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Author Topic:   Molecular Population Genetics and Diversity through Mutation
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


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:
 Message 92 by NoNukes, posted 05-29-2016 1:12 PM PaulK has replied

  
NoNukes
Inactive Member


Message 92 of 455 (785203)
05-29-2016 1:12 PM
Reply to: Message 91 by PaulK
05-29-2016 5:02 AM


Re: Faith begins to understand evolution..
She might even get to understand why her "motley collection of phenotypes"
Actually, a 'motley collection of phenotypes' sounds like a pretty good description for any large population of human beings. Subgroups of humans are not a collection of homogeneous clones. Getting us to look alike or to have similar traits as Faith seems to think is 'evolution' that would require a deliberate eugenics program. Which is what dog breeders actually do engage in.
I'm curious to see how long the ever patient Genomicus can deal with her insistence on this erroneous path.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams

This message is a reply to:
 Message 91 by PaulK, posted 05-29-2016 5:02 AM PaulK has replied

Replies to this message:
 Message 93 by PaulK, posted 05-29-2016 1:27 PM NoNukes has seen this message but not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 93 of 455 (785206)
05-29-2016 1:27 PM
Reply to: Message 92 by NoNukes
05-29-2016 1:12 PM


Re: Faith begins to understand evolution..
I guess she could be just ignoring existing variation. But of course it is obviously daft to think that restoring variation to the same level as the parent species would make the daughter species anything but a "nice clear species" (to the extent that real species are "clear"). After all the parent species had the same level of variation.
Edited by PaulK, : No reason given.

This message is a reply to:
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 94 of 455 (785208)
05-29-2016 5:48 PM
Reply to: Message 76 by Faith
05-28-2016 3:34 AM


Re: Faith - Why the fuss?
You have a big problem with context. 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.
And since mutations add diversity, there is no reason why this process should ever stop.

This message is a reply to:
 Message 76 by Faith, posted 05-28-2016 3:34 AM Faith has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 95 of 455 (785209)
05-29-2016 5:50 PM
Reply to: Message 42 by Faith
05-26-2016 1:59 PM


Re: Why neutral and deleterious mutations count
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. You could double the genetic diversity in a stable population and still, when selection or the random selection of the splitting off of a subpopulation occurs, new phenotypes are going to emerge simply from the new higher gene frequencies, and former phenotypes that are now low frequency will fade away, while alleles competing with the new phenotypes will necessarily also be reduced and perhaps disappear. You may (hypothetically) have lots of mutated alleles to begin with, but when you are getting evolution there's no more genetic increase, just reduction. And evolution IS the point, isn't it?
You can, if you wish, contrary to all accepted usage, exclude mutations from your own private definition of evolution. But this does not prevent them from happening, so you still have to deal with that.

This message is a reply to:
 Message 42 by Faith, posted 05-26-2016 1:59 PM Faith has not replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


(1)
Message 96 of 455 (785214)
05-30-2016 9:41 AM
Reply to: Message 80 by NoNukes
05-28-2016 3:23 PM


Re: You are looking at the wrong part of the system
I'm a bit suspicious of this idea. Sometimes populations do not intermingle thoroughly even over large periods of time.
This is just a matter of the 'largeness' of the time, and definitions of 'population'. Subpopulations that don't share genetic material with other parts of the population might simply not be considered part of the population. This would be a 'daughter' group as it were.
For example there are large segments of the US human population that have historically resisted intermingling due to social circumstances despite the fact that they are inter-fertile, and accordingly I would not expect some alleles not to be evenly distributed through out the population. I suspect we can find examples of animal populations behaving similarly.
Sure but the US is only a couple of centuries old. So any alleles unique to this group are alleles that were not present in the main population of Europe before their ancestors adopted a resistance to intermingling. The alleles might be 'old' relative to say, my shoes. But they are 'new' relative to the human race.
What we can say is that distributing a new allele will take time, and perhaps that means at a minimum that the term "new" is somewhat subjective.
For clarity, 'new' was being used relative to the population.
Also we're talking about perturbations from Hardy-Weinberg which has a large population with non-random mating (ie., anybody in the population has the same probabilities to have sex with any other member of population as any other member of the population). This is to isolate the effects we're talking about.
Faith believes that that a subgroup with different allele frequencies becomes isolated, and because of their allele frequency differences they are morphologically different and that over time these differences exacerbate and by {magic} the two populations are eventually unable to successfully interbreed.
Of course in the complete HW scenario, the original population is infinitely large and so every possible combination of alleles exists in the original population. Thus the original dog population, were it to be infinite, would contain all possible breeds that don't require mutations to express them (according to Faith therefore, all breeds). So the daughter population, if it somehow manage to be selective in which animals went to join it, will only contain a subset of the animals in the original population. So even on the face of it, this cannot lead to speciation in the sense of the two species are genetically incompatible.
The argument seems to be trying to both have its cake and eat it.

