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Author Topic:   Molecular Population Genetics and Diversity through Mutation
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 318 of 455 (785921)
06-13-2016 2:08 PM
Reply to: Message 317 by herebedragons
06-13-2016 1:11 PM


Re: Mutations are not alleles
There is no excuse whatever for your straw man versions of my argument, and Dr. A's are even worse. NN does the same, but then he does it on every subject imaginable.
The Wikipedia article concerned ONLY disease processes, why is that? You'd think such an article would make an attempt to be inclusive of all the forms but no it only mentions three diseases. ONE mention of a normal variant in the fur color illustrated by the mice in the picture.
My reaction was quite honest to that article.
Defining a disease allele as an allele is what is dishonest even if every geneticist does it. All it proves is that the ToE has a stranglehold on you all.
Here is a link to a couple of pages discussion the ABNORMALITIES connected with Runx-2. You asked, I'm answering:
Runx2 Targeted Allele Detail MGI Mouse (MGI:3043791)
Perhaps you can show that other versions do not produce abnormalities?
craniofacial
abnormal cranium morphology
large anterior fontanelle
absent occipital bone
absent zygomatic arch
abnormal hyoid bone morphology
abnormal nasal bone morphology
growth/size/body
decreased birth body size
decreased birth weight
limbs/digits/tail
abnormal phalanx morphology
abnormal tibia morphology
mortality/aging
postnatal lethality, incomplete penetrance
premature death
skeleton
Edited by Faith, : No reason given.

This message is a reply to:
 Message 317 by herebedragons, posted 06-13-2016 1:11 PM herebedragons has replied

Replies to this message:
 Message 319 by Dr Adequate, posted 06-13-2016 2:24 PM Faith has replied
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 Message 336 by herebedragons, posted 06-13-2016 11:06 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


(1)
Message 327 of 455 (785941)
06-13-2016 3:38 PM
Reply to: Message 324 by Taq
06-13-2016 3:09 PM


Re: Mutations are not alleles
Now, would you define this as a loss in genetic diversity?
That would be an increase in genetic diversity.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 324 by Taq, posted 06-13-2016 3:09 PM Taq has replied

Replies to this message:
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Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 328 of 455 (785947)
06-13-2016 4:11 PM
Reply to: Message 319 by Dr Adequate
06-13-2016 2:24 PM


Re: Mutations are not alleles
THe point, which you have clearly managed to overlook or intentionally garble, is that the adjectives are not used, while the word "allele" is used alone to designate every sequence found at a gene locus no matter what its origin.

This message is a reply to:
 Message 319 by Dr Adequate, posted 06-13-2016 2:24 PM Dr Adequate has replied

Replies to this message:
 Message 333 by Dr Adequate, posted 06-13-2016 5:23 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 329 of 455 (785948)
06-13-2016 4:12 PM
Reply to: Message 325 by Dr Adequate
06-13-2016 3:14 PM


Re: Mutations are not alleles
Oh, that's easy. In the Faith Theory Of Evolution And Not Reading Good, the only bit that counts is the bit highlighted in red, which is a loss of genetic diversity. The other stuff is irrelevant, as is the fact that genetic diversity has increased.
Perfect misrepresentation of my argument.

This message is a reply to:
 Message 325 by Dr Adequate, posted 06-13-2016 3:14 PM Dr Adequate has replied

Replies to this message:
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Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 330 of 455 (785949)
06-13-2016 4:16 PM
Reply to: Message 323 by Taq
06-13-2016 3:04 PM


Re: Mutations are not alleles
I don't get the point of your example. I also don't doubt that mutations can make all kinds of changes, why not? They're just mistakes that seem to occur more or less willy-nilly, with some apparent preference for certain locations for some reason. But why would I doubt that sequences could not be changed by a single base or any other chunk?

