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Author Topic:   Molecular Population Genetics and Diversity through Mutation
PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 6 of 455 (784835)
05-24-2016 7:55 AM
Reply to: Message 4 by Faith
05-24-2016 6:04 AM


Re: But I'm just as mathematically challenged as ever
quote:

Well, now I see that you are saying the same thing I’ve answered many times in this argument already: it doesn’t matter how much new genetic variability you can put into, or put back into, a population, when it is evolving a new population of new phenotypes, a new look, the trend is going to be to loss of genetic diversity, no matter how much new diversity may have been added.

As Modulous has pointed out this is a bad argument for reasons that have been pointed out before - and which are implicit in the post you are answering. The times when a new species is forming is just a fraction of the lifetime of a successful species - and the rest of that time is when we expect the increases to occur.
(For good reason. Losses should slow when a species is increasing in population, and the number of mutations appearing is proportional to population size.)

And, of course, this is one of the points that you haven't been able to refute.


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 Message 4 by Faith, posted 05-24-2016 6:04 AM Faith has responded

Replies to this message:
 Message 10 by Faith, posted 05-24-2016 4:52 PM PaulK has responded

  
PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 9 of 455 (784848)
05-24-2016 4:45 PM
Reply to: Message 8 by Faith
05-24-2016 4:29 PM


Re: Fitness graphic
quote:

Again, what I am focusing on is what happens when you are getting the active production of new phenotypes in reproductive isolation, because that is the clearest expression of evolution, usually believed to be THE way all life evolved from former life. But the fact is that this leads ultimately to genetic depletion, yes even with all the additions you can throw at it -- as long as new phenotypes are being produced you are getting a loss of genetic diversity.

But it does not lead to "genetic depletion" because variation IS added. if you insist on only looking at the - relatively short - periods when diversity is declining you will not see the increases - but that doesn't mean they don't happen.

You have yet to offer any valid reason why diversity cannot be restored between speciation events. So what if it contradicts your ideas about evolution - I'll stick with the evidence that says that your ideas are wrong.


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PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


(1)
Message 12 of 455 (784851)
05-24-2016 5:13 PM
Reply to: Message 10 by Faith
05-24-2016 4:52 PM


Re: The endless dance of the wishful refutation
quote:

And I've answered that I don't know how many times. You can get all the increases you want, taking all the time you want, it makes no difference to the point I'm making.

Simply stating your opinion is hardly sufficient - especially when that opinion seems to be obviously wrong. And refusing to consider the problems in your argument helps nobody (well it helps us win the argument but only because you disqualify yourself, which isn't really what I want)

quote:

Leaving aside the crucial question of just what sort of mutations are appearing in just what proportions to just what purpose, losses will slow when a population is genetically STABLE, increasing in numbers or not. If it's an evolving subpopulation, with new gene frequencies that have yet to be reproductively worked through the whole population, then the population will be increasing while the losses may be increasing at the same time by drift.

And there is a failure to think things through. In an increasing population a larger proportion of the offspring survive. That will reduce losses from drift and selection.

quote:

You keep saying that and I keep saying you're wrong.

You can keep saying it as long as you like, but that won't make it true. An opinion held against the evidence is not and never will be a successful refutation.

quote:

I never said it couldn't be restored. What I'm saying is that it makes no difference because when the population is actively evolving all that increase gets pared down to favor a few phenotypes with the concomitant loss of genetic diversity

Except that it does make a difference. Obviously it does. If genetic diversity is restored between speciation events we have no continuous decline in diversity, just a cycle between higher and lower levels of diversity.

Edited by PaulK, : Added a response to Faith's addition


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PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


(1)
Message 28 of 455 (784880)
05-25-2016 12:55 AM
Reply to: Message 15 by Faith
05-24-2016 5:34 PM


Re: The endless dance of the wishful refutation
quote:

But it can't reduce the original loss of genetic diversity from the new gene frequencies caused by the formation of the new subpopulation in the first place.

It will not bring back the lost alleles, it may well not add diversity at the loci of those alleles. But your argument is not concerned with those details, only with overall diversity, which can be increased by adding new alleles at other loci. And we still await a sound argument that overall diversity must decrease despite the evidence


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 Message 15 by Faith, posted 05-24-2016 5:34 PM Faith has responded

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 Message 30 by Faith, posted 05-25-2016 4:33 AM PaulK has responded

  
PaulK
Member
Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 31 of 455 (784886)
05-25-2016 5:16 AM
Reply to: Message 30 by Faith
05-25-2016 4:33 AM


Re: The endless dance of the wishful refutation
quote:

There is no such evidence.

Your refusal to accept the evidence does not make it go away. It is still a fact that genetic diversity is greater than you can easily account for even given your own views, never mind the history of life that the evidence really shows to us.

quote:

Mutation is the only thing that could increase the genetic diversity and I dispute that you could get a single beneficial mutation in the short time frame for all the above to occur.

Which is a complete irrelevance since we do not need beneficial mutations, nor do we need to restrict the timescale to the short periods of time that you are prepared to look at.

