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Author Topic:   Extent of Mutational Capability
Dr Adequate
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Posts: 15936
Joined: 07-20-2006
Member Rating: 3.4


Message 196 of 279 (793912)
11-07-2016 3:22 AM
Reply to: Message 194 by CRR
11-07-2016 2:42 AM


Re: The Maths
Who has refuted ReMine's paper?

See this thread, passim.


This message is a reply to:
 Message 194 by CRR, posted 11-07-2016 2:42 AM CRR has not yet responded

Replies to this message:
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Pressie
Member
Posts: 1627
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.6


Message 197 of 279 (793924)
11-07-2016 5:46 AM
Reply to: Message 196 by Dr Adequate
11-07-2016 3:22 AM


Re: The Maths
It seems as if CRR is not ever going to to the basic maths he was talking about. I think that he/she didn't tell the truth. CRR, like all those creationists, seems to be a bit scared when having to confront people who actually know what's going on.

Hey, CRR, please present the maths supporting your claim. Do the sums.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.


This message is a reply to:
 Message 196 by Dr Adequate, posted 11-07-2016 3:22 AM Dr Adequate has not yet responded

    
Pressie
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Posts: 1627
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.6


Message 198 of 279 (793925)
11-07-2016 6:18 AM
Reply to: Message 194 by CRR
11-07-2016 2:42 AM


Re: The Maths
This one was funny.

CRR writes:

Who has refuted ReMine's paper? No one that I know of.

Well, maybe he has to start presenting his paper in some relevant peer-reviewed journal...without that it's like presenting a "paper" on Noddy in TJ.

Do the maths for us, CRR. Here.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.


This message is a reply to:
 Message 194 by CRR, posted 11-07-2016 2:42 AM CRR has responded

Replies to this message:
 Message 200 by CRR, posted 11-12-2016 2:09 AM Pressie has responded

    
CRR
Member
Posts: 357
From: Australia
Joined: 10-19-2016
Member Rating: 1.3


Message 199 of 279 (794234)
11-12-2016 1:50 AM
Reply to: Message 195 by Dr Adequate
11-07-2016 3:21 AM


Re: The Maths
Prematurely condescending? Quite possibly, but it is a good way to learn.

However there is still a hole in your argument. You calculation relies on the estimated number that would become fixed in infinite time, but we only have the supposed time since separation of the species.

The mean time to fixity is T(mean) ≈ 4 Ne generations, so for Ne>90,000 less than half of the potential would become fixed in 350,000 generations, and this number becomes progressively smaller with each generation. Conversely the population has generally increased over time. It is estimated that around 50–60 million people lived in the combined eastern and western Roman Empire in the 4th century AD and a similar number in China, plus the rest of the world. So no mutations occurring since 1AD would have been fixed in the human population.

Estimates of the population of the world at the time agriculture emerged in around 10,000 BCE have ranged between 1 million and 15 million so it is unlikely any of those have been fixed either.

So even neutral drift is is going to come up well short of the number of genetic differences between humans and chimps.

Do you have any evidence that a significant number of mutations are currently being fixed by genetic drift? Sufficient to be consistent with your proposition?

[edit]
According to ReMine "Using straightforward data and theory supplied by Motoo Kimura himself (the author of the neutral theory), this chapter shows that in ten million years a human-like population could, at best, substitute 25,000 expressed neutral mutations."

Edited by CRR, : as marked


This message is a reply to:
 Message 195 by Dr Adequate, posted 11-07-2016 3:21 AM Dr Adequate has responded

Replies to this message:
 Message 202 by Dr Adequate, posted 11-12-2016 11:32 AM CRR has responded
 Message 203 by Dr Adequate, posted 11-12-2016 1:21 PM CRR has responded
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CRR
Member
Posts: 357
From: Australia
Joined: 10-19-2016
Member Rating: 1.3


Message 200 of 279 (794235)
11-12-2016 2:09 AM
Reply to: Message 198 by Pressie
11-07-2016 6:18 AM


Re: The Maths
It was published in Journal of Creation, (Previously called TJ)
Volume 19, Issue 1, Published April 2005

The paper was submitted previously to the journal Theoretical Population Biology, where renowned evolutionary geneticists Warren J. Ewens and James F. Crow reviewed it, along with Alexey Kondrashov and John Sanford. They all acknowledged this paper is essentially correct in all matters of substance. However, Ewens and Crow rejected it from publication on the grounds that it is not sufficiently new or different from what was known by themselves and some of their colleagues in the 1970s.