This message is a reply to:
 Message 323 by Taq, posted 06-13-2016 3:04 PM Taq has replied

Replies to this message:
 Message 332 by Taq, posted 06-13-2016 5:15 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 339 of 455 (785977)
06-14-2016 4:35 AM
Reply to: Message 337 by NoNukes
06-13-2016 11:25 PM


Re: Bad alleles are not really alleles...?
Yes Dr A has been egregiously misinterpreting my argument and that's a case of it.
I made ONE error in my answer to something about genotypes that I backed down on. ONE. You have a habit of misinterpreting me in the most ridiculous ways it's tiresome having to keep correcting you. Except for the one about genotype, there are no contradictions in your quotes of me, it's all in your own head. I've explained my argument and all its parts so many times if you don't get it by now, there is no hope you'll ever get it. Or Dr. A or HBD or any of the rest who keep getting it wrong.
If it's that hard to understand what I think of as a very simple argument -- rather counterintuitive but simple -- I don't see any point in trying to correct it any more. I've repeated the argument dozens of times, maybe even hundreds by now. There must be some terminological problem I'm not recognizing, in which case I can't do anything about it until that is revealed, or it's just the usual blinded evos who won't stop to figure anything out if it goes against evolution. Perhaps both.

This message is a reply to:
 Message 337 by NoNukes, posted 06-13-2016 11:25 PM NoNukes has replied

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Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 340 of 455 (785978)
06-14-2016 4:48 AM
Reply to: Message 336 by herebedragons
06-13-2016 11:06 PM


Re: Mutations are not alleles
If it's called "Runx-2" why should it matter whether it's in mice or dogs? Shouldn't one expect it to do similar things?
Isn't one of your examples of it the changing craniofacial forms of dogs? You present it as normal but that gene is presented as creating abnormal craniofacial structures in mice. Why should those be abnormal but the dogs' be normal?
Isn't one of your examples from the head of a bulldog? Are you aware that the face of that dog, as well as its general body build, are detrimental to the animal?
Here's a 2014 Scientific American article on problems with purebred dogs. It doesn't mention the Runx-2 gene but since bulldogs seem to be afflicted with the same abnormalities attributed to it in the article about mice, perhaps there's a connection.
In the 1850s, . . . the bulldog looked more like today’s pit bull terriersturdy, energetic and athletic with a more elongated muzzle. But by the early 20th century, when dog shows became popular, the bulldog had acquired squat, bandy legs and a large head with a flattened muzzle. This altered figure makes it nearly impossible for them to reproduce without assistance, and the facial changes cause severe breathing problems in a third of all bulldogs. Breeders frequently turn to artificial insemination because the female bulldog’s bone structure cannot support the male’s weight during mating. Most cannot give birth naturally either, because the puppies’ heads are too big for the birth canal.
Large head size and short legs are part of the written standard, so Serpell believes these standards would have forced the bulldog into extinction if breeders did not rely on artificial insemination. By essentially requiring judges to select animals that are the written standard, the club, in a way, signed the bulldog’s death warrant, Serpell says
Breathing problems, mating problems, birth problems. Are these products of your normal Runx-2 gene?
Edited by Faith, : No reason given.

This message is a reply to:
 Message 336 by herebedragons, posted 06-13-2016 11:06 PM herebedragons has replied

Replies to this message:
 Message 342 by Taq, posted 06-14-2016 10:52 AM Faith has replied
 Message 343 by herebedragons, posted 06-14-2016 2:39 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 345 of 455 (786008)
06-14-2016 4:42 PM
Reply to: Message 343 by herebedragons
06-14-2016 2:39 PM


Re: Mutations are not alleles
I don't have as much of a problem defining disease as you do. I can even say that human beings are weird enough to like some products of disease, as food, or pets for instance. That doesn't make them undiseased, it just means human beings are a weird lot. Ya know, it's just ToE definitions that you're talking about when you say it's hard to make a distinction between normality or health and abnormality or unhealth.
Did you just say that since bulldogs are selected for their unhealthy traits that makes it hard to call them unhealthy? After all it facilitates their survival through their reproductive advantage through human intervention. Ai yi yi HBD. That's because the ToE defines selection as the road to evolution, defines survival/reproductive success as the fruit of selection. Parasites that harm the health of many animals and human beings are of course highly selected, highly reproductively successful, but I'm not going to call them good no matter what Evo Madness says about them. By definition nothing that is selected can be unhealthy or abnormal. But the ToE is basically a crackpot worldview, it shouldn't be allowed to dictate such things but it's that sort of irrationality we creationists are up against.
I was hoping it was the runx-2 gene that was responsible for the bulldog's unhealthy condition, meaning a mutation thereof, but apparently it was simple human selection.
I've forgotten your original question. Didn't you say the Runx-2 is a mutation? Isn't that what I was supposed to be answering? So the mouse experiment was doing a mutation to a mutation?
I'm coming to the conclusion that even where a mutation produces something at least superficially beneficial, all that's happened is that it's a mutation to a particular locus that makes a product that it would be hard to corrupt. Such as fur color. What could it do but change the color? Or kill the allele I guess, which is one common thing mutations seem to do. "Benign" mutations that don't change what the gene codes for seem to me to be benign because the allele under attack is flexible enough to resist change to the product. It's hard to imagine a deleterious form of a fur color gene in other words, one that produces a disease of fur color. Do you know of any?
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 343 by herebedragons, posted 06-14-2016 2:39 PM herebedragons has replied

