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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 46 of 455 (784960)
05-26-2016 2:38 PM
Reply to: Message 23 by herebedragons
05-24-2016 11:08 PM


You are looking at the wrong part of the system
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.
Geographic isolation prevents or limits gene flow, but by itself, isolation does not bring about genetic change. All combinations of alleles present in the daughter population are also present in the parent population.
A change in gene frequencies does indeed bring about genetic change, it's even given as a definition of evolution. Put "Evolution as a change in gene frequency" into Google. The first line of the Berkeley page on the subject says "Microevolution is a change in gene frequency in a population." (Windows 10 doesn't let me copy links or I haven't figure out how to yet)
And even Genomicus agrees, which is why I prefer to debate her rather than anyone else here:
Genomicus in message 22 writes:
... I should also add that new phenotypes can arise through novel allele combinations in a diploid organism, so this wouldn't technically be a mutation.
HBD writes:
Orchids - 80,000 +/- species... no sign of genetic depletion
Dogs - 100s of breeds... no sign of genetic depletion
Fruit flies (Drosophilidae) - 4,000 species... no signs of genetic depletion
Cats (Felidae) - 41 species... cheetahs have severe genetic depletion, but not domestic cats
So how have these species maintained genetic diversity according to your hypothesis?
You insist on talking about the ENTIRE population of a species, which I'm NEVER talking about. Sure you can have lots of genetic diversity in the whole population, and dogs as a whole species certainly have lots of genetic diversity. AS I'VE SAID MANY TIMES.
What you are failing to get is that I'm only talking about EVOLVING populations, that is, populations where you are getting new phenotypes due to new gene frequencies, which requires losing alleles for competing phenotypes. The point is to illustrate what EVOLUTION does, and what it does is reduce genetic diversity in the service of producing a new subspecies. It's from this sort of observed evolution (microevolution of course), that is, the observed production of new variations, that the ToE takes its idea that there is nothing to stop variation from continuing indefinitely, but if in fact there is a trend to decreased genetic diversity, that must NECESSARILY occur with the production of new variations, the ToE has been refuted. Doesn't matter how much genetic variation remains in stable populations, or gets added wherever you want to add it, the processes of EVOLUTION, meaning the production of new species or subspecies from whatever genetic diversity is present, MUST reduce genetic diversity. Evolution itself must bring evolution to a stop.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 23 by herebedragons, posted 05-24-2016 11:08 PM herebedragons has replied

Replies to this message:
 Message 52 by herebedragons, posted 05-26-2016 4:03 PM Faith has replied

  
caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(1)
Message 47 of 455 (784963)
05-26-2016 2:54 PM
Reply to: Message 39 by Faith
05-26-2016 3:03 AM


Some very simple maths.
I'm having difficulty understanding exactly where your misunderstanding stems from here, but maybe some very simple maths can help.
No, because NO source of additional genetic diversity can overcome the processes that of necessity must reduce it in order to produce new phenotypes. The rarity of mutations is a separate topic.
But this is of course nonsense. Of course the rate of mutations matter. If an average of ten alleles are vanishing each generation due to drift or selection, while an average of 5 alleles are added by mutations, then of course the genetic diversity of the population will decline.
To say that nothing can overcome this decline however is fairly obviously wrong. If instead of 5 new alleles appearing each generation through mutation, there were 15, then diversity would be increasing. 15 is larger than 10. What's difficult about this?
On the subject of the real world:
OK, I see, and this is so as a TREND and with respect to the salient characteristics of the subspecies that is developing. There could still be great diversity for other characteristics of the creature that don’t show up in the new phenotype. The estimate of heterozygosity for human beings now is something like 7% IIRC, but taking a wild guess back a few thousand years it could have been as much as 50% or 70% or higher, and some loci could have retained a higher percentage than others even now.
I don't think the idea of an estimate of heterozygosity in humans is coherent. You can't be homozygous in the abstract; you are homozygous or hetrerozygous at a specific locus. Everyone will be homozygous at certain loci and heterozygous at others. A quick Google search to figure out where you might have got this statistic from led me to an estimate that the average protein coding gene is heterzygous about 9% of the time in humans (cited to this 1999 article from Nature Genetics for anyone interested who has access), so maybe this is what you heard.
The idea that humans were much more genetically diverse a few thousand years ago, however, is almost certainly wrong, and for a very simple reason. The human population has expanded exponentially over the last few thousand years, which implies a few things.
1. An expanding population is generally under less selection pressure. When a population starts expanding rapidly (as ours is) then it means that factors which used to kill people before they could reproduce or which reduced fertility through other means are apparently less of a problem. These pressures which might otherwise be driving fitter alleles to fixation are not as pressing (there is clearly a much better way to express than I'm managing!)
2. Genetic drift is less powerful in larger populations. This is fairly obvious. If an allele is present in 10% of a population of ten individuals, it can go extinct by a rock falling on someone's head. If it's present at 10% in the modern human population then it's present in double the population of the US. It would take a much longer time for it to dwindle by chance.
3. Adding more people to the population means adding more mutations. More babies are born every week than would be annually in the Palaeolithic, and every one of them carries new mutations. Regardless of the probability of any mutation arising, it's obviously going to happen more if there are more opportunities for it to happen.
I'm sure Gemonicus is able to demonstrate these concepts more rigorously if necessary, but I know you hate maths and this all seems intuitive without even glancing at algebra (though maybe not the ham-fisted way I describe it...).