This message is a reply to:
 Message 198 by Pressie, posted 11-07-2016 6:18 AM Pressie has responded

Replies to this message:
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 Message 209 by Pressie, posted 11-14-2016 5:51 AM CRR has not yet responded

  
Admin
Director
Posts: 12516
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.9


Message 201 of 279 (794239)
11-12-2016 7:22 AM
Reply to: Message 200 by CRR
11-12-2016 2:09 AM


Re: The Maths
CRR writes:

The paper was submitted previously to the journal Theoretical Population Biology, where renowned evolutionary geneticists Warren J. Ewens and James F. Crow reviewed it, along with Alexey Kondrashov and John Sanford. They all acknowledged this paper is essentially correct in all matters of substance. However, Ewens and Crow rejected it from publication on the grounds that it is not sufficiently new or different from what was known by themselves and some of their colleagues in the 1970s.

One of my roles as moderator is as fact checker. These aren't your words. They're the words of Walter J. Remine as quoted at Cost theory and the cost of substitution—a clarification at Creation Ministries International. From the Forum Guidelines:

    Never include material not your own without attribution to the original source.

Remine goes on to say:

quote:
"However, they never communicated this knowledge to the greater scientific community, nor to the public at large. There were rare correct insights scattered sparsely in the literature, but those were incomplete, overwhelmed by confusion, and never communicated together in a coherent manner. This has all been very unfortunate, as there continues to be widespread misunderstanding within the scientific community regarding these important matters, even among those who have studied the cost literature for years. It is hoped that the clarifications presented in this paper, which are sound, will eventually reach the greater scientific community."—Walter J. ReMine.

Your task in this thread should be explain where lies the misunderstanding referred to by Remine, and why his objections are valid.


--Percy
EvC Forum Director

This message is a reply to:
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Dr Adequate
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Posts: 15936
Joined: 07-20-2006
Member Rating: 3.4


(1)
Message 202 of 279 (794252)
11-12-2016 11:32 AM
Reply to: Message 199 by CRR
11-12-2016 1:50 AM


Re: The Maths
However there is still a hole in your argument. You calculation relies on the estimated number that would become fixed in infinite time ...

No, what in the world gave you that idea?

As for the rest of your post, I would point out that the figures are not perfectly known, we're just ballparking it here. When we're looking at millions of years, does it matter what might or might not have happened since 1 AD? That would only been important if we were going for a factitiously precise figure. The fact remains, we expect millions of differences between chimps and humans as a result of neutral mutation and drift alone, and so anyone ignoring this has messed up.

ETA: Note that whenever we start the clock on the process, there is already neutral variation in the gene pool. It is true that a neutral mutation that happened yesterday will not have been fixed yet, bit now consider what's going to happen at the other end of the process.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 199 by CRR, posted 11-12-2016 1:50 AM CRR has responded

Replies to this message:
 Message 206 by CRR, posted 11-13-2016 5:21 PM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 15936
Joined: 07-20-2006
Member Rating: 3.4


(1)
Message 203 of 279 (794253)
11-12-2016 1:21 PM
Reply to: Message 199 by CRR
11-12-2016 1:50 AM


Re: The Maths
But if fixation is too confusing, let's think about two individuals, let's say me and this chimpanzee.

I have of course acquired μ mutations of my own. But what did I get from my parents? Well, they each acquired μ mutations of their own. What with diploidly, they each passed on ˝μ mutations to me, and since I have two parents, that makes a grand total of μ. But what did they get from their parents? Well of course the same reasoning applies

So if there have been G generations between now and the chimp-human split, then I have had time to accumulate μG mutations. As similar processes have affected the chimp line, the chimp in the photo has also had time to accumulate μG mutations (ballparking generation time as the same for both species). The difference between me and the chimp should therefore be 2μG mutations. Which is what I said.

(Note that to a very good first approximation, because the genome is so big all the mutations we're talking about will be different; for our ballpark figure we can neglect the occasional coincidence.)

---

As we don't exactly know μ and G, there's no point in striving for a high level of accuracy. What we can say is that the difference between me and the chimp should be of the order of 2μG.

