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Author Topic:   Extent of Mutational Capability
CRR
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Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 241 of 279 (798207)
02-01-2017 6:34 AM
Reply to: Message 238 by Dr Adequate
01-31-2017 9:42 AM


Re: The Maths
As you said “Usually this will involve fixation in the two populations as a whole.” We are talking about fixed mutations. What you haven't considered is population size and time to fixity.

So what would have been the population of chimps?
Millions of chimpanzees used to live throughout equatorial Africa from southern Senegal through Central Africa to western Tanzania. This is an area almost the size of the United States. Today, there are estimated to be merely 170,000-300,000 chimpanzees left in Africa, and their population is decreasing. rapidly.www.savethechimps.org/about-us/chimp-facts/

A female chimp will usually have her first child at around the age of 14 years old. A female chimp will not be fertile again until her child is fully weaned, so at most a female chimp will give birth every five years. She may have approximately 4-6 children in her lifetime. http://www.savethechimps.org/about-us/chimp-facts/ So the original estimate back at #176 of 20 years/generation is reasonable.

The average estimated population is ~235,000 so even today the mean time to fixity in chimps is 4Ne~=4*235,00=940,000 generations, or 18 million years.
In other words there has been time to accumulate the required number of mutations but not enough time to fix more than a small fraction.

How about the human population? Unless you assume dramatically small population sizes once again there has not been enough time to fix more than a small fraction. My previous estimate of ~25% was very generous; it would be much smaller.

So the conclusion is that the proposition that genetic differences between humans and chimps can be explained by genetic drift fails by at least an order of magnitude.


This message is a reply to:
 Message 238 by Dr Adequate, posted 01-31-2017 9:42 AM Dr Adequate has responded

Replies to this message:
 Message 243 by PaulK, posted 02-01-2017 7:00 AM CRR has responded
 Message 246 by Dr Adequate, posted 02-01-2017 9:58 AM CRR has responded

  
CRR
Member
Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 242 of 279 (798208)
02-01-2017 6:35 AM
Reply to: Message 240 by Dr Adequate
01-31-2017 9:41 PM


Re: The Maths
btw. Thanks for what you've taught me.
This message is a reply to:
 Message 240 by Dr Adequate, posted 01-31-2017 9:41 PM Dr Adequate has not yet responded

  
PaulK
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Posts: 13228
Joined: 01-10-2003
Member Rating: 1.9


Message 243 of 279 (798212)
02-01-2017 7:00 AM
Reply to: Message 241 by CRR
02-01-2017 6:34 AM


Re: The Maths
You seem to have missed the significance of the context:

quote:

This is an underestimate. Why? Because it doesn't take into account the diversity which existed before the split, which will have been lost in different ways on the way to me and the chimp. (Usually this will involve fixation in the two populations as a whole. )

This refers to alleles already in the population at the time of the common ancestor, so mean time to fixation is not really relevant (because there is no fixed start point). The correct way to handle it is to look at the number of alleles fixed by drift in the time period since the split without reference to time to fixation.

(Granted it is possible that an allele will independently fixed in both populations but I think that is uncommon enough that it can be ignored for an estimate)


This message is a reply to:
 Message 241 by CRR, posted 02-01-2017 6:34 AM CRR has responded

Replies to this message:
 Message 244 by CRR, posted 02-01-2017 8:20 AM PaulK has responded

    
CRR
Member
Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 244 of 279 (798224)
02-01-2017 8:20 AM
Reply to: Message 243 by PaulK
02-01-2017 7:00 AM


Re: The Maths @PaulK
Taking into account the diversity which existed before the split is not going to save the situation. You would have to consider the amount that were "partially fixed" but common and the effect that would have. Then you have to consider minimum time to fixity and that the mean time to fixity can not be linearly extrapolated to 100% mutations fixed.

Of course you can make the proposition work if you make enough dubious assumptions along the way.

As well as the 35 million base pair differences there are also over 700 non-homologous genes to be explained, the increase in brain mass, as well as the obvious ability to walk on two feet and talk.


This message is a reply to:
 Message 243 by PaulK, posted 02-01-2017 7:00 AM PaulK has responded

Replies to this message:
 Message 245 by PaulK, posted 02-01-2017 8:45 AM CRR has not yet responded
 Message 247 by Dr Adequate, posted 02-01-2017 10:04 AM CRR has not yet responded

  
PaulK
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Posts: 13228
Joined: 01-10-2003
Member Rating: 1.9


Message 245 of 279 (798226)
02-01-2017 8:45 AM
Reply to: Message 244 by CRR
02-01-2017 8:20 AM


Re: The Maths @PaulK
quote:

Taking into account the diversity which existed before the split is not going to save the situation. You would have to consider the amount that were "partially fixed" but common and the effect that would have.

