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Author Topic:   Molecular Population Genetics and Diversity through Mutation
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 76 of 455 (785118)
05-28-2016 3:34 AM
Reply to: Message 75 by PaulK
05-28-2016 2:57 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.

This message is a reply to:
 Message 75 by PaulK, posted 05-28-2016 2:57 AM PaulK has replied

Replies to this message:
 Message 77 by PaulK, posted 05-28-2016 3:45 AM Faith has not replied
 Message 94 by Dr Adequate, posted 05-29-2016 5:48 PM Faith has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.3


(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.

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

Replies to this message:
 Message 81 by NoNukes, posted 05-28-2016 5:43 PM PaulK has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 78 of 455 (785140)
05-28-2016 9:20 AM
Reply to: Message 65 by Faith
05-27-2016 1:48 PM


Re: You are looking at the wrong part of the system
You aren't going to get "new" genotypes, just a new frequency of genotypes.
Precisely! That is exactly my point. But we need to explain new genotypes... how do new genotypes arise? So, back to my example of cytochrome C (cytC). This is a coding gene that is widely used for species identification, aka. a bar coding gene. (Note: unfortunately it is not a universal bar code meaning it doesn't work with all types of organisms. We don't use it for fungi, for example, but it is widely used for plants and animals). Every species has a unique cytC sequence(s) that can be used to identify an organism as a member of a species. Say you discover an organism that you are not quite sure what species it is, maybe it has a unique morphology or form that makes it difficult to place it with a particular group. Or maybe the distinction between species requires the analysis of very obscure characteristics. You could sequence the cytC and compare that sequence to a database in order to identify what species the organism is.
OK, let's start with a single mating pair with maximum number of alleles at the cytC locus - a, b, c, d. These alleles could segregate into sub-populations so that 4 species, subspecies, varieties, breeds, whatever you want to call them have a unique cytC identifier.
THE PROBLEM. There are many, many more species than 4 that would have come from a single ark pair. Even working from the genus level in Canis or Drosophila, there are dozens of species with unique cytC sequences. Even being generous and considering there to be 10 actual unique species within each of those genus, that would mean there needs to be 6 alleles of cytC that have arisen since the ark kind.
Yes, your hypothesis would only involve shuffling alleles around and altering allele frequency, which is sufficient to explain evolution within a population, that is, how a population with brown fur becomes a population with white fur. But it is a small part of the big picture and it doesn't explain how we have the actual genetic diversity that we observe today.
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.

This message is a reply to:
 Message 65 by Faith, posted 05-27-2016 1:48 PM Faith has replied

Replies to this message:
 Message 84 by NoNukes, posted 05-28-2016 9:56 PM herebedragons has not replied
 Message 124 by Faith, posted 06-03-2016 1:52 AM herebedragons has replied
 Message 136 by Faith, posted 06-03-2016 7:38 PM herebedragons has not replied

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


(1)
Message 79 of 455 (785146)
05-28-2016 10:01 AM
Reply to: Message 71 by Faith
05-28-2016 12:03 AM


