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Author Topic:   The Great Debate: Molecular Population Genetics and Diversity in Evolution
Faith 
Suspended Member (Idle past 343 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 24 of 30 (785395)
06-04-2016 1:32 AM
Reply to: Message 19 by Genomicus
06-03-2016 10:44 PM


Unproven net increase in genetic diversity
It is interesting that some species may become genetically incompatible with so little change. This is, however, a very odd piece of logic, in that such a low requirement for a reproductive barrier to arise doesn’t imply anything about changes in other genes, whether required or not. Are we talking two particular genes or any two genes? In any case I fail to see how this is a problem for my argument.

We're talking about changes to two particular genes.

OK, which particular two?

And this is deeply problematic for your position because if only changes to two genes are required for speciation in this case, then all other chromosomal loci can diversify through mutation, such that there is a net increase in genomic diversity.

1) You haven't proved this happens

2) How does mutation choose to change only some loci and not others?

3) Even if it did happen, managing not to affect the salient characteristics of the breed or species, it doesn't change the fact that to get that breed or species required the loss of genetic diversity for those evolving new traits. THAT is where the changes are occurring, the new phenotypes and the loss of diversity. Of course it MUST occur throughout the genome anyway just because reduced numbers has to bring about a change in gene frequencies wherever in the genome this can happen, and that in turn has to bring about the loss of genetic diversity I'm talking about. Etc etc etc

4) It also fails to add diversity where the ToE would need it if further evolution beyond any species really were possible -- in those traits that most clearly characterize the breed or species. That is, net diversity that leaves the new species intact doesn't help the ToE at all. Blurring the species with mutations destroys evolution, and so does leaving the species intact, with or without increased diversity. But of course overall decreased genetic diversity is what brings evolution to a natural stopping point.

5) Since apparently Sardinia had lots of gene flow over the centuries although your referenced study said it didn't, and the elephant seals are also still considered to be genetically depleted despite their great increase in population, although your study there said their genetic diversity had increased, I'm beginning to wonder how good all those supposed markers of genetic diversity in those studies really are. Microsatellite information for instance. Mitochondrial information for instance. What do you really learn from those things about the organism's overall genetic diversity?
Etc
etc
etc

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
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Faith 
Suspended Member (Idle past 343 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 25 of 30 (785400)
06-04-2016 7:05 AM
Reply to: Message 19 by Genomicus
06-03-2016 10:44 PM


The evidence for mutations oddly questionable
(Great Debate)

The problem is that unless you are counting on mutation to make random changes in two genes there is no explanation for how this comes about.

Yeah, I have no problem with "counting on mutation to make random changes in two genes," given the preponderance of evidence that mutation is a major diversifying force in biology.

I'm wondering more and more just how good this "evidence" is that mutation is a major diversifying force. I mean there is something wrong with your evidence in relation to Sardinia and the elephant seal, and there is also something wrong with the study Tangle came up with for mutation as the cause of the change from the light to the dark peppered moths. I presented my objections to that on his thread but will repeat them here because I'd really like your response to this:

Tangle writes:

The peppered moth's evolution from white to black and back to white again is pure observation. That's how we know about it - it is documented.

The mechanism that allows the selective survival of black moths over white moths has been observed - the darkening of the trees on which the moths rest during the day leaving them open to predation against the newly black trunks. The predation process was reversed when the trees were no longer black. Observed and documented.

[Faith] That much is common knowledge, and quite easily explained in terms of a built-in allele for the black moth.

Mutation is in fact harder to explain. See my post to jar above. There is something very very weird about the idea that it was a mutation instead of built-in for the reasons I give there. You either need many same or similar mutations at the same locus to counteract the constant loss to predation, which doesn't fit with the general observations of mutations as random accidents of replication, or you have to count on one mutation surviving against ridiculous odds, or showing up so exactly at the right time that only a teleological mechanism could explain it. Not what the ToE normally has in mind.

There has to be something wrong with the science that supposedly "observed" this mutation.

Also seems to be the case with many other studies that find mutations to be the cause of genetic changes.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
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Faith 
Suspended Member (Idle past 343 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 26 of 30 (785499)
06-06-2016 8:35 AM
Reply to: Message 19 by Genomicus
06-03-2016 10:44 PM


Re: General Responses
Just so you know, I am still working on your post although also being distracted. I hope it's not a problem breaking it up into small bites; it seems to help me get my responses organized. But I'm working on a bigger bite next time. I'll post it in this box.

This message is a reply to:
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Faith 
Suspended Member (Idle past 343 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 29 of 30 (785562)
06-07-2016 7:39 AM
Reply to: Message 28 by Genomicus
06-07-2016 7:00 AM


Re: On the Evidence from Elephant Seal mtDNA
I'm sorry to inform you that this is not exactly "A Scientific Debate" as I am not a scientist and not required to be one to debate at EvC. Scientific American ought to be an acceptable reference, and whether you accept it or not I'm considering it so for purposes of this discussion.

What do these results tell us? Both haplotype diversity and nucleotide diversity of modern northern elephant seals are significantly higher than that of the elephant seal population from 1892, when the population hit an all-time low.

Nobody has explained to me what either haplotype or nucleotide diversity has to do with anything, what it actually is, why I should regard it as more important than the usual measures of genetic diversity. But I think I get some idea from this post.

