairs out of whole cloth, invented me saying that "bp" doesn't mean base pairs, and ignored all attempts to point out your mistakes. What's the point? You're talking about your own fantasies, not science.

Yes Steve I do understand and all this semantical slight of hand doesn't change anything. I didn't just bust in here and jump into someone elses conversation. I've been asking you about the indels for sometime and you have yet to answer a fundamental question, how did the divergance get there with an observed rate of 2 x 10^-8/bp/generation? The obvious answer is that it didn't happen at 3 x that rate. So you guys just pretend that a 1 bp mutation is the same thing as one a million base pairs long!!!!

Time could have made a mistake when they said 98% of the DNA was the same. Nature might have only been counting the single nucleotide substitutions when they said the same thing. This is a direct contradiction, you either made a mistake or you lied:

"No, like counting all the base pairs in the indels and applying them to the mutation rate as measured in mutation events, which is what you've just done here. The 2x10^-8/bp/generation is the number of mutation events, not the number of base pairs. (It's also just the single-base substitution rate, but that's less important.) It doesn't matter how many times you make that comparison: it will be wrong every time you do."

You said that bp does not mean base pairs. I know what you were trying to do, you were trying to take the observed mutation rate and squeeze all of the divergance into it. It doesn't work and I do know what I'm talking about because I learned to find, isolate and emphasis other peoples fatal errors from experts

 This message is a reply to: Message 143 by sfs, posted 11-05-2006 10:54 PM sfs has not yet responded

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Member (Idle past 45 days)
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 Message 145 of 157 (362527) 11-07-2006 11:09 PM Reply to: Message 144 by eggasai11-07-2006 7:21 PM

Re: bp does not mean base pair no matter what
 Yes Steve I do understand and all this semantical slight of hand doesn't change anything. I didn't just bust in here and jump into someone elses conversation. I've been asking you about the indels for sometime and you have yet to answer a fundamental question, how did the divergance get there with an observed rate of 2 x 10^-8/bp/generation? The obvious answer is that it didn't happen at 3 x that rate.

Actually, the obvious answer is contained in my previous post, where I point out your childish error.

 So you guys just pretend that a 1 bp mutation is the same thing as one a million base pairs long!!!!

No-one has said this. You made that up.

 You said that bp does not mean base pairs.

Wounded King did not say that. You made that up.

 I do know what I'm talking about because I learned to find, isolate and emphasis other peoples fatal errors from experts

This delusion seems to be at the root of all your other delusions.

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Wounded King
Member (Idle past 2723 days)
Posts: 4149
From: Edinburgh, Scotland
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 Message 146 of 157 (362558) 11-08-2006 4:53 AM Reply to: Message 145 by Dr Adequate11-07-2006 11:09 PM

Re: bp does not mean base pair no matter what
 Wounded King did not say that. You made that up.

He was actually talking about something Sfs said, but what Sfs said wasn't 'bp does not mean base pairs' either.

TTFN,

WK

 This message is a reply to: Message 145 by Dr Adequate, posted 11-07-2006 11:09 PM Dr Adequate has not yet responded

Wounded King
Member (Idle past 2723 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003

 Message 147 of 157 (362624) 11-08-2006 11:41 AM Reply to: Message 144 by eggasai11-07-2006 7:21 PM

Re: bp does not mean base pair no matter what
Could you finally once and for all give us a source for your mutation rate? I have mentioned a number of papers which have similar values derived principally from single nucleotide substitutions. The mutation rate for indels is estimated to be ~10 fold less than that for single nucleotide substitutions (Nachman and Crowell, 2000) where the rate of single nucleotide substitutions is measured as 2.3X10-8 substitutions/bp/generation and that for length mutations as 2.3X10-9 indels/bp/generation, giving an overall mutation rate of 2.5X10-8 mutations/bp/generation.