Re: You are looking at the wrong part of the system
Dear dear Moddy, I said nothing about H-W equilibrium.
quote:
When you have a population of over a million individuals, say of black wildebeests, you are probably getting something like Hardy-Weinberg equilibrium in reality.
quote:
This quote from the Wikipedia article on Genotype Frequency doesn't treat the H-W equilibrium as an ideal but as a reality.
If for some reason it SHOULD be in equilibrium, though I don't know why it should, then adjusting the percentages is fine with me.
The reason I posted that was not to be pedantic, per se, but to try and inspire you to think about this very point.
Are the gene frequencies changing from generation to generation in the parent population in the scenario you envisage? If the answer is basically 'no' then they are at equilibrium. The default equilibrium for a population to be in is the H-W equilibrium. This is because of the maths involved.
You can play with the maths at this website:
Hardy-Weinberg Equilibrium Calculator | Science Primer
You enter the allele frequencies and it tells you how those frequencies can exist in a population that is not evolving. That is, it will tell you the distribution of heterozygotes and homozygotes.
This is the H-W equilibrium when the allele frequencies are 50/50
p is one allele q is the other. p squared means it has two p's and therefore is homozygous. 2pq covers the heterozygous cases. Here we see that if Blue Eyes gene is 'p' then if it has 50% frequency in the population, it will be homozygous and expressed only 25% of the time. When the distribution is even the dominant trait gets expressed 75% of the time. It's a little like the maths when you flip two coins. 25% of the time you will get two Heads, the rest will have at least one Tail.
Anyway, from the parent population you propose a split off:
quote:
20% bb, 70%Bb and 10% BB
Which is not a Hardy-Weinberg Equilibrium. So because of Mendel's laws of inheritance (totally evolution neutral stuff, no shenanigans) the next generation will be different. The exact details depend on information about our population we haven't defined, but I will illustrate the point thusly.
First of all, there's too much heterozygosity, that's definitely going to change next generation. Suppose it drops to 40%Bb leaving us with 35%bb and 25%BB (I distributed the 30% evenly just for ease). This isn't quite stable so it changes to 55%Bb 25%bb 15%BB. Still not stable the next generation comes out to
Which is H-W equilibrium of 60% blue eyed genes, and this is where it will stay until something changes. That's just how Mendel's work applies to large populations. This is a gene frequency change. It is by migration alone. It is not a sufficient picture of evolution.
Parent lots of blue eyes, daughter an increase in brown eyes which should increase even more down the generations.
And that's the point of equilibria, there is no 'should increase even more down the generations' unless something makes that happen. The laws of inheritance provide a default frequency distribution, there is no tendency towards loss of an allele through this process.
from which the daughter population randomly selected most of the B's which would give it a new set of genotypes
But how would that happen? And why couldn't that daughter population later have a split which 'randomly selects' most of the b's?
There's no tendency to loss of allele here.
The only time allele loss happens is when the migratory population happens to have 0 of an allele represented. This can only realistically happen if the allele was not distributed evenly throughout the population. An allele can only realistically not be distributed evenly through the entire population if it is an allele that is new to the population.
So again, how does a daughter population migrate with such radically different allele distributions? Why can't a granddaughter population use this same mechanism to restore the frequencies? Where is the allelic loss in this situation? I think you are picturing domestic breeding too closely, where daughter populations are chosen on purpose towards some end.
HBD's point is that the genotypes in your parent population are:
BB
bb
Bb
bB
And the genotypes in your daughter population are the same. How the genotypes are distributed in the population is different, but the genotypes are the same.
Edited by Modulous, : No reason given.

This message is a reply to:
 Message 71 by Faith, posted 05-28-2016 12:03 AM Faith has not replied

Replies to this message:
 Message 80 by NoNukes, posted 05-28-2016 3:23 PM Modulous has replied

  
NoNukes
Inactive Member


Message 80 of 455 (785178)
05-28-2016 3:23 PM
Reply to: Message 79 by Modulous
05-28-2016 10:01 AM


Re: You are looking at the wrong part of the system
An allele can only realistically not be distributed evenly through the entire population if it is an allele that is new to the population.
I'm a bit suspicious of this idea. Sometimes populations do not intermingle thoroughly even over large periods of time. 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.
But I have to admit that no additional examples comes to mind. 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.
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 79 by Modulous, posted 05-28-2016 10:01 AM Modulous has replied

Replies to this message:
 Message 96 by Modulous, posted 05-30-2016 9:41 AM NoNukes has replied

  
NoNukes
Inactive Member


Message 81 of 455 (785183)
05-28-2016 5:43 PM
Reply to: Message 77 by PaulK
05-28-2016 3:45 AM