And this is sufficient on its own to undermine ReMine's nonsense about Haldane's dilemma: there is simply no need at all to suppose that all the mutations (or even more than a tiny fraction of them) that separate us from chimps are beneficial mutations fixed by selection; but these are the only mutations to which Haldane's dilemma applies.

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 199 by CRR, posted 11-12-2016 1:50 AM CRR has responded

Replies to this message:
 Message 220 by CRR, posted 01-21-2017 8:40 PM Dr Adequate has responded

  
caffeine
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Posts: 1289
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 5.6


(2)
Message 204 of 279 (794256)
11-12-2016 3:29 PM
Reply to: Message 199 by CRR
11-12-2016 1:50 AM


Re: The Maths
Estimates of the population of the world at the time agriculture emerged in around 10,000 BCE have ranged between 1 million and 15 million so it is unlikely any of those have been fixed either.

The probability of any allele reaching fixation in the human population in the last 10,000 years is very low. However, this time period represents about 0.2% of the time elapsed since the estimated divergence from chimps; and humans 10,000 years ago were already human and in possession of the full set of alleles that distinguish humans from chimps, so I am unclear why this would matter.

Edited by caffeine, : No reason given.


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Replies to this message:
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PaulK
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Posts: 12770
Joined: 01-10-2003
Member Rating: 3.0


Message 205 of 279 (794257)
11-12-2016 5:12 PM
Reply to: Message 204 by caffeine
11-12-2016 3:29 PM


Re: The Maths
It's even worse for CCR than that.

If you want to consider differences in the genomes there will be some from mutations that occurred before the split. If one allele is fixed in the human lineage, and another in the chimpanzee lineage - or even if an allele is fixed in one lineage and lost in the other - that would contribute to the differences.


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CRR
Member
Posts: 357
From: Australia
Joined: 10-19-2016
Member Rating: 1.3


Message 206 of 279 (794277)
11-13-2016 5:21 PM
Reply to: Message 202 by Dr Adequate
11-12-2016 11:32 AM


Re: The Maths
What in the world gave me that idea? https://en.wikipedia.org/wiki/Fixation_(population_genetics)

"Because the effect of natural selection is stipulated to be negligible, the probability at any given time that an allele will ultimately become fixed at its locus is simply its frequency {\displaystyle p} p in the population at that time. " Note ULTIMATELY.
https://en.wikipedia.org/wiki/Fixation_(population_genetics)#Probability_of_fixation

"Additionally, research has been done into the average time it takes for a neutral mutation to become fixed. Kimura and Ohta (1969) showed that a new mutation that eventually fixes will spend an average of 4Ne generations as a polymorphism in the population." Note AVERAGE.
https://en.wikipedia.org/wiki/Fixation_(population_genetics)#Time_to_fixation

At the time of separation when the clock is started much of the neutral mutation is already substantially established and you can't appeal to that to make up the gap.

I agree that population figures are not perfectly known, actually they are very rough estimates. However that works both ways since it also limits the precision of your calculations. To rescue your proposition you would have to assume that population numbers have been very small for most of the time to allow fixation to occur, and the evidence for that is scant.

A very rough estimate assuming an average population of 90,000 is that 1/2 of the first generation neutral mutations would have been fixed (T,mean=4Ne), and less in each succeeding generation so that perhaps 1/4 of potential mutations would have bee fixed in the 350,000 generations available.

Note that ReMine gave a much smaller figure than this. I'm not sufficiently across the maths of neutral theory to say if he is right or wrong.

Overall I believe you have failed to substantiate your claim that genetic drift alone is sufficient to explain the number of genetic differences between humans and chimps. Perhaps you can direct me to a published source to back up your position.


This message is a reply to:
 Message 202 by Dr Adequate, posted 11-12-2016 11:32 AM Dr Adequate has responded

Replies to this message:
 Message 207 by Dr Adequate, posted 11-13-2016 8:58 PM CRR has not yet responded

  
Dr Adequate
Member
Posts: 15936
Joined: 07-20-2006
Member Rating: 3.4


Message 207 of 279 (794282)
11-13-2016 8:58 PM
Reply to: Message 206 by CRR
11-13-2016 5:21 PM


Re: The Maths
What in the world gave me that idea? https://en.wikipedia.org/wiki/Fixation_(population_genetics)
"Because the effect of natural selection is stipulated to be negligible, the probability at any given time that an allele will ultimately become fixed at its locus is simply its frequency {\displaystyle p} p in the population at that time. " Note ULTIMATELY.