This message is a reply to:
 Message 80 by NoNukes, posted 05-28-2016 3:23 PM NoNukes has replied

Replies to this message:
 Message 97 by NoNukes, posted 05-30-2016 1:14 PM Modulous has seen this message but not replied

  
NoNukes
Inactive Member


Message 97 of 455 (785218)
05-30-2016 1:14 PM
Reply to: Message 96 by Modulous
05-30-2016 9:41 AM


Re: You are looking at the wrong part of the system
This is just a matter of the 'largeness' of the time, and definitions of 'population'. Subpopulations that don't share genetic material with other parts of the population might simply not be considered part of the population. This would be a 'daughter' group as it were.
Of course we can define any subpopulation that we want.
In the case of humans living among each other, I think this distinction would be a fairly artificial one I would think. Would not defining population to be the groups of people that have all the same characteristics amount to simply defining population in a way to make your statement true? I'm still chewing on this, but currently I am leaning away from accepting.
Sure but the US is only a couple of centuries old.
You are not the first person from the UK that has reminded me of how little 'history' our country has. But here you understate things. Blacks and whites have been living together in at least some of what became the current country for well over twice that amount of time. As I mentioned in my post, my objection this does raise the issue of what is to be considered new. Also, for the most part, we are not talking about new alleles, we are instead talking about how long it has been since the population came together again. Presumably we all came from a single small group of humans originally. If "new" really means up to 4-500 years, that is probably something worth mentioning.
Also we're talking about perturbations from Hardy-Weinberg which has a large population with non-random mating (ie., anybody in the population has the same probabilities to have sex with any other member of population as any other member of the population). This is to isolate the effects we're talking about.
I understand the basis of the mathematics, but I think deviations from that theoretical model are worth noting. It may be important to note that traits that are held by a small percentage of the population may take long time periods to become distributed through a large population. Even in a perfect situation, "new" is a relative term.
Faith believes that that a subgroup with different allele frequencies becomes isolated, and because of their allele frequency differences they are morphologically different and that over time these differences exacerbate and by {magic} the two populations are eventually unable to successfully interbreed.
I know. And surely we agree that her belief is wrong. You have made a number of arguments I personally find compelling, but I'm not sure insisting that non-new (by a nebulous definition) traits must be evenly distributed in a population is necessary to reach your conclusion. In fact I might well argue that the earth is covered with subgroups that are only cosmetically different from each other in the most minor ways. We are all inter fertile. Apparently not even 6000 years (yeah, I know that we mean hundreds of thousands of years) to accomplish what Faith claims happens.
I note that Faith's belief involves not only some goofy mechanism that does not seem to produce what she claims (for example dogs are generally inter fertile) but also excludes any real role for natural selection via competition in addition to excluding mutation. Faith will only acknowledge evolution as a phenomenon that magically shows up when you subset a population and enforce the subset. There must be dozens of lines of inquiry that show that her explanation does not fit the facts and even more ways to show that she is not even attacking the real theory of evolution.
So the daughter population, if it somehow manage to be selective in which animals went to join it, will only contain a subset of the animals in the original population. So even on the face of it, this cannot lead to speciation in the sense of the two species are genetically incompatible.
Totally agree. My experience is that dogs, when left to their own devices are not all that selective. When I was a kid, we had a female mutt that most closely resembled some type of chow. The dog ran off for a couple of days and some time later delivered about six puppies that all looked exactly like the chocolate lab down the street, but each with the same bad temper as their mama chow. Of course our neighbor refused to pay us any puppy support even when we presented the blood test.[1]
The point is that even with humans spaying/neutering, using buckets of cold water etc., to keep breeds intact, or just plain passing no mixing laws, humans and dogs don't end up speciating in the sense Faith claims. She's just plain wrong. It is difficult to express exactly how wrong without using adjectives/adverbs, but that would not really be productive.
[1] Yeah, I know that letting your dogs loose like this is irresponsible. Please spay/neuter your pets if you don't want them to sire/birth offspring. There is no such thing as puppy support.
Edited by NoNukes, : No reason given.
Edited by NoNukes, : No reason given.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams

