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Author Topic:   Molecular Population Genetics and Diversity through Mutation
Modulous
Member (Idle past 521 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 16 of 455 (784855)
05-24-2016 6:28 PM
Reply to: Message 14 by Faith
05-24-2016 5:23 PM


Re: Fitness graphic
That's how increases in genetic diversity are proved by math, by simply assuming it's possible when it's not.

Nope. The mathematics does not make this assumption. The maths tells us under what conditions of selection and mutation an increase in diversity is possible, indeed inevitable. It also tells us under what conditions genetic diversity will decrease.

The graphic in your post is no doubt a case of the same error.

I'm going to say that your errors are bigger than its errors are.

Oh yeah yeab yeah, EVERYTHING is evolution, yeah yeah, but that's why I keep saying ACTIVE evolution, because I'm describing the specific process where you are getting new characteristic phenotypes and ultimately a new subspecies based on those phenotypes.

Come up with all the new terms you like, the fact is that the net result of the process that evolutionists say is responsible for biological change can be an increase in diversity. Maybe some part of it is subtractive, but some parts of it are additive.

If you want to argue that the mathematics that supports evolution is wrong you can't just say 'I assume the mathematics behind the evolutionary process biologists are talking about proves it is wrong'.

Until you can watch that video and understand what it's saying and how it relates to your objection I can't present the argument any better. I am happy to answer questions, but simple denial makes for a boring discussion. I didn't understand this stuff when I started at EvC Forum, you can learn it if you are motivated, but I feel your religious objections may interfere with that motivation.



Here is a diagram

This is a simplified version of the graph in the video. Let's, for the sake of argument, say it measures 'beak thickness'. The horizontal axis represents thickness, the y axis represents fitness. If the population is at the point where the red arrows start, it will tend to go towards peak B.

Imagine every single member of the population marked on the graph. Some will have thicker beaks some smaller. The phenotypic variation is measured approximately by the length measured from the thinnest beak to the thickest beak. The ones close to B reproduce more and so the population 'crawls' towards B over time.

If a subpopulation breaks off and goes to say, an island, the curve of the graph may well be different. Let's make it simple though, just for illustration purposes. Let's say the curve is basically the same, except that everything to the left of B is 'pushed up' the y axis relative to B (so B can drop it doesn't matter exactly). Now the population that split off may be less diverse, but through mutation and selection it too will crawl up towards A instead of B. The length of the population can remain the same, it's just evolving in a different direction because the fitness landscape differs on the island. The length can remain the same under certain conditions, this is mathematically proven. Now the two populations are separate and Active evolution has occurred, but the length/width of the population on the graph (distance between thinnest and thickest beak thickness) can, under certain circumstances stay the same in both populations. Thus it is possible for diversity to remain. It's just a diverse range of thinner beaks rather than a diverse range if middling beaks.

The only real challenge you face is now to show that those certain circumstances can't exist. We've looked and as far as we can see, they can.


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Genomicus
Member (Idle past 359 days)
Posts: 852
Joined: 02-15-2012


Message 17 of 455 (784856)
05-24-2016 6:41 PM
Reply to: Message 11 by caffeine
05-24-2016 4:56 PM


Re: Nitpick alert
Certain types of selection can work to maintain diversity, such as in cases of heterozygote advantage.

You are right, of course, so your nitpick is well-taken


This message is a reply to:
 Message 11 by caffeine, posted 05-24-2016 4:56 PM caffeine has acknowledged this reply

  
Genomicus
Member (Idle past 359 days)
Posts: 852
Joined: 02-15-2012


(2)
Message 18 of 455 (784858)
05-24-2016 7:51 PM
Reply to: Message 4 by Faith
05-24-2016 6:04 AM


Re: But I'm just as mathematically challenged as ever
If necessary, I'll endeavor to walk you through the math. For now, though, I'll stick with word-based reasoning. Here's what I'm going to respond to:

Well, now I see that you are saying the same thing I’ve answered many times in this argument already: it doesn’t matter how much new genetic variability you can put into, or put back into, a population, when it is evolving a new population of new phenotypes, a new look, the trend is going to be to loss of genetic diversity, no matter how much new diversity may have been added. As I put it above, you can't get the phenotypic changes without removing the genetic diversity. So if you are adding genetic diversity, you are obviously not removing genetic diversity.