Peanut Gallery comments.
You're wrong, as usual, and obviously so.
Faith is of course wrong, but it seems to me that it will be impossible for her to budge from her current position. She's saying exactly the same thing in her Great Debate.
Faith writes:
Yes of course, "if genetic diversity is determined by a combination of mutation rate, population size, genetic drift, and selection" you'll get increased heterozygosity. But that isn't evolution, that isn't how new species come about. That's a see-saw between adding and subtracting that overall gets called evolution but it's only the subtractive processes that form the new species. I think it's in your next post that you talk about new phenotypes spreading in a population and I agree that is also evolution, and for that to happen requires the competing alleles to drop out. THAT's what makes it evolution.
Not only does she deny that such any steps adding diversity are part of evolution. She denies that adding diversity is even an aspect of evolution or that Darwin ever considered it to be. This after all of the citing of biologists including Darwin who say otherwise. In my view the kinds of comments in the following excerpt border on being dishonest.
That is by way of condensing my argument, which is of course what I'll continue to be arguing in this thread. The idea that adding and subtracting genetic diversity, one step forward, two steps back etc., is any way to run a theory of evolution is not exactly what Darwin had in mind, or anybody else for that matter.

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 77 by PaulK, posted 05-28-2016 3:45 AM PaulK has not replied

Replies to this message:
 Message 82 by Faith, posted 05-28-2016 7:33 PM NoNukes has replied

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


Message 82 of 455 (785186)
05-28-2016 7:33 PM
Reply to: Message 81 by NoNukes
05-28-2016 5:43 PM


Re: Peanut Gallery comments.
I think you should start a separate Peanut Gallery thread because I've been posting to this one and that's not supposed to happen on the Peanut Gallery.

This message is a reply to:
 Message 81 by NoNukes, posted 05-28-2016 5:43 PM NoNukes has replied

Replies to this message:
 Message 83 by NoNukes, posted 05-28-2016 9:47 PM Faith has replied

  
NoNukes
Inactive Member


Message 83 of 455 (785189)
05-28-2016 9:47 PM
Reply to: Message 82 by Faith
05-28-2016 7:33 PM


Re: Peanut Gallery comments.
I think you should start a separate Peanut Gallery thread because I've been posting to this one and that's not supposed to happen on the Peanut Gallery.
That's a good point. My question to you is why would you post here?
I thought the purpose of the Great Debate was to provide a more comfortable forum for you because the group discussion is not working for you. If you are going to continue to post here, I think my comment to PaulK is still relevant. You are just as welcome to comment on my post as you are to post anything else here.
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 82 by Faith, posted 05-28-2016 7:33 PM Faith has replied

Replies to this message:
 Message 85 by Faith, posted 05-29-2016 12:47 AM NoNukes has replied

  
NoNukes
Inactive Member


Message 84 of 455 (785190)
05-28-2016 9:56 PM
Reply to: Message 78 by herebedragons
05-28-2016 9:20 AM


Re: You are looking at the wrong part of the system
Precisely! That is exactly my point. But we need to explain new genotypes... how do new genotypes arise?
Faith's answer is probably along the lines of 'generating new genotypes is not evolution' or something similar to that.

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 78 by herebedragons, posted 05-28-2016 9:20 AM herebedragons has not replied

Replies to this message:
 Message 86 by Faith, posted 05-29-2016 1:02 AM NoNukes has replied

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


Message 85 of 455 (785191)
05-29-2016 12:47 AM
Reply to: Message 83 by NoNukes
05-28-2016 9:47 PM


Re: Peanut Gallery comments.
I don't feel the stress or pressure of posting here now that the Great Debate is set up.
But answering people's posts to me is not the same thing as responding to the comments about the debate on the Peanut Gallery where the debaters are specifically not supposed to post according to the rules, so I won't respond to your comment about the debate.
It may seem a small point and maybe I should just stop posting here altogether but if I have a thought in response to someone then I post it and don't have a sense of obligation to post if I don't want to. It also keeps my brain in gear for the debate itself because I'm pondering my next answer at the same time. Hm. It's a little like playing a game of Free Cell while I'm pondering a post, which I used to do before Windows 10 took away my games.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 83 by NoNukes, posted 05-28-2016 9:47 PM NoNukes has replied

Replies to this message:
 Message 87 by NoNukes, posted 05-29-2016 1:57 AM Faith has not replied

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


Message 86 of 455 (785192)
05-29-2016 1:02 AM
Reply to: Message 84 by NoNukes
05-28-2016 9:56 PM


Re: You are looking at the wrong part of the system
Generating a new phenotype is definitely evolution. I suppose you think you understand my argument? Just proved you haven't a clue.