This message is a reply to:
 Message 39 by Faith, posted 05-26-2016 3:03 AM Faith has replied

Replies to this message:
 Message 48 by Faith, posted 05-26-2016 3:05 PM caffeine has replied
 Message 53 by 14174dm, posted 05-26-2016 4:46 PM caffeine has replied

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


Message 48 of 455 (784965)
05-26-2016 3:05 PM
Reply to: Message 47 by caffeine
05-26-2016 2:54 PM


Re: Some very simple maths.
You are missing the whole point of why adding genetic diversity makes no difference to what I'm saying.
I just explained it to HBD again. Please read the last paragraph of that Message 46 to him.

This message is a reply to:
 Message 47 by caffeine, posted 05-26-2016 2:54 PM caffeine has replied

Replies to this message:
 Message 49 by PaulK, posted 05-26-2016 3:13 PM Faith has not replied
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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


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.

This message is a reply to:
 Message 48 by Faith, posted 05-26-2016 3:05 PM Faith has not replied

  
caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 50 of 455 (784970)
05-26-2016 4:00 PM
Reply to: Message 48 by Faith
05-26-2016 3:05 PM


Re: Some very simple maths.
You are missing the whole point of why adding genetic diversity makes no difference to what I'm saying.
I just explained it to HBD again. Please read the last paragraph of that Message 46 to him.
I did read that, and your view of evolution is confused - it doesn't only happen in small, isolated populations.
But the important point is that this does not matter! Even on your confused version of evolution there's no required, long term decline in diversity. Think about your small isolated population which experiences a loss of genetic diversity because some alleles spread to fixation quickly, in the process making a specific phenotype characteristic of the population. What happens afterwards? If this is a successful phenotype, and the population is able to expand, new alleles can appear and spread, restorng genetic diversity to the population.
Why would this not be able to happen?

This message is a reply to:
 Message 48 by Faith, posted 05-26-2016 3:05 PM Faith has not replied

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


(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...

This message is a reply to:
 Message 44 by Faith, posted 05-26-2016 2:17 PM Faith has not replied

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


Message 52 of 455 (784972)
05-26-2016 4:03 PM
Reply to: Message 46 by Faith
05-26-2016 2:38 PM