The processes that bring about the new phenotypes, that is, that are actively evolving the population, have to get rid of whatever genetic diversity doesn’t support the new phenotypes, and the end is going to be the same no matter how much diversity is added: a subspecies with reduced genetic diversity, and if many daughter populations succeed one another eventually the loss of genetic diversity should be quite dramatic. And if during all these evolutionary changes new genetic diversity is added, all that can do is interfere with the formation of the phenotypes that is underway. It can happen, of course, but then it isn’t evolution.

You state that the process giving rise to novel phenotypes "have to get rid of whatever genetic diversity doesn’t support the new phenotypes." I'm not sure if this is a typo on your part or a genuine misunderstanding of terminology. The only process that gives rise to new phenotypes (barring epigenetic mechanisms) is mutation; natural selection and genetic drift only determines the distribution of that new phenotype in the population.

That being said, your argument is fatally flawed, and here's why.

It is indeed true that while a new trait is increasing in frequency throughout the population, there is a loss in heterozygosity among the relevant alleles (that is, the alleles which encode the specific proteins that constitute the novel trait on a molecular level). There are some exceptions, as caffeine noted, but these aren't relevant here and the exceptions would further refute your argument anyway.

So, from that perspective, you're right: as a new trait is evolving, there is a decay in heterozygosity among the relevant alleles. However, what you apparently fail to take into consideration is the entire diversity of the population's gene pool. In other words, while one set of alleles might become increasingly homozygous in the population by virtue of so-called "active evolution" of a trait, there are literally thousands of other chromosomal loci which are witnessing an increase in allelic heterozygosity (that is, an increase in diversity). What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).

The experimental facts of life, however, demonstrate that as one beneficial phenotype gains in frequency in the population, plenty of other selectively neutral phenotypes will emerge in the population -- phenotypes which are not related to the function of the beneficial phenotype. And these selectively neutral phenotypes, too, will -- fueled by mutation -- spread through the population according to the statistics of population genetics. These phenotypes, then, provide the "raw genetic material" -- or the genetic diversity -- for further evolution to continue. In short, while one particular beneficial trait will gain in frequency at the expense of other alleles, selection will only "weed out" the alleles which are selectively relevant to the function of the beneficial trait.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 4 by Faith, posted 05-24-2016 6:04 AM Faith has responded

Replies to this message:
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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006


Message 19 of 455 (784864)
05-24-2016 9:15 PM
Reply to: Message 14 by Faith
05-24-2016 5:23 PM


Re: Fitness graphic
That's how increases in genetic diversity are proved by math, by simply assuming it's possible when it's not.

But mutation does occur. This is not an assumption; that is known. Models that take this into account are in that respect correct; models that ignore it are a fine example of what is meant by "garbage in, garbage out".


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NoNukes
Inactive Member


Message 20 of 455 (784866)
05-24-2016 9:22 PM
Reply to: Message 18 by Genomicus
05-24-2016 7:51 PM


Re: But I'm just as mathematically challenged as ever
The only process that gives rise to new phenotypes (barring epigenetic mechanisms) is mutation

That's probably not a correct statement.

https://en.wikipedia.org/wiki/Phenotype

A phenotype results from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorph.

I think a better way of dealing with things is to note that Faith really means genetic diversity as only the loss of genetic diversity can really count as a permanent loss to a population. Of course mutations directly add to genetic diversity. Faith's responses to that fact are total nonsense. But she will never see that regardless of how much rigorous your math is.

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 18 by Genomicus, posted 05-24-2016 7:51 PM Genomicus has responded

Replies to this message:
 Message 21 by Dr Adequate, posted 05-24-2016 10:00 PM NoNukes has responded
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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006


Message 21 of 455 (784870)
05-24-2016 10:00 PM
Reply to: Message 20 by NoNukes
05-24-2016 9:22 PM


Re: But I'm just as mathematically challenged as ever
Well, it's a subtle point. To the extent that a white guy with a tan can be considered to be phenotypically different from a guy with the same genes for skin color but an indoor job ... well, I think we can neglect that for the purposes of this discussion.