This message is a reply to:
 Message 96 by Modulous, posted 05-30-2016 9:41 AM Modulous has seen this message but not replied

  
NoNukes
Inactive Member


(3)
Message 98 of 455 (785222)
05-30-2016 5:05 PM


Some pretty telling quotes from the Great Debate.
No commentary needed.
Faith writes:
To show an increase would require knowledge of its level in the past, and I don't trust DNA analysis to tell us that, the same way I don't trust the "fossil record" or radiometric dating to tell me how old the earth is -- because there's no way to test the test when it's about the unwitnessed past. And I can't trust somebody who's immersed in Evo assumptions to interpret things accurately either. Sorry.
And...
Genomicus writes:
Sure it is. These are all factors that contribute to the formation of new species.
Faith writes:
Yeah yeah yeah, why do you feel the need to repeat the party line which I've been at pains to divide into its relevant opposing activities because that's what makes my point? Anything to obscure my point perhaps? You don't have to like my way of dealing with the party line, but honesty should compel you to recognize the logic of it so you can follow my argument.
And...
As for bacteria, yeah, I don't trust bacteria, that's what it comes down to. I doubt that what can be learned from them can be meaningfully applied to mammals or other higher animals.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams

  
NoNukes
Inactive Member


(1)
Message 99 of 455 (785226)
05-30-2016 10:10 PM


Faith on evidence
Faith writes:
My evidence that human genetic diversity has been decreasing is more a necessary deduction from my argument than direct evidence. However, I'd include the huge amount of junk DNA in the genome as evidence myself, which isn't likely to convince you of the point because you could only believe it's explained sufficiently by Evo Theory.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


(4)
Message 100 of 455 (785233)
05-31-2016 3:23 AM


The inevitable decline in world temperature
I've taken an interest in the season of Winter, specifically in the changes that mark its beginning. I have observed that every year, as we enter winter the temperature inevitably does down. And it turns out that this is true everywhere in the world, even in the Southern Hemisphere where the seasons are reversed.
Obviously this means that world temperatures are on an inevitable downward trend.
Some people tali about other seasons, or even invoking the dubious "science" of global warming. But that is just a tactic to confuse the issue. By thinking only of Winter we can see the clear downward trend, which will inevitably end when the temperature reaches absolute zero.

  
NoNukes
Inactive Member


(1)
Message 101 of 455 (785267)
06-01-2016 4:15 PM


I do have this nagging question how it is that you can count on mutations at other chromosomal loci to keep up the genetic diversity while not affecting the collection of loci that determine the breed or species.
1) Possible responses:
Sheer numbers. There are a lot more loci that can vary without affect the species than are required to maintain whatever few traits distinguish species from their ancestors. So the probability is high that any particular loci will be unaffected by a random mutation. Plus the mutation rate is low anyway.
2) Species, unlike breeds, are not composed of homogeneous collections of critters. It turns out that not all black people look alike, have inherited the trait to pass on sickle cell anemia, lack persistent lactase intoleracne, not all Chinese people are identical, not all have creased eyelids, the same lactase intolerance, or the same enzyme balance.
As PaulK has expressed it, if a certain level of phenotypic variability exists in the parent group, and that group is a species, why is there some limit on how much variation we can add to a daughter species once speciation has ended.
3) The record already includes cited examples of variations among new species, and of variation in a single race of folks increasing over time. Your denials do not deal with the evidence and in fact your own proposition is contrary to the evidence and deserves little to no respect.
4) Say what?
Edited by NoNukes, : No reason given.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams

  
14174dm
Member (Idle past 1108 days)
Posts: 161
From: Cincinnati OH
Joined: 10-12-2015