Re: You are looking at the wrong part of the system
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.
Yes, "probably" "something like" HW, if all the conditions meet the HW assumptions; 1 million individuals is pretty much an infinite population size, and if all other assumptions were met then geneotypic frequencies would be very close to HW equilibrium. Also keep in mind that HW is calculated for a single locus. The gene for coat color may be in equilibrium while the gene for horn length may be under selection and so the genotype frequency may be out of equilibrium.
And even Genomicus agrees, which is why I prefer to debate her rather than anyone else here:
First off, I have agreed with you on occasion as well such as in the very post you are responding to.
HBD writes:
I think we have all agreed that isolation of a population, especially a small one, will likely result in the loss of genetic diversity. I think we would all agree that selection removes undesirable alleles and so reduces genetic diversity within a population (except in a few special cases where selection can increase or maintain diversity). I think we all agree that drift can bring alleles to fixation and therefore reduce genetic diversity.
But your claim goes beyond those things, and when I address them, you say they are irrelevant. If your whole argument is that a population split can (and usually does) reduce genetic diversity, then the debate is over and we all agree.
A change in gene frequencies does indeed bring about genetic change, it's even given as a definition of evolution. Put Evolution as a change in gene frequency into Google. The first line of the Berkeley page on the subject says Microevolution is a change in gene frequency in a population.
And even Genomicus agrees, which is why I prefer to debate her rather than anyone else here:
Genomicus in message 22 writes:
... I should also add that new phenotypes can arise through novel allele combinations in a diploid organism, so this wouldn't technically be a mutation.
A couple things are being conflated here.
1) The Berkeley page refers to microevolution, which means evolution WITHIN a population. Changes in allele frequency causes the phenotypic composition of a population to change over time. This could even apply to sub-populations, as you are doing, which may be considered a subspecies, a variety, a morph, etc.
2) Genomicus said that "new phenotypes can arise from novel allele combinations" not that new genotypes could arise. And I agree with that, novel phenotypes can arise and become more prevalent as allele frequencies change. But new genotypes do not arise from changing allele frequencies. What new genotypes exist in the daughter population that don't exist in the parent population for the following example?
Parent: {90% a1, 10% a2, 60% b1, 40% b2, 40% c1, 60% c2, 10% d1, 90% d2}
Subpopulation: {60% a1, 40% a2, 100% b2, 60% c1, 40% c2, 100% d1}
Changing allele frequencies and eliminating alleles does not create new genotypes.
You insist on talking about the ENTIRE population of a species, which I'm NEVER talking about. Sure you can have lots of genetic diversity in the whole population
No, I am talking about speciation. Although you keep referring to "sub-populations" and avoid calling them separate species, that is what your hypothesis is attempting to explain right? How we went from a single mating pair to all the species (or sub-species) that we have today. Your hypothesis requires that when new species are formed, genetic diversity is removed until evolution comes to an ultimate standstill because it is utterly depleted of genetic diversity. The examples I gave are meant to show that is not what we observe in natural populations. There is not "genetic depletion" despite thousands of population splits.
What you are failing to get is that I'm only talking about EVOLVING populations, that is, populations where you are getting new phenotypes due to new gene frequencies, which requires losing alleles for competing phenotypes.
I get it, Faith, I get it. But that's not the whole story, is it? How does your "genetic depletion" hypothesis explain how we got from an ancestral population (parental) to the species of the genus Canis ( the grey wolf, coyote, red wolf, and several species of jackals). Or how about the species within the genus Drosophila? Or any other genus of plants, animals or fungi that you care to address. How does shuffling alleles around create those different genomes?? (in less than 4000 years, no less)
the processes of EVOLUTION, meaning the production of new species or subspecies from whatever genetic diversity is present, MUST reduce genetic diversity. Evolution itself must bring evolution to a stop.
You must be missing something because this "bringing to a stop" bit is not observed in natural populations.
(Windows 10 doesn't let me copy links or I haven't figure out how to yet)
You updated to Windows 10, huh? I remember when you were debating about upgrading and I meant to advise against it, but didn't get the chance. How is it working out so far? I would guess you will probably want to upgrade your memory to the maximum your setup will allow in order to keep it from bogging down really bad.
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 46 by Faith, posted 05-26-2016 2:38 PM Faith has replied

Replies to this message:
 Message 54 by Faith, posted 05-27-2016 4:31 AM herebedragons has replied

  
14174dm
Member (Idle past 1109 days)
Posts: 161
From: Cincinnati OH
Joined: 10-12-2015


Message 53 of 455 (784976)
05-26-2016 4:46 PM
Reply to: Message 47 by caffeine
05-26-2016 2:54 PM