This message is a reply to:
 Message 20 by NoNukes, posted 05-24-2016 9:22 PM NoNukes has responded

Replies to this message:
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Genomicus
Member (Idle past 359 days)
Posts: 852
Joined: 02-15-2012


Message 22 of 455 (784871)
05-24-2016 10:05 PM
Reply to: Message 20 by NoNukes
05-24-2016 9:22 PM


Re: But I'm just as mathematically challenged as ever
Hey NoNukes,

The only process that gives rise to new phenotypes (barring epigenetic mechanisms) is mutation

That's probably not a correct statement.

https://en.wikipedia.org/wiki/Phenotype

I believe you will find my original statement correct in the light of this explanation:

1. While I have a disdain for quoting from Wikipedia, here's Wikipedia's definition of phenotype:

"A phenotype (from Greek phainein, meaning "to show", and typos, meaning "type") is the composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird's nest)."

So what kind of processes can give rise to new phenotypes? Well, as I stated, barring epigenetic mechanisms, only mutations can result in new phenotypes. In the Wikipedia quote you cited, it is stated that phenotype results from genes and the influence of environmental factors. If a new phenotype is to arise, then (a) it is the result of changes in genes (mutation), or (b) the result of environmental factors (or a combination of the two). If it is the result of environmental factors -- e.g., diet affecting DNA methylation patterns -- then these are epigenetic mechanisms.

Having said that, 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. But it's not like genetic drift or selection produces new phenotypes; these only impact the distribution of phenotypes in the population.


This message is a reply to:
 Message 20 by NoNukes, posted 05-24-2016 9:22 PM NoNukes has responded

Replies to this message:
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herebedragons
Member (Idle past 149 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 23 of 455 (784873)
05-24-2016 11:08 PM
Reply to: Message 8 by Faith
05-24-2016 4:29 PM


Re: Fitness graphic
There are conditions in which populations are stable, that is, NOT EVOLVING, which is what Hardy-Weinberg is describing. It is actually described AS not evolving.

Hardy-Weinberg is based on idealized conditions 1) infinite population size 2) completely random mating 3) no mutation 4) no selection pressure and 5) no migration (gene flow). It is not intended to describe any real populations as there is no populations that would fully meet these 5 conditions. The equation is used to identify what forces are acting upon a population since any of these conditions not being met would cause deviations from HW equilibrium.

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. Below is an example of a subpopulaton derived from a parental population complete with the loss of 2 alleles in the subpopulation due to sampling error (ie., those alleles were not represented in the founding population that established the subpopulation or perhaps they were lost to drift shortly after establishment).

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}

What genotypes exist in the subpopulation that don't exist in the parental population?

Again, what I am focusing on is what happens when you are getting the active production of new phenotypes in reproductive isolation, because that is the clearest expression of evolution,

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 the fact is that this leads ultimately to genetic depletion, yes even with all the additions you can throw at it -- as long as new phenotypes are being produced you are getting a loss of genetic diversity.

But this "genetic depletion" is not something we observe, it is not a thing. There is not this massive lack of genetic diversity in natural systems. Sure there are examples of species where genetic diversity has been depleted (such as the cheetah) but those are the exception not the rule. Your "hypothesis" predicts that we should detect "genetic depletion" in species where there has been rapid speciation or that there are large numbers of species that probably originated from an original population (or common ancestor).

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?

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 8 by Faith, posted 05-24-2016 4:29 PM Faith has responded

Replies to this message:
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NoNukes
Inactive Member


Message 24 of 455 (784875)
05-24-2016 11:44 PM
Reply to: Message 21 by Dr Adequate
05-24-2016 10:00 PM


Re: But I'm just as mathematically challenged as ever
Well, it's a subtle point. To the extent that a white guy with a tan can be considered to be phenotypically different from a guy with the same genes for skin color but an indoor job ... well, I think we can neglect that for the purposes of this discussion.

I agree with the tanning example, but I think we can come up with something more significant than something that comes and goes with exposure to the sun. I am struggling to come up with examples, but maybe the development of allergies based on exposure to some irritant might be something that does not fade away immediately, or perhaps an exposure to some chemical in the environment that suppresses the immune system.

I am not sure what the Wikipedia article was getting at, but I don't want the impression to be that all examples are as trivial as tanning. Perhaps my examples are not good ones.


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:
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NoNukes
Inactive Member


Message 25 of 455 (784876)
05-24-2016 11:50 PM
Reply to: Message 22 by Genomicus
05-24-2016 10:05 PM


Re: But I'm just as mathematically challenged as ever
If it is the result of environmental factors -- e.g., diet affecting DNA methylation patterns -- then these are epigenetic mechanisms.