It's past time you stopped dancing and tried to engage in honest discussion


This message is a reply to:
 Message 30 by Faith, posted 05-25-2016 4:33 AM Faith has responded

Replies to this message:
 Message 32 by Faith, posted 05-25-2016 5:20 AM PaulK has responded

  
PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


(3)
Message 33 of 455 (784889)
05-25-2016 6:39 AM
Reply to: Message 32 by Faith
05-25-2016 5:20 AM


Re: The endless dance of the wishful refutation
quote:

Evidence of what genetic diversity where? You don't know what you are talking about.

You mean that YOU don't know what I'm talking about despite all the discussion here.

Odd how you can't even remember how you have difficulty finding any examples of your "genetic depletion" - and how one of the examples you tried to give us is due to a bottleneck in historical times - and you can't even show that it produced the phenotypic changes you expect (elephant seals because you probably won't remember that unless I remind you)

And, you propose that there was a major bottleneck in the recent past such that some populations were reduced to single pairs - and that the descendants of these pairs became multiple modern species. The cytochrome-C argument given recently shows that genetic diversity at the level of sequences can't be easily explained without allowing for mutations to appear and become fixed since your bottleneck. And let us not forget that there are human genes with large numbers of alleles (hundreds IIRC - but certainly many more than the maximum of 10 we'd expect from an effective population of 5 people)

Edited by PaulK, : One clarification


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 Message 44 by Faith, posted 05-26-2016 2:17 PM PaulK has responded

  
PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 40 of 455 (784933)
05-26-2016 8:07 AM


Why neutral and deleterious mutations count
It should be obvious.

The heterozygosity measure in no way depends on fitness measures. The only question is whether the two alleles at the locus in question are the same or different. If they are the same, the individual is homozygous, if not heterozygous.

If we measure diversity by counting the range of alleles again, fitness does not matter.

Or again diversity is about the current state of the population. We should not count an allele differently if it was the product of a mutation or not (and what counts as "not" and how do we tell ?)

Or again, if the loss of an allele counts as a loss of diversity the gain of that allele should count as an increase. Alleles lost through selection are necessarily less fit - equivalent to a deleterious mutation. (Granted there are complications but they don't really impact the point)

So, I think that it is quite obvious to anyone who considers the matter that simply for considering their contribution to diversity all mutations count. Or rather that all alleles in the population count, whether they are considered mutant or not.

To forestall the obvious objection, what happens in future generations matters but that is a different question from the diversity of the current generation and it can only be prejudged in the case of the more severe deleterious mutations - even mildly deleterious mutations may be retained and spread by drift. And so long as the mutant allele is present it should be counted.


Replies to this message:
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PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 45 of 455 (784959)
05-26-2016 2:17 PM
Reply to: Message 42 by Faith
05-26-2016 1:59 PM


Re: Why neutral and deleterious mutations count
quote:

I agree with this post in general. But I still take the position that mutations aren't going to make a difference in the outcome of reduced genetic diversity in an evolving population.

We're all pretty much agreed that diversity will decrease during speciation events. The question is to what degree it can recover afterwards. I take the position that it can recover sufficiently that evolution will not cease for lack of diversity. At least not as a consequence of evolution rather than. say, human interference or the sun becoming a Red Giant star, as it will eventually.


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PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 49 of 455 (784966)
05-26-2016 3:13 PM
Reply to: Message 48 by Faith
05-26-2016 3:05 PM


Re: Some very simple maths.
quote:

You are missing the whole point of why adding genetic diversity makes no difference to what I'm saying.

The only "reason" seems to be that you refuse to consider it and insist on only thinking about times when diversity is decreasing. That is not exactly a good reason.


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PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


(1)
Message 51 of 455 (784971)
05-26-2016 4:00 PM
Reply to: Message 44 by Faith
05-26-2016 2:17 PM


Re: The endless dance of the wishful refutation
quote:

Oh I remember elephant seals as an example of depleted genetic diversity, but how am I know what you are referring to with your general statements?

I don't really see how you can recognise that elephant seals were one of your examples of genetic depletion while being completely unable to understand that you had difficulty finding such examples. As I remember you only had one other - which was also attributed to a bottleneck.

The other point was your claim that simply reducing genetic diversity would produce speciation - in fact you even tried to claim the cheetahs speed as an example. And yet - despite the fact that the elephant seal suffered its bottleneck relatively recently - so "before" and "after" versions should be findable you produced no evidence that modern elephant seals should be considered a different species - or "species" if you prefer - from their pre-bottleneck ancestors.

quote:

...it doesn't make such a huge difference when the genetic diversity starts out extremely high as it would have back then, such as for instance there likely having been many more genes for a given trait than there are now (most of that genetic diversity now in the Junk DNA cemetery)

In other words a questionable ad-hoc explanation - lacking in evidence. Supporting my point.

quote:

It was six, so twelve

No, it was five. Noah, his wife and their sons wives. The sons get all their alleles from Noah and his wife, so they add nothing. You can appeal to mutations if you like but you aren't going to get many more variations (if any) at that locus.

quote:

And I've many times allowed that there had to have been some kind of "mutation" to bring about the increase in alleles per locus. Something more orderly than random accidents I would suppose.