Re: Some very simple maths.
Instead of arguing math and semantics, could we find examples?
Otzi the Iceman and King Tutankhamun & family have had dna analyses. I've tried but haven't found what I'm looking for.
My thought is whether these analyses of ancient dna show differences from modern dna. Does Otzi from 5,200 years ago (guess 260 generations) have alleles that don't exist in modern times? Does he have more chromosomes and/or functioning genes?
One site I did find seems to say that Otzi is pretty much the same as modern people. OTZI, THE ICEMAN | Facts and Details
The genetic results add both information and intrigue. From his genes, we now know that the Iceman had brown hair and brown eyes and that he was probably lactose intolerant and thus could not digest milk’somewhat ironic, given theories that he was a shepherd. Not surprisingly, he is more related to people living in southern Europe today than to those in North Africa or the Middle East, with close connections to geographically isolated modern populations in Sardinia, Sicily, and the Iberian Peninsula. The DNA analysis also revealed several genetic variants that placed the Iceman at high risk for hardening of the arteries. ("If he hadn't been shot," Zink remarked, "he probably would have died of a heart attack or stroke in ten years.") Perhaps most surprising, researchers found the genetic footprint of bacteria known as Borrelia burgdorferi in his DNA---making the Iceman the earliest known human infected by the bug that causes Lyme disease.
That seems to say that human genetics haven't lost diversity.
A different look would be to examine isolated animal populations. I did find what should be a good candidate - Ossabaw Island pig. Spanish explorers dropped pigs off in the 1500s for later food stops. From what I could find, little cross breeding has occurred since then.
http://wildpiginfo.msstate.edu/...aw%20Island-Case_Study.pdf
The pigs are distinctive with small size, upright ears, and coarse bristles. Of interest to medicine is their genetic tendencies to high fat levels. They actually get pre-diabetic similar to humans. Additionally they are very tolerant of salt in their drinking water and diet.
If I understand Faith's proposal, the Ossabaw Island pig is using pre-existing genes that are now active due to the deletion of genes used by other pigs. To show this, comparisons with ancestor breeds would show no new genes in the Ossabaw Island pigs.
I tried to find comparisons of Ossabaw Island pigs with their presumed ancestors - Canary Island and Iberian pigs. Pretty much all I learned is that I don't know anything about biology and genetics.

This message is a reply to:
 Message 47 by caffeine, posted 05-26-2016 2:54 PM caffeine has replied

Replies to this message:
 Message 66 by caffeine, posted 05-27-2016 2:06 PM 14174dm has not replied

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


Message 54 of 455 (785003)
05-27-2016 4:31 AM
Reply to: Message 52 by herebedragons
05-26-2016 4:03 PM


