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Author Topic:   Evolution Requires Reduction in Genetic Diversity
Taq
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Message 182 of 1034 (692159)
02-28-2013 10:47 AM
Reply to: Message 155 by Faith
02-27-2013 7:41 PM


Re: Mutations Don't Add Anything That Could Rescue the ToE
I have not ignored them I've explained that they don't stop the march to genetic depletion, . . .
Where did you back this claim with evidence?

This message is a reply to:
 Message 155 by Faith, posted 02-27-2013 7:41 PM Faith has not replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 183 of 1034 (692160)
02-28-2013 10:53 AM
Reply to: Message 160 by Faith
02-27-2013 8:31 PM


Re: Constant Increase In Genetic Diversity
Deleterious can mean doing damage that doesn't show up in a changed function except after many mutations have accumulated, and I'd guess such sleeper mutations as it were constitute the majority of the mutations out there. Just a guess.
The vast majority of mutations do not occur in genes, promoters, or transcription factors so I would say that the vast majority are neutral. Of the mutations that change protein sequences I would think that a fair amount are deleterious, much more so than those that occur in non-coding and non-regulatory DNA. We can also see negative selection removing these mutations by comparing the genomes of species. When we do so we find something very interesting. We find that mutations which do not change the amino acid sequence of proteins are more common in a gene than those that do change the amino acid sequence. This tells us that selection is removing deleterious mutations.
This doesn't change the fact that the DNA differences seen between species contain mutations that are beneficial to each species. We KNOW that they exist because we can see them. We can find them.
Prediction from this guess is that we'll be seeing lots more genetic diseases in the near future.
Why wouldn't selection remove them just as selection has been removing deleterious mutations since evolution started?

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 Message 160 by Faith, posted 02-27-2013 8:31 PM Faith has replied

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 184 of 1034 (692161)
02-28-2013 10:58 AM
Reply to: Message 176 by Faith
02-28-2013 9:28 AM


Re: Mutations Don't Add Anything That Could Rescue the ToE
Not if evolution is the production of new species/varieties/breeds. All you get from the addition of mutations is more traits that COULD be the basis of a new species, but as long as they aren't being selected, no, you aren't getting evolution.
They are being selected for, and this is shown by comparing our genomes to that of other apes. We can find patterns of positive and negative selection. I even highlighted evidence of positive selection in the case of the mc1r gene in pocket mice. Remember that?
No, it isn't a simple addition-subtraction thing. If alleles are flowing in you get stasis.
If alleles are flowing in and selection is changing allele frequencies then you have change in a species over time, otherwise known as evolution.
It is the BASIS for phenotypic change, because the gene pool IS the basis for phenotypic change, but you aren't GETTING phenotypic change until you get reproductive isolation and selection.
The phenotypic change shows up in the first organism that carries the mutation. The first pocket mouse with the mutation conferring black fur had black fur.

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 Message 176 by Faith, posted 02-28-2013 9:28 AM Faith has replied

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 Message 207 by Faith, posted 03-01-2013 2:48 PM Taq has replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 189 of 1034 (692173)
02-28-2013 12:50 PM
Reply to: Message 185 by Faith
02-28-2013 11:00 AM


Re: Mutations Don't Add Anything That Could Rescue the ToE
I don't know what you would get in this scenario but it's something blurry and constantly changing, NOT an identifiable new species which is what happens IN REALITY.
In reality, species do change over time. We call it evolution.
Is evolution about forming new SPECIES or about the myriad of different traits that show up in all populations? New traits show up in individuals in my scenario too, WITHOUT mutations.
Evolution is about speciation AND how traits appear in populations. It is both. Also, new traits also show up due to mutation. You are once again ignoring this fact. The black mice with the mc1r mutation are an example of this.
But to GET that new species the traits have to be SELECTED AND ISOLATED. That's my point. The traits that constantly crop up in individuals in any fairly genetically diverse population, whether by mutation or by what I think it is, simply new combinations of existing alleles, do not constitute a new SPECIES unless selected, isolated and worked through the entire new gene pool. And THAT happens only when all the alleles for OTHER traits are suppressed, reduced, or eliminated = REDUCED GENETIC DIVERSITY REQUIRED TO FORM A NEW SPECIES.
Before the reduction due to selection you get an increase in genetic diversity due to the accumulation of mutations. It is a sine wave, not an ever decreasing curve.
What you are calling new "species" is really just varieties or breeds of existing species, presumably having reached a point where they no longer interbreed with their mother populations, probably due to severe genetic depletion in some cases.
What we are calling species are genetically isolated gene pools. This causes different mutations to accumulate in each population, either through chance (neutral drift), or different selection pressures. What results is divergence. The two isolated populations become more diverse when compared to one another because they are accumulating different mutations.
What you guys seem not to appreciate is that the existing alleles and genes in a genetically diverse population are more than sufficient to form many many subspecies through selection and isolation of portions of the gene pool.
What you fail to appreciate is that species who share a common ancestor are more divergent than can be produced by a single ancestral gene pool. The differences between human and chimp genes is not due to different alleles in our common ancestor. Those differences are due to lineage specific mutations.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 197 of 1034 (692255)
03-01-2013 12:31 PM
Reply to: Message 195 by Faith
03-01-2013 11:40 AM