Epigenetic functions are specifically factors that switch gene expression on or off. I am not sure that this covers every possible every possible environmental mechanism, but perhaps I am wrong. I appreciate that you've added novel allele combinations. I think it is important to do so because that addition is the closest to things that Faith is claiming are the 'real' mechanisms for new phenotypes.

I'm satisfied with your position.


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 22 by Genomicus, posted 05-24-2016 10:05 PM Genomicus has acknowledged this reply

  
Faith
Member
Posts: 34711
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.2


Message 26 of 455 (784878)
05-25-2016 12:16 AM
Reply to: Message 18 by Genomicus
05-24-2016 7:51 PM


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

Edited by Faith, : No reason given.


This message is a reply to:
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Faith
Member
Posts: 34711
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.2


Message 27 of 455 (784879)
05-25-2016 12:18 AM
Reply to: Message 18 by Genomicus
05-24-2016 7:51 PM


Re: But I'm just as mathematically challenged as ever
If necessary, I'll endeavor to walk you through the math.

Not necessary but thanks.

For now, though, I'll stick with word-based reasoning. Here's what I'm going to respond to:

Well, now I see that you are saying the same thing I’ve answered many times in this argument already: it doesn’t matter how much new genetic variability you can put into, or put back into, a population, when it is evolving a new population of new phenotypes, a new look, the trend is going to be to loss of genetic diversity, no matter how much new diversity may have been added. As I put it above, you can't get the phenotypic changes without removing the genetic diversity. So if you are adding genetic diversity, you are obviously not removing genetic diversity.

The processes that bring about the new phenotypes, that is, that are actively evolving the population, have to get rid of whatever genetic diversity doesn’t support the new phenotypes, and the end is going to be the same no matter how much diversity is added: a subspecies with reduced genetic diversity, and if many daughter populations succeed one another eventually the loss of genetic diversity should be quite dramatic. And if during all these evolutionary changes new genetic diversity is added, all that can do is interfere with the formation of the phenotypes that is underway. It can happen, of course, but then it isn’t evolution.

You state that the process giving rise to novel phenotypes "have to get rid of whatever genetic diversity doesn’t support the new phenotypes." I'm not sure if this is a typo on your part or a genuine misunderstanding of terminology. The only process that gives rise to new phenotypes (barring epigenetic mechanisms) is mutation; natural selection and genetic drift only determines the distribution of that new phenotype in the population.

I sometimes don't get the whole thought expressed. You will get new phenotypes simply from a new set of gene frequencies. Not new in the sense of novel but new to the population. If the parent population was characterized by brown fur the new subpopulation may have more alleles for gray fur and after some period of mixing of the new gene frequencies over some number of generations the new population will now look gray or mostly gray, differing from the original population by that particular trait. And the same thing should be happening with other traits, some now being more frequent and coming to contribute to the new population while others that were frequent in the original population are now less frequent and may even disappear. Thus you get a new set or new mix of phenotypes in your new population, eventually amounting to a new subspecies. Of course it's an oversimplification but the logic should be correct enough. And the smaller the subpopulation the more dramatic the new appearance will be, and the greater the loss of genetic diversity.

That being said, your argument is fatally flawed, and here's why.

It is indeed true that while a new trait is increasing in frequency throughout the population, there is a loss in heterozygosity among the relevant alleles (that is, the alleles which encode the specific proteins that constitute the novel trait on a molecular level). There are some exceptions, as caffeine noted, but these aren't relevant here and the exceptions would further refute your argument anyway.

So, from that perspective, you're right: as a new trait is evolving, there is a decay in heterozygosity among the relevant alleles.

Good, your specificity is welcome.

However, what you apparently fail to take into consideration is the entire diversity of the population's gene pool. In other words, while one set of alleles might become increasingly homozygous in the population by virtue of so-called "active evolution" of a trait, there are literally thousands of other chromosomal loci which are witnessing an increase in allelic heterozygosity (that is, an increase in diversity). What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).