Re: You are looking at the wrong part of the system
The Hardy—Weinberg law describes the relationship between allele and genotype frequencies when a population is not evolving.
This quote from the Wikipedia article on Genotype Frequency doesn't treat the H-W equilibrium as an ideal but as a reality.
And even Genomicus agrees, which is why I prefer to debate her rather than anyone else here:
First off, I have agreed with you on occasion as well such as in the very post you are responding to.
Not about how new gene frequencies from a population split bring about phenotypic variation.
HBD writes:
I think we have all agreed that isolation of a population, especially a small one, will likely result in the loss of genetic diversity. I think we would all agree that selection removes undesirable alleles and so reduces genetic diversity within a population (except in a few special cases where selection can increase or maintain diversity). I think we all agree that drift can bring alleles to fixation and therefore reduce genetic diversity.
But your claim goes beyond those things, and when I address them, you say they are irrelevant. If your whole argument is that a population split can (and usually does) reduce genetic diversity, then the debate is over and we all agree.
I'm saying this is the main way new subspecies or varieties are made.
A change in gene frequencies does indeed bring about genetic change, it's even given as a definition of evolution. Put Evolution as a change in gene frequency into Google. The first line of the Berkeley page on the subject says Microevolution is a change in gene frequency in a population.
And even Genomicus agrees, which is why I prefer to debate her rather than anyone else here:
Genomicus in message 22 writes:
... I should also add that new phenotypes can arise through novel allele combinations in a diploid organism, so this wouldn't technically be a mutation.
A couple things are being conflated here.
1) The Berkeley page refers to microevolution, which means evolution WITHIN a population. Changes in allele frequency causes the phenotypic composition of a population to change over time. This could even apply to sub-populations, as you are doing, which may be considered a subspecies, a variety, a morph, etc.
Microevolution means "evolution within a population???" I have NO idea what you are saying. Microevolution IS evolution, it's what is happening wherever new varieties or subspecies are being formed from new gene frequencies.
2) Genomicus said that "new phenotypes can arise from novel allele combinations" not that new genotypes could arise. And I agree with that, novel phenotypes can arise and become more prevalent as allele frequencies change. But new genotypes do not arise from changing allele frequencies. What new genotypes exist in the daughter population that don't exist in the parent population for the following example?
Parent: {90% a1, 10% a2, 60% b1, 40% b2, 40% c1, 60% c2, 10% d1, 90% d2}
Subpopulation: {60% a1, 40% a2, 100% b2, 60% c1, 40% c2, 100% d1}
Changing allele frequencies and eliminating alleles does not create new genotypes.
You have absolutely lost me. You are talking gobbledygook as far as I can tell, making unimportant distinctions as far as my argument is concerned. It is "gene frequency" not "genotype frequency" that is defined as evolution, and it's evolution I'm talking about. *
You insist on talking about the ENTIRE population of a species, which I'm NEVER talking about. Sure you can have lots of genetic diversity in the whole population
No, I am talking about speciation.
Your list was of ALL species within a species or I guess family. You listed ALL the different breeds of dogs and claimed no loss of genetic diversity. That would only be true of the entire family of dogs, because separate breeds do in fact have sharply reduced genetic diversity and where selection has been severe genetic depletion that has brought about genetic diseases. I believe it was you who once posted that chart of dog breeds, absurdly claiming it disproved my argument when it didn't show for most of them which descended from which because that information was not known. Just another way you do NOT grasp what I'm arguing despite your insistence that you do.
lthough you keep referring to "sub-populations" and avoid calling them separate species, that is what your hypothesis is attempting to explain right?
NO!!! I'm talking about the TREND to reduced genetic diversity. It may or may not come to Speciation. I figure there could be many daughter populations in a series, as in "ring species," without actually reaching Speciation, just new geographically isolated subspecies with less genetic diversity than the parent population.
How we went from a single mating pair to all the species (or sub-species) that we have today. Your hypothesis requires that when new species are formed, genetic diversity is removed until evolution comes to an ultimate standstill because it is utterly depleted of genetic diversity. The examples I gave are meant to show that is not what we observe in natural populations. There is not "genetic depletion" despite thousands of population splits.
Since dog breeds certainly show often drastic genetic reduction what on earth are you talking about? That's why I use dog breeds. You don't get a breed without losing the alleles for all the other breeds, THAT'S THE POINT. I would assume the same is the case with your other examples, orchids and I forget the rest. How can you just blithely announce that what I'm describing is not shown in your example since I know it is with dogs?
What you are failing to get is that I'm only talking about EVOLVING populations, that is, populations where you are getting new phenotypes due to new gene frequencies, which requires losing alleles for competing phenotypes.
I get it, Faith, I get it.
NO YOU DO NOT GET IT!!!! You seem to get it and then you show that you clearly don't.
But that's not the whole story, is it? How does your "genetic depletion" hypothesis explain how we got from an ancestral population (parental) to the species of the genus Canis ( the grey wolf, coyote, red wolf, and several species of jackals).
What IS the problem? Extrapolating back from the loss of genetic diversity brought about by selection, random or artificial or natural (it's all the same effect), I add back the genetic diversity lost down the generations and arrive at LOTS of genetic diversity at the starting point from which all the types and breeds descended. A lot more heterozygosity I've many times suggested. WHAT'S THE PROBLEM?
Or how about the species within the genus Drosophila? Or any other genus of plants, animals or fungi that you care to address. How does shuffling alleles around create those different genomes?? (in less than 4000 years, no less)
WHAAAAAAT? WHAT ARE YOU TALKING ABOUT? "Shuffling alleles around" proves you have no idea what I'm talking about. I've explained my idea about how we got from the ark to today many many times, and explained it again above. Since I have no idea what your problem is you are going to have to make it a lot clearer if you really want an answer.
the processes of EVOLUTION, meaning the production of new species or subspecies from whatever genetic diversity is present, MUST reduce genetic diversity. Evolution itself must bring evolution to a stop.
You must be missing something because this "bringing to a stop" bit is not observed in natural populations.
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. The stopping point is the natural ultimate consequence of that trend, and my guess is that there are examples of species in that condition too which are discoverable if you are looking in the right place for the right evidence.
(Windows 10 doesn't let me copy links or I haven't figure out how to yet)
You updated to Windows 10, huh? I remember when you were debating about upgrading and I meant to advise against it, but didn't get the chance. How is it working out so far? I would guess you will probably want to upgrade your memory to the maximum your setup will allow in order to keep it from bogging down really bad.
I answered this on the Computer Help Please thread.
Seems to me I've been able to copy links sometimes even since Windows 10 but last time I tried I couldn't.
===============================
* Sorry for getting impatient. You keep bringing up supposed problems that seem/are completely irrelevant, when a little extra thought might have shown you I've already dealt with the issue. I usually say that it takes some generations of inbreeding for the new look of the new population to emerge from its new set of gene frequencies. This answers your gene frequency versus genotype frequency "problem:" The new population has new gene frequencies; the genotype frequency will change over some generations as the new gene frequencies get mixed, and contrary to your expectation this WILL change the appearance of the daughter population in comparison with the parent population.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : add footnote on genotype frequency