Re: Mutations Don't Add Anything That Could Rescue the ToE
According to my model on the other hand, I would say that the odds favor its having been latent in the gene pool and then brought to expression in a combination that's rare for that gene pool through mere sexual recombination.
How is your model supported by the evidence?
What is best known is the mutations that cause genetic diseases.
Of course, because they are easy to find. This is a confirmation bias. We spend billions of dollars studying genetic diseases, but only a tiny bit of money finding mutations that are currently occuring that produce beneficial adaptations.
More to the point, can you show that the mutations that have occurred in humans over the last 100 years are all detrimental or neutral? We are talking about billions of mutations, and I doubt that you have checked them all.
Often deleterious ones.
Are the phenotypic differences between chimps and humans beneficial to both chimps and humans?
Are those differences in phenotypes due to differences in DNA sequence?
The conclusion seems obvious to me. Changes in DNA sequence can and do result in beneficial phenotypes. Mutations are observed to change DNA sequence.

This message is a reply to:
 Message 195 by Faith, posted 03-01-2013 11:40 AM Faith has replied

Replies to this message:
 Message 215 by Faith, posted 03-01-2013 5:52 PM Taq has replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 204 of 1034 (692270)
03-01-2013 2:30 PM
Reply to: Message 203 by Faith
03-01-2013 2:19 PM


Re: Mutations Don't Add Anything That Could Rescue the ToE
My model, which you doubt I possess, but anyway, my model says that you get reduced GENETIC diversity with the formation of new phenotypes.
The current human population is around 7 billion. It was around 4 billion when I was a kid. So let's say that the last generation had 3 billion kids. We also know that each human is born with between 50 and 100 mutations specific to them.
So that is 200 to 400 billion mutations in just one generation of humans. How is this not an increase in genetic diversity?

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 Message 203 by Faith, posted 03-01-2013 2:19 PM Faith has replied

Replies to this message:
 Message 206 by Faith, posted 03-01-2013 2:40 PM Taq has replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 208 of 1034 (692278)
03-01-2013 2:56 PM
Reply to: Message 206 by Faith
03-01-2013 2:40 PM


Re: Mutations Don't Add Anything That Could Rescue the ToE
If you KNOW they are mutations and not just normal variations thrown up by sexual recombination then it would be enormous truly novel diversity,
We do know this. We have sequenced the genomes of parents and their children. The children have mutations in their genome that are not found in either parent.
quote:
Here we present, to our knowledge, the first direct comparative analysis of male and female germline mutation rates from the complete genome sequences of two parent-offspring trios. Through extensive validation, we identified 49 and 35 germline de novo mutations (DNMs) in two trio offspring, as well as 1,586 non-germline DNMs arising either somatically or in the cell lines from which the DNA was derived. Most strikingly, in one family, we observed that 92% of germline DNMs were from the paternal germline, whereas, in contrast, in the other family, 64% of DNMs were from the maternal germline.
http://www.nature.com/...f/ng.862.pdf%3FWT.ec_id%3DNG-201107
quote:
We analyzed the whole genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors, and identify very rare SNVs. We also directly estimated a human intergeneration mutation rate of ∼1.110-8 per position per haploid genome.
Analysis of Genetic Inheritance in a Family Quartet by Whole Genome Sequencing - PMC
There is no reason to think that these families are the exception. There is every expectation that every child is born with mutations. So yes, we do know that these numbers are about right. In the very large current human population we are getting hundreds of billions of mutations per generation that did not exist in the generation before them. Every person is born with a human genome that has never existed before in the history of the universe (excluding identical twins, of course).