Your whole argument is about denying increases in variation...


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PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 55 of 455 (785004)
05-27-2016 7:35 AM
Reply to: Message 54 by Faith
05-27-2016 4:31 AM


Re: You are looking at the wrong part of the system
quote:

It would be if you understood what I'm talking about and looked in the right place for the right evidence. It would also help if you understood that I'm talking about a TREND in that direction. That's what you would look for rather than the stopping point itself.

I think that I can speak for pretty much everyone when I tell you that we are still waiting for you to produce the evidence justifying your claims.

So far as I can see your main arguments are that you won't look at periods when diversity is exacted to increase (because they don't fit your idea of evolution - although why that should matter I have no idea) and that you say that the increases in diversity cannot be sufficient, although without any clear argument or evidence for that conclusion.

So instead of trying to blame everyone else perhaps you should actually make a real case for this alleged declining trend.

Edited by PaulK, : No reason given.


This message is a reply to:
 Message 54 by Faith, posted 05-27-2016 4:31 AM Faith has responded

Replies to this message:
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PaulK
Member
Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 60 of 455 (785052)
05-27-2016 1:16 PM
Reply to: Message 58 by Faith
05-27-2016 12:51 PM


Re: You are looking at the wrong part of the system
quote:

The necessity of loss of genetic diversity in breeding, such as dog breeding and the known fact that selection reduces genetic diversity are evidence for starters. Funny you haven't noticed.

Those certainly aren't being ignored, they are just nowhere near sufficient. So where is the evidence that HBD supposedly isn't looking at ?

quote:

can repeat it I guess. My focus is on the processes that bring about new subspecies from new gene frequencies, which is what evolution is., Evoilution is not going on in the periods of stability

But you cannot work out what is going on with genetic diversity by just cherry-picking the periods where it is declining. So all you are saying is that I was correct and you are refusing to consider periods where diversity is increasing. Your excuse - and it is transparently an excuse - holds no water.

quote:

All those who keep pointing to the genetic increases need to show that you could get evolution out of them


Well no. All we need to show is that they add genetic diversity, which they obviously do.

quote:

Sorry if it hasn't been clear but I've certainly made the argument many times.

All I remember is some vague rambling about "interfering" with speciation - without any explanation of how (and I must suspect the reason for that is you have no idea of how that could be true either). If you can point to anything sensible I'd like to see it, but I'm sure you never managed that.


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PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 75 of 455 (785116)
05-28-2016 2:57 AM


Faith - Why the fuss?
Faith you have admitted that you are not interested in the question of long-term trends in diversity, only what happens to diversity in speciation events.

why then, are you claiming to have discovered such a trend when you aren't interested enough to investigate the question properly ?

Wouldn't it be far easier to just admit that you aren't interested and drop the point right at the start instead of spending - literally - years arguing over something you claim not to care about ?


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PaulK
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Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


(4)
Message 77 of 455 (785121)
05-28-2016 3:45 AM
Reply to: Message 76 by Faith
05-28-2016 3:34 AM


Re: Faith - Why the fuss?
quote:

You have a big problem with context.

You're wrong, as usual, and obviously so.

quote:

The context is that selection, random or otherwise, gets new gene frequencies, new gene frequencies bring out new phenotypes, getting new phenotypes requires losing alleles, reproductive isolation of these phenotypes can produce a new subspecies which must trend toward reduced genetic diversity as a result. This is evolution. There's no point in examining other contexts when I know this is evolution and it costs genetic diversity.

In other words you see no point in considering anything other than your idea of evolution. But if you were actually interested in long term trends in genetic diversity you would consider everything that contributes, whether you considered it "evolution" or not.

So, in fact you have simply confirmed my point. You have not properly investigated the question of long term trends because you aren't interested in it. And yet you have spent years arguing about it.


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PaulK
Member
Posts: 16061
Joined: 01-10-2003
Member Rating: 2.1


Message 91 of 455 (785199)
05-29-2016 5:02 AM


Faith begins to understand evolution..
...she's still fighting against understanding.

Message 10


Although these four are all identified as “evolutionary processes” They do entirely different things. The additive processes contribute to genetic diversity in a haphazard way, adding a variety of phenotypes to a population for a motley appearance, while the subtractive processes select and bring out a new homogeneous collection of phenotypes, even a completely new subspecies, which is what I mean by active evolution.

As was recently pointed out:
Message 913


As Dr Adequate and Modulous and NoNukes have demonstrated, evolutionary theory has, ever since Darwin, been depicted as the interplay of two forces. One introducing new variations and one culling them.

Faith would find it much easier if she listened, and worked on understanding. She might even get to understand why her "motley collection of phenotypes" objection applies more to dogs than to wild species.

Edited by PaulK, : Clarification


Replies to this message:
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