This message is a reply to:
 Message 52 by herebedragons, posted 05-26-2016 4:03 PM herebedragons has replied

Replies to this message:
 Message 55 by PaulK, posted 05-27-2016 7:35 AM Faith has replied
 Message 57 by Modulous, posted 05-27-2016 12:41 PM Faith has replied
 Message 63 by herebedragons, posted 05-27-2016 1:32 PM Faith has replied

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


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 replied

Replies to this message:
 Message 56 by jar, posted 05-27-2016 7:54 AM PaulK has not replied
 Message 58 by Faith, posted 05-27-2016 12:51 PM PaulK has replied

  
jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 56 of 455 (785005)
05-27-2016 7:54 AM
Reply to: Message 55 by PaulK
05-27-2016 7:35 AM


Reality really should be taken into consideration.
I would think that the simple fact that evolution has continued for over three billion years in the one sample we have studied might be sufficient to indicate the process does not decrease diversity to the point it must halt.
Yes, the assertion that life on this earth is not billions of years old can be made but that position too has been soundly refuted by reality and discarded by all scientists and all of the major Christian denominations.
PaulK writes:
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.
But I think pretty much everyone also understands that it is impossible to present evidence in support of Faith's position so we will of necessity continue waiting.

Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 55 by PaulK, posted 05-27-2016 7:35 AM PaulK has not replied

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


Message 57 of 455 (785038)
05-27-2016 12:41 PM
Reply to: Message 54 by Faith
05-27-2016 4:31 AM