Well, no, I haven't failed to take into account that there are plenty of other genes that are being affected at the same time although it’s true I don’t spend time focusing on them. You stymied me for a while with your statement that an increase in allelic heterozygosity is an increase in diversity. It took a while for me to see that you made a mistake there: you are confusing gene frequency with genetic diversity. The former is just an increase in the quantity of an allele, the latter would be an increase in kinds of alleles, which isn’t going to happen in a reproductively isolated population, except by mutations of course.

What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).

Not sure what you are saying. Do you mean my argument requires ALL alleles to tend towards homozygosity or do you mean that this is to be expected in reality? My first take, I could be wrong, is that neither should be the case. Some genes should remain heterozygous, perhaps some become heterozygous, though I’m not sure about how that happens.

But to the general point, the whole genome should have new gene frequencies as a result of the population split, except for any that are always fixed, which you would know more about than I do, and just like the ones that are making the major changes in the look of the population by working through the population from generation to generation, all the alleles throughout the genome should have undergone the same changes: some higher frequency than they were in the original population, some lower, including many also not changed or much changed in frequency. Most of them probably wouldn’t affect the phenotype, but there should be some differences that do contribute to the change in appearance of the new population in relation to the original population.

In any case the decrease I have in mind is specifically due to the high frequency traits that will dominate the appearance of the new population.

The experimental facts of life, however, demonstrate that as one beneficial phenotype gains in frequency in the population, plenty of other selectively neutral phenotypes will emerge in the population -- phenotypes which are not related to the function of the beneficial phenotype.

I agree and I do take that into account. I don’t think it affects my basic argument so I don’t normally discuss it.
Also, more as a side issue perhaps, I don't think in terms of the emerging phenotypes as “{beneficial,” I guess because because I don't think much in terms of natural selection or of mutations, I'm thinking in terms of random changes in frequency of a species' built in genes/alleles as the driving element in evolution.

They are most likely neutral with respect to adaptation, at least adaptation that would come about from environmental pressure. I've come to see most adaptations as produced by these random genetic changes rather than by the environment, genetic changes which then lead the organism to gravitate to whatever in the environment suits it.

So: the lizards on Pod Mrcaru that developed the large heads and jaws and tougher digestive system didn't develop all that because of a loss of their usual food in their new environment or a greater abundance of food that required the heavier jaws and tougher digestive system, they simply evolved the new physical abilities by random genetic combinations from new gene frequencies and then gravitated to the food best suited to their new abilities.

Same with Darwin's finches. There was no lack of a range of foods available in the environments they inhabited, but some finches developed beaks suitable to berries, and some to nuts and some to insects and so on, simply from becoming geographically isolated from other populations and developing the new beaks from new gene frequencies. It's not a crucial point I guess, that is it doesn't particularly further my argument, it's just something I think is true, and it has the virtue of saving what could be an enormous cost to the organism from natural selection.

So I'd reword your statement: "plenty of other selectively neutral phenotypes will emerge in the population -- phenotypes which are not related to the function of the beneficial new dominating or high-frequency phenotype."

And that I agree with. I think some of the other “selectively neutral” phenotypes will also contribute something to the overall phenotypic presentation of the new population after it has thoroughly worked through all its new frequencies over some number of generations.

And these selectively neutral phenotypes, too, will -- fueled by mutation -- spread through the population according to the statistics of population genetics.

Even if the high-frequency phenotypes among them do spread, they would merely become part of the overall phenotypic presentation of the population after enough generations for the new presentation to emerge as more or less homogeneous, and they aren’t “selectively neutral” if they are that high frequency that they do in fact spread as you describe, they are in fact among the selected, and genetic diversity will be lost for them as for the more obvious phenotypes such as the gray fur that replaces the brown over some generations.

But as to mutations: in every discussion I've ever read, mutations are treated as sort of an article of faith, their actuality not being demonstrated, or the mere presence of a newly expressed phenotype gets it called a mutation without warrant. It’s science that describes them as so predominantly either deleterious or neutral and so extremely rarely of any value to the organism, but the obvious conclusion isn’t drawn from those facts. If I draw it I get accused of bias but the conclusion seems to me to be so inevitable I keep being amazed that mutations are so consistently invoked as the source of genetic variation. Not only is a beneficial mutation rare, it’s even rarer in the sex cells where it might have an impact on offspring, and the unlikelihood of its being selected makes it even rarer still, and the time frame required can be so enormous – as I keep noting, the cheetah has been waiting around forever for a mutation to get it out of its genetic purgatory --you might as well dismiss mutations as of no use at all. But no, they are constantly invoked as the fuel for evolution.