Message 102 of 455 (785268)
06-01-2016 5:04 PM


Was Adam Human?
Just a thought - The Great Debate: Molecular Population Genetics and Diversity in Evolution Message 18
EvC Forum: Information? control=msg&m=785265#m785265
Faith says about "Junk DNA"
It’s a lot of dead DNA, so I take it to represent a lot of dead creatures. It’s the greater part of at least the human genome and many others
If I understand Faith's proposal right, current humans have massive genetic depletion as evidenced by the "junk dna"
So what did Adam & Eve look like since they had so much more genetic material? Were they so different that they would be a different species than homo sapiens?
Edited by 14174dm, : Crappy title

Replies to this message:
 Message 103 by NoNukes, posted 06-01-2016 9:38 PM 14174dm has not replied
 Message 104 by New Cat's Eye, posted 06-01-2016 10:24 PM 14174dm has replied
 Message 106 by Faith, posted 06-01-2016 10:54 PM 14174dm has replied

  
NoNukes
Inactive Member


(1)
Message 103 of 455 (785275)
06-01-2016 9:38 PM
Reply to: Message 102 by 14174dm
06-01-2016 5:04 PM


Re: Was Adam Human?
If I understand Faith's proposal right, current humans have massive genetic depletion as evidenced by the "junk dna"
Exactly so. In short, Faith gives herself the right to speculate on the past based on her Biblical beliefs while denying others the right to evaluate even direct evidence from the past.
In this particular case, Faith has once again pushed an argument that she all but admitted she could not defend in a previous discussion. The last time she put forward the idea about genes dying off in the Flood I asked her how other people dying might affect Noah and his family's gametes and she admitted that her idea made no sense. Perhaps I will dig that up again.
It is pretty clear from her last couple of posts that Faith equates winning the debate with simply not ever being personally convinced that she is wrong.
ABE:
Here is that old admission Message 535 in response to Message 103
NN writes:
But the Flood loss could not represent any loss of function that Noah and his sons still possessed right? Surely those eight people possessed all of the vital functions for humans. Besides the silly notion that the people missing after the flood could have done something to the genes of living people, the flood itself could not have possible eliminated any essential human functions or else Noah and family would have had to be sickly.
Faith writes:
But that isn't what I thought. Really I hadn't thought it through at all, I just liked the idea, and when I finally did actually think it through I realized it wouldn't work. But what I sort of vaguely thought I thought was something like this: I thought the surviving eight, really the surviving three reproducing couples, had so little genetic diversity left (though they had enough to generate everyone living today, it's relative of course) that when later population splits occurred and some genes were reduced to fixed loci, that they'd become vulnerable to further loss and therefore keep adding to the junk DNA. But I finally realized that doesn't happen with population splits in general so there's no reason to expect it to happen as a result even of the Flood bottleneck. And as someone said here, it would only happen through mutations anyway.
Apparently no idea is too stupid not to have again.
Edited by NoNukes, : No reason given.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King
If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams

This message is a reply to:
 Message 102 by 14174dm, posted 06-01-2016 5:04 PM 14174dm has not replied

Replies to this message:
 Message 105 by Faith, posted 06-01-2016 10:46 PM NoNukes has replied

  
New Cat's Eye
Inactive Member


Message 104 of 455 (785277)
06-01-2016 10:24 PM
Reply to: Message 102 by 14174dm
06-01-2016 5:04 PM


Re: Was Adam Human?
Do humans live 900 years?

This message is a reply to:
 Message 102 by 14174dm, posted 06-01-2016 5:04 PM 14174dm has replied

Replies to this message:
 Message 184 by 14174dm, posted 06-07-2016 12:16 PM New Cat's Eye has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 105 of 455 (785278)
06-01-2016 10:46 PM
Reply to: Message 103 by NoNukes
06-01-2016 9:38 PM


Re: Was Adam Human?
I did think it through and discovered it is defensible.

This message is a reply to:
 Message 103 by NoNukes, posted 06-01-2016 9:38 PM NoNukes has replied

Replies to this message:
 Message 108 by NoNukes, posted 06-02-2016 1:26 AM Faith has not replied
 Message 110 by NoNukes, posted 06-02-2016 1:35 AM Faith has replied

  
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