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 Message 206 by Faith, posted 03-01-2013 2:40 PM Faith has replied

Replies to this message:
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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 209 of 1034 (692279)
03-01-2013 3:03 PM
Reply to: Message 207 by Faith
03-01-2013 2:48 PM


Re: Mutations Don't Add Anything That Could Rescue the ToE
I know that the production of a new trait is phenotypic change in an individual, but I've been using the idea of phenotypic change in relation only to whole populations.
Then you have been using it wrong. What you are looking at for the population is a change in how common one allele is compared to another. The phenotypic change has already occurred. It is a question of how common this mutation becomes in the population over time.
So again, in order for a new population to get a new phenotype that characterizes all its members so that it can be called a new breed or variety or species or subspecies that trait has to be selected and worked through an entire reproductively isolated population by inbreeding for some number of generations.
The change was already present in the population before selection even got started. It got there by mutation. Selection can only eliminate or spread a phenotypic change through the population.
If the new trait occurs only in the individual and is not selected it may stay in the population and be passed on to other individuals but it will not contribute to the formation of new species.
So you are saying that if a mutation is selected for it can lead to a new species?

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 223 of 1034 (692319)
03-01-2013 7:45 PM
Reply to: Message 215 by Faith
03-01-2013 5:52 PM


Re: Mutations Don't Add Anything That Could Rescue the ToE
Of course not, it's part of my model as your interpretations are of yours. My model IS internally consistent.
What is part of your model? Could you be specific?
Are beneficial mutations part of your model?
Also, I could care less if your model is internally consistent. What we are curious about is if it is consistent with the facts. The facts are that each person is born with 50 or so mutations. In a population of billions that is hundreds of billions of mutations in every generation. How does this NOT create genetic diversity?
Huh?
Chimps and humans are different. In those places where we are different, are those differences beneficial to each species? For example, a chimp has a much more robust wrist compared to humans. This allows the chimp to hang from branches and knuckle walk. In humans, the wrist is less robust and much more flexible. This allows us to use tools and have fine motor control in our hands.
Are these differences beneficial to each species? I would say yes.
Changes in DNA sequence include changes from simple sexual recombination of alleles, not necessarily and not even predominantly from mutations.
Are there combinations of chimp genes that can produce a human? I would say no. The only explanation is a change in sequence due to mutations in the alleles, not different combinations of alleles.
And it's really disingenuous of you to imply that all change in DNA sequence is beneficial when that's what is in question. Mutations change DNA sequence, the question is to what effect.
I never said that all mutations are beneficial. Nowhere did I say that. However, it is really disingenuous of you to imply that no change in DNA can be beneficial when obviously they can as a comparison of the human and chimp genomes illustrates. We can find the DNA that they share through common ancestry, and then find the mutations that have occurred in each lineage. We can also find the signal of negative selection in genes by comparing the rate of non-synonymous to synonymous mutations. We can see that deleterious mutations have been selected out of each lineage as they evolved.
The dishonesty of your model is that it ignores the reality of mutations. It is inconsistent with reality. In reality, mutations increase genetic diversity.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 224 of 1034 (692320)
03-01-2013 7:53 PM
Reply to: Message 218 by Faith
03-01-2013 6:24 PM


Re: Mutations Don't Add Anything That Could Rescue the ToE
Even if you maintain a fairly high level of genetic diversity in a particular population, nevertheless the production of a new subspecies REQUIRES reduced genetic diversity to whatever extent RELATIVE to the former population.
After the strong selection event or population bottleneck the non-stop accumulation of mutations increases genetic diversity over time. Not only that, but different mutations will accumulate in different subpopulations adding to the overall diversity of the clade.
And that's ALL you have, those imaginary beneficial mutations.
There is your bias again. We already know that these beneficial mutations exist. A comparison of the human and chimp genome shows us that these beneficial mutations exist.