Note that "ultimately" does not mean "after a infinite amount of time".

After an infinite amount of time all of the neutral mutations would have occurred.

I agree that population figures are not perfectly known, actually they are very rough estimates. However that works both ways since it also limits the precision of your calculations.

That's fine, I'm just establishing plausibility, which I have, it's not me going around claiming to have proved that there's been time for exactly 1,667 mutations.

A very rough estimate assuming an average population of 90,000 is that 1/2 of the first generation neutral mutations would have been fixed (T,mean=4Ne), and less in each succeeding generation so that perhaps 1/4 of potential mutations would have bee fixed in the 350,000 generations available.

No, you can't do that. Kimura's time is from when the mutation arises, when there's only one copy of it. So if it's already been around for some time the probability that at any given time there's still only one copy and that the same math applies is negligible.

Overall I believe you have failed to substantiate your claim that genetic drift alone is sufficient to explain the number of genetic differences between humans and chimps.

But you've been wrong a lot lately.

Any thoughts on message #203?

Edited by Dr Adequate, : No reason given.


This message is a reply to:
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Pressie
Member
Posts: 1627
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.6


Message 208 of 279 (794288)
11-14-2016 5:42 AM
Reply to: Message 200 by CRR
11-12-2016 2:09 AM


Re: The Maths
CRR writes:

It was published in Journal of Creation, (Previously called TJ) Volume 19, Issue 1, Published April 2005

I'm not too sure why you think this is going to advance your case. So, never published in any scientific journal as a first step?

Still not going to do the maths for us, here? The maths for your claims, CRR. Please do the maths here.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.


This message is a reply to:
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Pressie
Member
Posts: 1627
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.6


Message 209 of 279 (794289)
11-14-2016 5:51 AM
Reply to: Message 200 by CRR
11-12-2016 2:09 AM


Re: The Maths
CRR writes:

The paper was submitted previously to the journal Theoretical Population Biology, where renowned evolutionary geneticists Warren J. Ewens and James F. Crow reviewed it, along with Alexey Kondrashov and John Sanford. They all acknowledged this paper is essentially correct in all matters of substance. However, Ewens and Crow rejected it from publication on the grounds that it is not sufficiently new or different from what was known by themselves and some of their colleagues in the 1970s.

I don't believe you at all. You lie. Peer-reviewers are not named in journals.

But, interestingly is that they got Sanford was supposed to review according to you. Something smelly about it. Really, really smelly.

Please show us your maths, CRR.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.


This message is a reply to:
 Message 200 by CRR, posted 11-12-2016 2:09 AM CRR has not yet responded

Replies to this message:
 Message 210 by herebedragons, posted 11-14-2016 8:26 AM Pressie has not yet responded
 Message 211 by Dr Adequate, posted 11-14-2016 2:48 PM Pressie has responded

    
herebedragons
Member
Posts: 1328
From: Michigan
Joined: 11-22-2009
Member Rating: 5.9


Message 210 of 279 (794295)
11-14-2016 8:26 AM
Reply to: Message 209 by Pressie
11-14-2016 5:51 AM


Re: The Maths
I don't believe you at all. You lie. Peer-reviewers are not named in journals.

I agree that it's weird that the authors knew who the reviewers were, but maybe that journal's policy is not anonymity. (?) Most reputable journals do have a policy of reviewer anonymity though, so it is definately suspect. I doubt CRR is lying himself, though, he simply got this information from somewhere and is just repeating it.

But, interestingly is that they got Sanford was supposed to review according to you. Something smelly about it.

I think it depends on when during Sanford's career he reviewed it. I believe he started out as an atheist, then became a theistic evolutionist, then old earth creationist, then ID, then YEC (which is unusual in itself).

What bothers me is that they submitted it to a quite prestigious journal, with a pretty narrow focus and when it was rejected, they went ahead and published in a creationist journal... Anyone who has submitted anything for publication knows that even good articles can be rejected for various reasons not related to quality or accuracy. What most researchers do is submit to other reputable journals until someone picks it up, not go right for a junk journal. So you fix it up and/or submit it to another journal, not dump it in the Journal of Creation That's what is smelly about it to me.

However, not completely sure what specific article is being referred to here... I think I've look at it briefly, but I'm not sure. Maybe a link to the article? I don't think there has been any real discussion about it either... just that it was "essentially correct" yet rejected anyway (presecution complex?).

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


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