The diversity that existed before is certainly relevant - and I do not find your objection significant. Certainly there would be significant variation in the ancestral population, and even the population splits that occurred when the human and chimp lineages diverged should have caused some to move closer to fixation in each population.

quote:

Then you have to consider minimum time to fixity and that the mean time to fixity can not be linearly extrapolated to 100% mutations fixed.

Except that we obviously do not unless we have a clear starting point. What is wrong with taking the number of alleles we expect to be fixed in that time ? It is obviously a better estimate.

quote:

Of course you can make the proposition work if you make enough dubious assumptions along the way

You do realise that it is your arguments that rely on dubious assumptions ?

quote:

As well as the 35 million base pair differences there are also over 700 non-homologous genes to be explained, the increase in brain mass, as well as the obvious ability to walk on two feet and talk.

The increase in brain size is rather well documented in the fossil record. Chimpanzees have quite good communication skills for an animal and the increase in brain size is rather obviously related to improvements in the human lineage. And I don't see any problem in the change in locomotion either.

That leaves the (allegedly) non-homologous genes. I'd expect these to be generally genes lost in one lineage and not the other (horizontal transfer is not completely out of the question but I would not expect it to account for more than a very few, if any)


This message is a reply to:
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Dr Adequate
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Posts: 15960
Joined: 07-20-2006
Member Rating: 5.6


Message 246 of 279 (798239)
02-01-2017 9:58 AM
Reply to: Message 241 by CRR
02-01-2017 6:34 AM


Re: The Maths
As you said “Usually this will involve fixation in the two populations as a whole.” We are talking about fixed mutations.

NO WE ARE NOT. That was an addendum, a footnote, referring to a different process to the one I was discussing. The 2μG figure I just derived comes without any consideration of fixation.

You are in fact wrong about fixation as well, but is hardly worth going into since you are being wrong about the wrong thing.

Can you find any error in the calculation that I just presented, the one that involves neither fixation nor the human and chimp populations considered as a whole?


This message is a reply to:
 Message 241 by CRR, posted 02-01-2017 6:34 AM CRR has responded

Replies to this message:
 Message 248 by CRR, posted 02-01-2017 11:03 PM Dr Adequate has responded

  
Dr Adequate
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Posts: 15960
Joined: 07-20-2006
Member Rating: 5.6


Message 247 of 279 (798241)
02-01-2017 10:04 AM
Reply to: Message 244 by CRR
02-01-2017 8:20 AM


Re: The Maths @PaulK
Taking into account the diversity which existed before the split is not going to save the situation.

It would, in fact, but since we got to 2μG without any consideration of fixation, using only mutations which happened after the split, none of your quibbling about how fixation would work will "save the situation" for you.

Can you find anything wrong with the calculation I just presented, the one that doesn't involve fixation in any way shape or form? The calculation that I prefaced with the words "nor are we calculating the fixations that differentiate the populations as wholes"?

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 244 by CRR, posted 02-01-2017 8:20 AM CRR has not yet responded

  
CRR
Member
Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 248 of 279 (798355)
02-01-2017 11:03 PM
Reply to: Message 246 by Dr Adequate
02-01-2017 9:58 AM


Re: The Maths
No problem with your second calculation. It's a good example of genetic entropy.

However you started talking about fixed mutations and now you're talking about a gross number of mutations of which only a minority are fixed, so there has been a significant shift in your position during the conversation.


This message is a reply to:
 Message 246 by Dr Adequate, posted 02-01-2017 9:58 AM Dr Adequate has responded

Replies to this message:
 Message 249 by Dr Adequate, posted 02-02-2017 12:39 AM CRR has responded

  
Dr Adequate
Member
Posts: 15960
Joined: 07-20-2006
Member Rating: 5.6


Message 249 of 279 (798368)
02-02-2017 12:39 AM
Reply to: Message 248 by CRR
02-01-2017 11:03 PM


Re: The Maths
No problem with your second calculation.

Good. Then you must admit that mutation is sufficient to account for the genetic distance between me and a chimp.

However you started talking about fixed mutations and now you're talking about a gross number of mutations of which only a minority are fixed, so there has been a significant shift in your position during the conversation.

No there hasn't. Both things I said are still true. I have not shifted my position one inch: I have merely talked about two different things consecutively.


This message is a reply to:
 Message 248 by CRR, posted 02-01-2017 11:03 PM CRR has responded

Replies to this message:
 Message 250 by CRR, posted 02-05-2017 3:24 AM Dr Adequate has responded

  
CRR
Member
Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 250 of 279 (798721)
02-05-2017 3:24 AM
Reply to: Message 249 by Dr Adequate
02-02-2017 12:39 AM


Re: The Maths
Then you must admit that mutation is sufficient to account for the genetic distance between me and a chimp.