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 Message 218 by Faith, posted 03-01-2013 6:24 PM Faith has not replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(2)
Message 297 of 1034 (692532)
03-04-2013 2:06 PM
Reply to: Message 247 by Faith
03-02-2013 11:17 AM


Re: Mutations Don't Add Anything That Could Rescue the ToE
AS AN EXAMPLE OF HOW NATURE MAKES HOMOGENEOUS POPULATIONS OR SUBSPECIES WITH THEIR OWN CHARACTERISTICS. Which could not occur if mutations kept cropping to interfere.
At one time, there were no grizzly bears, so your example is a really poor one. At one time there were no bears period, and at a time even further back there were no mammals to speak of. Obviously, mutations do crop up and cause species to change.
Even more, we have cited peer reviewed papers where whole genomes of families have been sequenced in order to find the mutations, and they were there. We have cited dominant Mendelian traits in cats that are obvious mutations, and yet you still close your eyes and ears.
What do we need to do to convince you to accept the facts of mutation?

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 Message 247 by Faith, posted 03-02-2013 11:17 AM Faith has not replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 301 of 1034 (692545)
03-04-2013 6:26 PM
Reply to: Message 299 by nwr
03-04-2013 6:06 PM


Re: Faith is done with this thread ???
I think this blog post O O O That Evo ha looshinist Mizrabul Buh-loosyist Cantwinferlosinist Ra-ag
can be taken to indicate withdrawal of Faith from further participation.
And not one mention of mutations anywhere in the blog post. Go figure.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 382 of 1034 (727760)
05-20-2014 1:23 PM
Reply to: Message 377 by Faith
05-20-2014 10:53 AM


Re: No 'new functions'
Oh mutation happens all right, but what YOU can't prove is that it produces the changes you claim it does.
How could mutations not produce these changes?
Why do you think that humans and chimps are different? It is because their DNA is different, right?
Edited by Taq, : No reason given.

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 Message 377 by Faith, posted 05-20-2014 10:53 AM Faith has not replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 392 of 1034 (757730)
05-12-2015 6:55 PM
Reply to: Message 385 by Faith
05-11-2015 7:16 PM


Re: No 'new functions'
Sorry, I don't accept anything about bacterial genetics (your E. coli example) as applying in this discussion. You have to use examples from sexually reproducing creatures.
Why does that matter?
Besides, you won't address evidence from sexually reproducing creatures either. All you do is make up these fantasies, and pretend that your made up fantasies trump real evidence.
Here is something really simple that you can address that I have asked before. Why do you think chimps and humans look different? Isn't it due to the differences in their genomes?

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 Message 385 by Faith, posted 05-11-2015 7:16 PM Faith has not replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 492 of 1034 (758040)
05-18-2015 9:22 PM
Reply to: Message 481 by herebedragons
05-18-2015 3:31 PM


Re: Moderator Introduced Definitions
"Junk DNA" was a very unfortunate term coined in the early days of genetic sequencing when it was thought that DNA --> Protein was the major player. It is now known that it is not anywhere near that simplistic. We now suspect that the majority of "non-coding" sequences actually have a function.
Junk DNA is a perfect term. It is disposable DNA. It is DNA we can throw out.
We now suspect that less than 10% of the human genome has selectable function. The problem is that the ENCODE group tried to make their data look more important than it was by conflating function with "does something". Those aren't the same thing. This is where it all comes full circle. The trash in your kitchen trash can does something. It releases odor molecules into the air in your kitche. It is still trash, even though it does something. What it doesn't do is perform a function that is important to your kitchen. Junk DNA is like the boxes of old stuff we have jammed in our garage that we have accumulated over the years but no longer have a use for.
In fact, some species have chucked a majority of their junk DNA. In the case of the bladderwort, it is probably due to the lack of phosphates in the environment.
"Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. "
Architecture and evolution of a minute plant genome | Nature
82 million bases, that's it. And it has a genome with the normal number of genes for a plant. The onion, for comparison, has a 100 billion base genome. Billion, with a B.
In the end, I think junk DNA is a perfect term.
I suspect that most evolutionary change is due to regulatory changes rather than changes in protein coding sequences.
Those are not mutually exclusive. Changes in the protein coding sequence of a regulator protein can change the expression of other genes.

This message is a reply to:
 Message 481 by herebedragons, posted 05-18-2015 3:31 PM herebedragons has replied

Replies to this message:
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