Re: You are looking at the wrong part of the system
Not about how new gene frequencies from a population split bring about phenotypic variation.
Gene frequency changes from a population split don't result in phenotypic variation. If variability is lower, it simply restricts the possible phenotypes that can be made and it may make some fairly different looking phenotypes more probability of being expressed through recombination, but this isn't the full picture.
For reasons that can be explained using Game Theory, a mixture of phenotypes is likely to reach a stable equilibrium in a population. There are some great examples of these 'mixed phenotypic strategies' in the world of fish and kleptogamy. The idea is that when males typically spend some energy growing large and brightly coloured and doing flashy things to get clearance from a female to fertilise her eggs, there is an alternative strategy available - to not bother with all that - stay small and female looking sneak in and fertilise the eggs while the other fish are ritualising. Of course, if EVERYBODY did that, the females would be able to fend them off, and males would be competing again. But if some people are doing it, a balance can emerge where the strategy works if say 10% of fish are sneaky, but if the next generation has 15% sneaky fish, they all do worse for it, reducing their numbers.
This isn't evolutionary by the way, sneaky fish have the same genes as straight players, the phenotypic changes but it shows in a very stark way that the success of certain phenotypes can influence the success of another within a species which results in a balance of strategies where presumably both strategies work out as being approximately equally successful.
Let's say brown fur/grey fur is in this category and it's influenced by a single gene F. F makes brown and is dominant. f makes grey and is recessive. Perhaps brown fur is good for hunting wheras grey fur is bad for hunting but is 'sexy' to female foxes because if you can live to reproductive age AND have grey fur, your other genes are probably pretty good to compensate.
We have a stable population that is not experiencing phenotypic change or genotypic change. The population has 100,000 members and we find there are 9,000 grey wolves when we count them. Using the maths of Hardy Weinberg we calculate that this means the Allele Frequency is 70% Brown Fur and 30% Grey Fur.
We watch, and occasionally there are 10,000 grey wolves, then 8,000 but it bounces around the 9,000 point. The sexiness of the gene makes sure that 30% of wolves have it, but when it gets too common the disadvantages to hunting become a bigger factor and this pushes them back to lower numbers where sexiness matters more which pushes them up and so on.
Even if a subpopulation of say, 10,000 wolves of 3,000 brown and 7,000 grey were to somehow split off, everything else being the same, if this population grows to 100,000 we'd expect there to only be 9,000 grey wolves. Brown wolves do very well at hunting in a grey wolf world and while they get more of the girls when they grow up, more of them die trying to grow up than brown wolves.
So evolution doesn't happen by pushing the population out of equilibrium. The population just tends towards the same equilibrium. This is evolution, but it's the conservative part of evolution, tending towards the current equilibrium.
Forget the subpopulation thing now, and we'll watch how evolution is said to happen.
The equilibrium point shifts. Right now, the balance is between two opposing forces: Hunting prowess versus sexual attraction. So let's flip things around. Let's say the forest land dies away and the area the population lives in becomes rockier and more prone to snow. Climate change it seems. Grey fur now aids in hunting, but brown fur is considered sexy because of the handicap effect. The dominant/recessive stays.
So the next generation is going to have more f alleles and F is going to decrease. f alleles are getting the big benefits of surviving to adulthood, and although F loses that, it gains something by being sexy. The next generation has 40% f rather than 30%. What does the population look like? Now there are 16,000 homozygous f and thus Grey Wolves rather than 9,000.
Selection carries on, pushing the population towards the new equilibrium. Grey has more force than Brown in the struggle and pushes it back....
When 50% of wolves carry f there are 25,000 grey wolves in our 100,000 population
When 60% of wolves carry f 36,000 grey wolves
At 70% we reach approximately 50,000 grey 50,000 brown
At 90% we reach 80,000 grey wolves
When 96% of the population has f, then we see approximately 92,000 grey wolves and 8,000 brown wolves and the phenotypic balance of sexiness and hunting skill is restored, the allele frequencies have change from 30% f to 96% f but we still have both F and f. Homozygosity has increased (and thus variability has decreased). But then, if the process was reversed Homozygosity would decrease.
So randomly 'selecting' a population with different frequencies out of a larger population doesn't cause evolution, isn't said to be the main element of evolution. Changes in the equilibrium point, results in selection and this can result in either a more homozygous or less homozygous population around that loci.
Your list was of ALL species within a species or I guess family. You listed ALL the different breeds of dogs and claimed no loss of genetic diversity. That would only be true of the entire family of dogs, because separate breeds do in fact have sharply reduced genetic diversity and where selection has been severe genetic depletion that has brought about genetic diseases.
quote:
According to the pairwise genetic distances, Greyhounds and German Shepherds had longer diverse evolutionary histories than Greyhounds and Labradors or Labradors and German Shepherds. Although a few breed-specific alleles were observed, the significant differences between breeds are in their relative frequencies and distribution of the alleles across a locus. None of the three pure dog breeds corresponds to Hardy-Weinberg equilibrium. A considerable reduction in intrapopulation variation was observed within three pure breeds, compared with the population of individuals belonging to 15 dog breeds. This reduction was especially pronounced in the Greyhound breed, which expressed the lowest degree of variation. Intrapopulation variations of Labradors and German Shepherds did not differ significantly, that of Labradors being only slightly higher. The intra-species variation of dogs is lower than in humans, mouse, or rat, but similar to that in domestic animals, probably reflecting similarly high inbreeding coefficients.
Domestic animals have other effects on variability, especially when you consider the Platonic fantasy that the 'purebreed' culture revolves around. Ultimately the differences aren't because alleles are lost between breeds. Some alleles do get lost due to stringent breeding programs which are essentially replications of the Noachic flood bottleneck.
For example:
quote:
All modern Thoroughbreds can trace their pedigrees to three stallions originally imported into England in the 17th century and 18th century,
Thoroughbred - Wikipedia
quote:
During the 1880s, the 3rd Earl of Malmesbury, the 6th Duke of Buccleuch and the 12th Earl of Home collaborated to develop and establish the modern Labrador breed.
Labrador Retriever - Wikipedia
Most labradors descending from an animal we have a photograph of:
Extrapolating back from the loss of genetic diversity brought about by selection, random or artificial or natural (it's all the same effect), I add back the genetic diversity lost down the generations and arrive at LOTS of genetic diversity at the starting point from which all the types and breeds descended. A lot more heterozygosity I've many times suggested.
The problem is that the most heterozygosity there can be in a population is 50%. The maximum number of alleles in a population is determined by its size - there can only be at most two alleles per individual. Take any population today and go back in time and the population collapses back towards some smaller pool of common ancestors (for you, this is the Flood for the sake of ease). In this scenario everyone may well be heterozygotic, but there are only two alleles per individual. So maximum 12 alleles in the Noachic ancestors. There's a lot of variety there, but I don't think it's enough to account for what we see. Particularly that there are more than 12 alleles for some genes.
So the problem is that your model ends up with there being less alleles in the past with no way for alleles to be added...
WHAAAAAAT? WHAT ARE YOU TALKING ABOUT? "Shuffling alleles around" proves you have no idea what I'm talking about. I've explained my idea about how we got from the ark to today many many times, and explained it again above.
Indeed, the problem is that you need to introduce variability into the system one way or another to explain what we see.
You have *something God related no doubt*
We have observed random noise.
But random noise is all we need, because there are those equilibria and gradiants towards them and a tip in the wrong direction does nothing, but tip the population towards the gradiant and it settles at that new equilibria.
Both explain what we see, and you can't just dismiss the noise.
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.
Yes, but the TREND of genetic variability depends on a number of factors and you are only looking a part of it.
It's like looking at a TV and saying that the image on the screen is about vanish because there is a way for the electricity causing them to escape the TV without considering that its part of a circuit and more electricity is entering it.
Edited by Modulous, : No reason given.