This message is a reply to:
 Message 84 by NoNukes, posted 05-28-2016 9:56 PM NoNukes has replied

Replies to this message:
 Message 88 by NoNukes, posted 05-29-2016 1:58 AM Faith has replied

  
NoNukes
Inactive Member


Message 87 of 455 (785193)
05-29-2016 1:57 AM
Reply to: Message 85 by Faith
05-29-2016 12:47 AM


Re: Peanut Gallery comments.
But answering people's posts to me is not the same thing as responding to the comments about the debate on the Peanut Gallery where the debaters are specifically not supposed to post according to the rules, so I won't respond to your comment about the debate.
Fair enough.

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 85 by Faith, posted 05-29-2016 12:47 AM Faith has not replied

  
NoNukes
Inactive Member


Message 88 of 455 (785194)
05-29-2016 1:58 AM
Reply to: Message 86 by Faith
05-29-2016 1:02 AM


Re: You are looking at the wrong part of the system
Generating a new phenotype is definitely evolution. I suppose you think you understand my argument? Just proved you haven't a clue.
Faith, perhaps you should re-read my comment. I did not mention or say anything about generating a new phenotype. That also wasn't mentioned in the portion of the comment I responded to. Perhaps then we can discuss whether or not I have a clue.
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 86 by Faith, posted 05-29-2016 1:02 AM Faith has replied

Replies to this message:
 Message 89 by Faith, posted 05-29-2016 2:28 AM NoNukes has replied

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


Message 89 of 455 (785195)
05-29-2016 2:28 AM
Reply to: Message 88 by NoNukes
05-29-2016 1:58 AM


Re: You are looking at the wrong part of the system
Meant genotype.

This message is a reply to:
 Message 88 by NoNukes, posted 05-29-2016 1:58 AM NoNukes has replied

Replies to this message:
 Message 90 by NoNukes, posted 05-29-2016 2:30 AM Faith has not replied

  
NoNukes
Inactive Member


Message 90 of 455 (785196)
05-29-2016 2:30 AM
Reply to: Message 89 by Faith
05-29-2016 2:28 AM


Re: You are looking at the wrong part of the system
Meant genotype.
Thank you. Now is the creation of new genotypes evolution? Mutations create new genotypes by definition. Does that, according to you, constitute evolution? Does my comment seem more reasonable in that light?
From the Wikipedia article on evolution:
Evolution - Wikipedia
quote:
Precise mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of pangenesis.[54] In 1865, Gregor Mendel reported that traits were inherited in a predictable manner through the independent assortment and segregation of elements (later known as genes). Mendel's laws of inheritance eventually supplanted most of Darwin's pangenesis theory.[55] August Weismann made the important distinction between germ cells that give rise to gametes (such as sperm and egg cells) and the somatic cells of the body, demonstrating that heredity passes through the germ line only. Hugo de Vries connected Darwin's pangenesis theory to Weismann's germ/soma cell distinction and proposed that Darwin's pangenes were concentrated in the cell nucleus and when expressed they could move into the cytoplasm to change the cells structure. De Vries was also one of the researchers who made Mendel's work well-known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline.[56] To explain how new variants originate, de Vries developed a mutation theory that led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries.[41][57][58] In the 1930s, pioneers in the field of population genetics, such as Ronald Fisher, Sewall Wright and J. B. S. Haldane set the foundations of evolution onto a robust statistical philosophy.
The false contradiction between Darwin's theory, genetic mutations, and Mendelian inheritance was thus reconciled.
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 89 by Faith, posted 05-29-2016 2:28 AM Faith has not replied

  
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