Mutations are needed if the ToE is correct about evolution beyond the Kind or evolution from a dog to something that is not a dog, but for microevolution built-in alleles are all that is needed, their combinations are just about endless in themselves, can produce an enormous variety of dogs or whatever organism is evolving. 1) There is no need for mutations, and 2) if they arose while a population was evolving they'd only interfere with the new phenotypes that are forming, and 3) the fact, that I didn't make up, that most are by far deleterious or neutral and anything at all beneficial is rare to the point of vanishing, means to me that mutations contribute nothing to the evolution of new varieties.

These phenotypes, then, provide the "raw genetic material" -- or the genetic diversity -- for further evolution to continue. In short, while one particular beneficial trait will gain in frequency at the expense of other alleles, selection will only "weed out" the alleles which are selectively relevant to the function of the beneficial trait.

This last statement is correct according to my thinking too, but despite the presence of other traits in the population it depends on the size of the population whether they will come to affect the phenotype or not. The low frequency ones won’t. But evolution doesn't continue once a population is established from its particular set of gene frequencies after some number of generations of inbreeding. It could even settle down to a Hardy-Weinberg stability for some great period of time. What would cause evolution to resume would be the selection, random or otherwise, of another small population to become reproductively isolated with a new set of gene frequencies that may allow expression to those that have been dormant, genetic diversity will be lost with respect to those other traits in the new population and the beat goes on.

Edited by Faith, : No reason given.


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PaulK
Member
Posts: 15932
Joined: 01-10-2003
Member Rating: 2.3


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


Re: The endless dance of the wishful refutation
quote:

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

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


This message is a reply to:
 Message 15 by Faith, posted 05-24-2016 5:34 PM Faith has responded

Replies to this message:
 Message 29 by NoNukes, posted 05-25-2016 3:17 AM PaulK has not yet responded
 Message 30 by Faith, posted 05-25-2016 4:33 AM PaulK has responded

  
NoNukes
Inactive Member


Message 29 of 455 (784882)
05-25-2016 3:17 AM
Reply to: Message 28 by PaulK
05-25-2016 12:55 AM


Re: The endless dance of the wishful refutation
It will not bring back the lost alleles, it may well not add diversity at the loci of those alleles.

I would add that the only reason for this is that there are so many other loci available that it is only unlikely that the an immediately previous one generated again in a random process. There is no natural equivalent of a 'breeder' working to prevent any old allele to come back. If in fact, we got to a point where a large percentage of loci had been mutated in an evolutionary branch, we should expect to start seeing some reruns.


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This message is a reply to:
 Message 28 by PaulK, posted 05-25-2016 12:55 AM PaulK has not yet responded

  
Faith
Member
Posts: 34711
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.2


Message 30 of 455 (784884)
05-25-2016 4:33 AM
Reply to: Message 28 by PaulK
05-25-2016 12:55 AM


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

There is no such evidence.

If all the alleles in a parent population except one come over to a reproductively isolated daughter population, that will be a reduction in genetic diversity. If the daughter population is significantly smaller than the parent there should be a decrease of more than one allele. Then as higher frequency alleles bring out new phenotypes in the population over some number of generations, more low frequency alleles may begin to drop out. Drift has the same effect.

Nothing is going to "add new alleles at other loci" in a population split. All loci are subject to new gene frequencies. Some alleles will be higher frequency than before and may contribute a new phenotype to the population but it won't involve an increase in genetic diversity, and since any remaining competing allele may eventually drop out that will add to the decrease in genetic diversity.

Mutation is the only thing that could increase the genetic diversity and I dispute that you could get a single beneficial mutation in the short time frame for all the above to occur. But if it did it would also have to be selected and that means some other allele will probably have to drop out, so after many generations of mixing of the alleles you may have a new subspecies including one mutated allele in the mix, and an overall loss of genetic diversity.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 28 by PaulK, posted 05-25-2016 12:55 AM PaulK has responded

Replies to this message:
 Message 31 by PaulK, posted 05-25-2016 5:16 AM Faith has responded
 Message 35 by herebedragons, posted 05-25-2016 9:38 AM Faith has not yet responded

  
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