Then I think you don't understand your own argument. Try going back to taws and work through it again. Decide whether you are talking about fixed or unfixed mutations and include time to fixity and reasonable estimates of population size.


This message is a reply to:
 Message 249 by Dr Adequate, posted 02-02-2017 12:39 AM Dr Adequate has responded

Replies to this message:
 Message 251 by PaulK, posted 02-05-2017 3:42 AM CRR has responded
 Message 254 by Dr Adequate, posted 02-06-2017 1:22 AM CRR has not yet responded

  
PaulK
Member
Posts: 13228
Joined: 01-10-2003
Member Rating: 1.9


Message 251 of 279 (798726)
02-05-2017 3:42 AM
Reply to: Message 250 by CRR
02-05-2017 3:24 AM


Re: The Maths
A better suggestion would be for you to deal honestly with the situation.

Dr. Adequate has been perfectly clear on when he is talking about fixed alleles and when he is not. He cannot be blamed for your confusion.

Demanding that the completely irrelevant issue of time to fixity be included doesn't help either.


This message is a reply to:
 Message 250 by CRR, posted 02-05-2017 3:24 AM CRR has responded

Replies to this message:
 Message 252 by CRR, posted 02-06-2017 12:39 AM PaulK has responded

    
CRR
Member
Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 252 of 279 (798851)
02-06-2017 12:39 AM
Reply to: Message 251 by PaulK
02-05-2017 3:42 AM


Re: The Maths
Pardon me PaulK, but if you think time to fixity is not relevant when discussing the number of mutations which could become fixed in a certain period then you don't understand what you're talking about.
This message is a reply to:
 Message 251 by PaulK, posted 02-05-2017 3:42 AM PaulK has responded

Replies to this message:
 Message 253 by PaulK, posted 02-06-2017 12:43 AM CRR has responded

  
PaulK
Member
Posts: 13228
Joined: 01-10-2003
Member Rating: 1.9


Message 253 of 279 (798852)
02-06-2017 12:43 AM
Reply to: Message 252 by CRR
02-06-2017 12:39 AM


Re: The Maths
If you have a case that time to fixity should be used rather than the number of mutations that are expected to be fixed within the time period then make it. The fact that I've made the point and you have failed to answer rather suggests that it is your knowledge that is lacking.
This message is a reply to:
 Message 252 by CRR, posted 02-06-2017 12:39 AM CRR has responded

Replies to this message:
 Message 255 by CRR, posted 02-06-2017 1:23 AM PaulK has responded

    
Dr Adequate
Member
Posts: 15960
Joined: 07-20-2006
Member Rating: 5.6


Message 254 of 279 (798858)
02-06-2017 1:22 AM
Reply to: Message 250 by CRR
02-05-2017 3:24 AM


Re: The Maths
Then I think you don't understand your own argument. Try going back to taws and work through it again.

I do understand my own arguments. I do not understand what you mean by taws.

One thing you don't seem to understand --- despite me explaining it repeatedly with a patience that would do credit to a saint --- is that I have in fact presented two completely different arguments. The second of these does not involve fixation, and so cannot possibly involve time to fixation, and so is entirely unaffected by population size and all the other semi-digested ideas by means of which you hope to misunderstand the first argument.

Can you find anything wrong with the second argument? If not, you must admit that mutation is sufficient to account for the genetic distance between me and a chimp.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 250 by CRR, posted 02-05-2017 3:24 AM CRR has not yet responded

  
CRR
Member
Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 255 of 279 (798859)
02-06-2017 1:23 AM
Reply to: Message 253 by PaulK
02-06-2017 12:43 AM


Re: The Maths
If you have a case that time to fixity should be used rather than the number of mutations that are expected to be fixed within the time period then make it.

Are you sure you thought about that response? Let me explain.

Say we are looking at a period of 100 generations with 100 mutations expected to be fixed from generation 1.
If the mean time to fixity is 100 generations then we would expect 50 of those mutations to be fixed in the time available.
If the mean time to fixity is 1000 generations then very few, possibly none, of those mutations will be fixed in the time time available.

The number of mutations that are expected to be fixed within the time period DEPENDS on the time to fixity.

Time to fixity is normally expressed as the Mean Time to Fixity for much the same reasons we measure radioactive decay as a half life.


This message is a reply to:
 Message 253 by PaulK, posted 02-06-2017 12:43 AM PaulK has responded

Replies to this message:
 Message 256 by PaulK, posted 02-06-2017 1:52 AM CRR has not yet responded
 Message 258 by Dr Adequate, posted 02-06-2017 3:44 PM CRR has not yet responded

  
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