And unlike heterozygosity, which is not necessarily the result of novel mutations, nucleotide diversity is the result of mutations introducing new DNA changes throughout the population.

So what I'm getting is that you get a lot of mutations at these locations. I understood that to be the case for MtDNA, which is the "haplotype" DNA, but the import of that wasn't apparent at the time. The fact that you get these mutations at this location you call an increase in genetic diversity, which technically of course it is I suppose, but I have no idea why it should be taken as any kind of measure of the genetic condition or general health of the seal population. What does this DNA do anyway? It seems to do nothing more than accumulate mutations. Does it do anything else in the organism? I can see why accumulating mutations so frequently could make cytochrome C a good marker of species since each would get its own mutations, and cytC has something to do with MtDNA, sorry I forget exactly what and I don't want to abandon my post to go find out.

Perhaps you will explain if that haplotype DNA actually DOES something. Because if it doesn't, if it does nothing but accumulate mutations, I don't see what it has to do with any kind of genetic diversity that would benefit the elephant seal.

The kind of genetic diversity that is needed is the kind that makes traits, phenotypes, changes in the animal itself that can benefit it by giving it options for variation, without which it remains in danger of extinction. THAT kind of genetic diversity is measured by heterozygosity: the more homozygosity the more endangered the animal, which is the problem for the cheetah as well as the elephant seal. Homoygosity at the loci that most characterize the animal used to be the criterion for a purebred until it became known that it put the animal at risk of genetic diseases. All this goes on in the genome where genes make phenotypes. What does MtDNA do?

I don't have a clear idea about nucleotide diversity except that it implies a change in the sequence of a gene, which would of course be the result of mutation. Mutations aren't very often a good thing so I don't see how this "increase in genetic diversity" bodes any good for the seal anyway. Since nothing is said about how it relates to the measure of heterozygosity I've always taken as the indicator of true genetic diversity, I'm going to assume that these mutations are generally bad for the seals and it's just a bit of word magic to call them an increase in genetic diversity as if they solved the poor creature's plight of genetic depletion. This of course means I'm saying some unkind things about scientists which I'm sure you'll take with your usual indignation, but really you should just take it as a reason to explain why I should regard this evidence as answering my argument that normal evolutionary processes lead to decreased genetic diversity.

Furthermore, in recent history, the northern elephant seal population has not been subjected to gene flow from other species, so the only way these observations can be explained is through mutations.

Yes you would have to be right about this. But nothing in these studies shows that either of these sources of increased genetic diversity is REAL increased genetic diversity that gives the genetically impoverished elephant seal any more genuine opportunities for further variation than it had before. I believe that Scientific American blog you so haughtily dismiss as unworthy of your scientific consideration is right: the elephant seal remains genetically endangered even with all this bogus increase in genetic diversity. Now, an increase in viable heterozygosity -- THAT would be SOMETHING.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 28 by Genomicus, posted 06-07-2016 7:00 AM Genomicus has not yet responded

  
Faith 
Suspended Member (Idle past 343 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 30 of 30 (785567)
06-07-2016 8:20 AM
Reply to: Message 27 by Genomicus
06-07-2016 6:44 AM


Re: On the Evidence from Human Genomics: The Case of Sardinia
In a beautiful piece of genomics research, Caramelli and colleagues (2007) analyzed mtDNA D-loop sequences (which are basically the most variable regions of the human genome) from ancient Sardinians who lived between 3,430 and 2,700 years ago (the DNA was extracted from teeth using a highly rigorous laboratory approach). The diversity of these sequences was then compared to the mtDNA of present-day Sardinians.

The haplotype diversity (a way to measure genetic diversity, and a form of heterozygosity) of the ancient population was 0.83, compared to a haplotype diversity of .96 for modern Sardinians (the larger the number, the greater the diversity). Revealingly, too, was the discovery that the average number of indels (a form of mutation) between sequences from the ancient population was a low 1.43, whereas the mean value for indels between modern Sardinian sequences was 4.68. This neatly demonstrates, again, that the modern Sardinian population has increased in genetic diversity, despite being isolated. The study by Caramelli and colleagues also provides evidence for clear genetic continuity between the ancient population and the modern Sardinian population, indicating a lack of gene flow from the “outside” world.

So how does your notion explain the above experimental results, Faith?

After answering the post about the seals maybe I just got an influx of cynicism but it hit me that what's being measured in both these studies has nothing whatever to do with REAL genetic diversity. MtDNA has nothing to do with anything related to normal evolution of traits so its accumulating mutations is just the usual accumulation of garbage, which is what most mutations are, nothing that could possibly contribute to the health of any organism or human being.

It's kind of like the logic of someone needing to measure the dimensions of a whole apartment who decides just to measure the broom closet because it's easier and it also is measurable in feet and inches just like the whole apartment so it should suffice as a measure of the apartment. Of course it's absurd but that's how it hits me. MtDNA has nothing to do with the evolution of traits that I've been talking about so how can it have anything to do with increasing the diversity that is lost through that process?

So you've got increased MTDNA diversity, which is nothing but a bunch of meaningless mutations absolutely unrelated to the genetic diversity that is lost in the evolutionary scenarios I've been describing. I realize this is too absurd to be true but I have no other way of making sense of this.

So this is your next project: proving me wrong about this.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 27 by Genomicus, posted 06-07-2016 6:44 AM Genomicus has not yet responded

  
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