Assuming your 2X10-8/bp/generation figure has a basis in similar numbers we should expect something slightly under 10% of mutations to be length mutations so of your 120-175 or however many mutations there are per generation we might expect ~10-15 of those to be length mutations of anywhere between 1bp up to several Kb. The average length of an indel has been calculated at 36bp (Britten et al, 2003) and the median length to be 3bp (Ogurtsov et al., 2003). Most such length mutations will therefore be on the lower end of the scale but there should be enough longer ones to make an assumption that there is a tenable one to one mapping between the number of mutations and the amount of difference in bps highly suspect. Indeed if we take the average length of indel 36bp and use it to calculate the amount of divergence in bp we might expect to see with an indel mutation rate of 2.3X10-9 indels/bp/generation we get a figure, 8.2X10-8 bp of difference/bp/generation, which is actually more than 3 times as high as the amount of bp change we would expect from the single nucleotide substitution rate. The average is a daft figure to use of course, the median is probably much more realistic but is still enough to produce an estimated divergence of ~3X10-8bp of difference/bp/generation, considerably above that for single nucleotide substitutions alone.

 So you guys just pretend that a 1 bp mutation is the same thing as one a million base pairs long!!!!

In terms of being a single mutational event it is. In terms of the effects of that mutation, especially on length, it isn't.

This could all be sorted out much more simply if you let us know exactly where your estimate of the mutation rate comes from so we can tell exactly what it is supposed to be measuring. You can trace all my numbers back to my references so why not give us the same courtesy.

TTFN,

WK

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 Replies to this message: Message 148 by derwood, posted 11-11-2006 9:49 AM Wounded King has not yet responded

derwood
Member (Idle past 505 days)
Posts: 1457
Joined: 12-27-2001

 Message 148 of 157 (363200) 11-11-2006 9:49 AM Reply to: Message 147 by Wounded King11-08-2006 11:41 AM

Re: bp does not mean base pair no matter what
This is hopeless. The difference between point mutation, indel as single event, etc. has been explained to Mark literally dozens of times - starting with my explanations to him at Christianforums over a year ago up to the several people providing several explanations to him here. He will not accept his error. He has Google expertise, and there is no topping that.

Edited by derwood, : typos

 This message is a reply to: Message 147 by Wounded King, posted 11-08-2006 11:41 AM Wounded King has not yet responded

Member
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Member Rating: 3.9

 Message 149 of 157 (363261) 11-11-2006 5:17 PM Reply to: Message 10 by eggasai10-24-2006 6:29 PM

Re: Genes affecting brain development
 eggasai writes:I see no reason that one cannot logically conclude that the differences are better accounted for by design rather then spontaneous mutations.

Of course you can logically conclude this. And not just 'better' accounted for; design PERFECTLY accounts for these differences. Of course, we're not talking about just any design and designer. Herbie tinkering in his garage down the street couldn't pull it off. We need a designer with almost perfect knowledge of what changes effect what results and how to implement those results, i. e., a god type of designer and a divine design. Of course, even if a crustacean genome had changed into an elephant genome in 27 days, the design inference is a perfectly logical explanation. If it was found that horses had PVC pipe for veins and a polyester bellows for a heart, the (divine) design inference is a perfectly logical explanation for such a finding. In fact, eggasai, this is exactly reason evolution is a SCIENTIFIC theory. Such findings would result in the theory of evolution being totally reworked or rejected. In fact, this is exactly why the design inference is NOT a scientific theory. It can pass any evidentiary test and thus cannot shed any light on what, how, or why anything exists the way it does.

The problem with the design inference is not that it is illogical, but that it is useless.

The evolutionary inference is pretty good but still IMperfect, primarily due to imperfect knowledge that is constantly being improved. Its real strength is that it is so extremely useful. In almost all fields of biology. Even if all the species were created 6000 years ago (or last tuesday for that matter) in exactly their current form and with exactly their current genome, the evolutionary inference would be extremely useful in systematizing biology, analyzing function through comparative anatomy, and determining developmental and biochemical pathways through comparative genomics. This is simply because whatever the process or agent that would have created them did so in a manner that makes the evolutionary paradigm work so extremely well.

 This message is a reply to: Message 10 by eggasai, posted 10-24-2006 6:29 PM eggasai has not yet responded

kuresu
Member (Idle past 1142 days)
Posts: 2544
Joined: 03-24-2006

 Message 150 of 157 (363337) 11-12-2006 1:42 AM

2x10^-8 mutations (per or /) base pairs (per or /) generation (per or /)?

under normal logic, that first (per or /) would invalidate the formula meaning 2x10^-8 base pairs. It's (per or /) base pairs, for crying out loud!

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