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

Replies to this message:
 Message 59 by Faith, posted 05-27-2016 1:02 PM Modulous has replied

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


Message 58 of 455 (785044)
05-27-2016 12:51 PM
Reply to: Message 55 by PaulK
05-27-2016 7:35 AM


Re: You are looking at the wrong part of the system
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.
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.
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)
I 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. I'm interested in the results of evolution, which are the production of new phenotypes that in reproductive isolation become a new subspecies with a different appearance from the parent population, which is what is normally pointed to as proof of evolution, and the fact that this costs alleles, of necessity reduces genetic diversity, which is the opposite of what the ToE needs to happen if its most popular tenet of Species-to-Species variation holds water. It doesn't hold water.
All those who keep pointing to the genetic increases need to show that you could get evolution out of them. There's no way you could get evolution out of Dr. A's American Curl, and there's no way you could get evolution out of a million wildebeests contentedly munching grass. You have to SELECT whole animals out of these groups and isolate them reproductively, and then and only then will you begin to see the variations that are called evolution. You may get drift, though that usually happens in smaller populations, and that's arguably a form of evolution, but it works exactly like the examples I'm giving anyway, by (randomly) selecting a phenotype that becomes characteristic over some number of generations as others drop out of the pool. But geographic isolation makes the case better.
and that you say that the increases in diversity cannot be sufficient, although without any clear argument or evidence for that conclusion.
Sorry if it hasn't been clear but I've certainly made the argument many times.
So instead of trying to blame everyone else perhaps you should actually make a real case for this alleged declining trend.
Funny, it's been made over and over and over, funny you 've missed it.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 55 by PaulK, posted 05-27-2016 7:35 AM PaulK has replied

Replies to this message:
 Message 60 by PaulK, posted 05-27-2016 1:16 PM Faith has not replied

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


Message 59 of 455 (785049)
05-27-2016 1:02 PM
Reply to: Message 57 by Modulous
05-27-2016 12:41 PM


genetic diversity on the ark
The problem is that the most heterozygosity there can be in a population is 50%. The maximum number of alleles in a population is determined by its size - there can only be at most two alleles per individual. Take any population today and go back in time and the population collapses back towards some smaller pool of common ancestors (for you, this is the Flood for the sake of ease). In this scenario everyone may well be heterozygotic, but there are only two alleles per individual. So maximum 12 alleles in the Noachic ancestors. There's a lot of variety there, but I don't think it's enough to account for what we see. Particularly that there are more than 12 alleles for some genes.
You act as if I'd never discussed this. Twelve is really a lot when you are talking about EVERY locus in the genome, or on the ark at least a majority, and when you assume, as I do, that there were lots more functioning genes for a given trait than is now the case, huge numbers having been lost to "junk DNA" since then. I do need to account for the extra alleles that now exist for a single locus nevertheless, so I've considered the possibility that there is some kind of mutation, just not the random accidental kind.
Interesting if maximum heterozygosity is 50% as you say. If so that would go back to Adam and Eve and I'd expect that on the ark to be somewhat lower. Something to ponder.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 57 by Modulous, posted 05-27-2016 12:41 PM Modulous has replied

Replies to this message:
 Message 61 by jar, posted 05-27-2016 1:19 PM Faith has replied
 Message 68 by Modulous, posted 05-27-2016 2:20 PM Faith has not replied

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


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.

This message is a reply to:
 Message 58 by Faith, posted 05-27-2016 12:51 PM Faith has not replied

  
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