Replies to this message:
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 Message 349 by herebedragons, posted 06-14-2016 6:11 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 346 of 455 (786009)
06-14-2016 5:04 PM
Reply to: Message 342 by Taq
06-14-2016 10:52 AM


Re: Mutations are not alleles
I've never said a thing about the rightness or wrongness of what breeders do, at least not as part of my argument about the processes involved. These I claim are the same processes that occur in the wild because the source of selection doesn't matter in regard to the processes involved.
Yes of course the sequence is what the allele DOES. I'm assuming Runx-2 is identified by its sequence. There are some variations in sequence that don't appear to change what it codes for of course.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 342 by Taq, posted 06-14-2016 10:52 AM Taq has replied

Replies to this message:
 Message 351 by Taq, posted 06-14-2016 6:55 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 350 of 455 (786018)
06-14-2016 6:44 PM
Reply to: Message 349 by herebedragons
06-14-2016 6:11 PM


Re: Mutations are not alleles
The testiness, the irritability, the anger, even the hate, are getting to me. I need to take a LOOOOONG break from this atmosphere, but stup-idly just *have to* answer this or that. It's getting to the point that I couldn't care less what you say or anybody says. You make so little effort to make sense of my posts. Does it ever occur to you that you really might be enslaved to a false worldview?
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 349 by herebedragons, posted 06-14-2016 6:11 PM herebedragons has not replied

Replies to this message:
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Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 353 of 455 (786024)
06-14-2016 8:57 PM
Reply to: Message 351 by Taq
06-14-2016 6:55 PM


Re: Mutations are not alleles
You keep making the claim that breeders are selecting for specific traits. If they are selecting for a short snout, and a mutation in Runx-2 produces the trait they were looking for, wouldn't that be a beneficial mutation? If not, what would be in this situation?
Not if it does harm to the animal. I don't define "beneficial" by human aesthetics. And this has nothing to do with my argument about genetic diversity.
Also, this would produce the very thing you called an increase in genetic complexity.
Genetic diversity. Meaning the sum of the genetic possibilities available in the population for creating new varieties of phenotypes (which you think of as mutations and I think of as Created for the purpose of variation of the Kind).
[qs] Prior to the mutation in Runx-2, you had several populations of dogs that shared similar alleles. Let's call that allele "A". Along came this new mutation and produce allele B. In the isolated bulldog population, this mutation was selected for and replaced the A allele.
Before
not bulldogs= allele A
bulldogs= allele A
After mutation and selection
not bulldogs= allele A
bulldogs= allele B
How is that not an increase in genetic complexity?
Genetic diversity, not complexity.
And I answered you that it is an increase in genetic diversity.
DNA sequence is not a verb. Sequence isn't something that a gene does. Sequence is what a gene is.
To try to be clearer then, the point is that it is the sequence that DETERMINES what the gene does. Yes? The protein it codes for and the phenotypic expression of that coding.
We are also talking about mutations in the Runx-2 gene that change the phenotype. You keep claiming that mutations can't produce changes in phenotype, yet here we have one.
Something is very unclear here too. I don't say mutations "can't produce changes in the phenotype," I just don't think they have much to do with that process in the normal run of things,
When I'm talking about the production of phenotypes I'm talking specifically about how that process reduces genetic diversity. I'm not focused on how the pool of genetic diversity originated from which the new population developed, but when mutations get into the picture I do acknowledge that of course they WOULD contribute to that diversity if they really do what you all say they do. I have acknowledged that much as a hypothetical situation I don't know how many times.
THEN I go on to my point which is how the isolated new population with its new gene frequencies (which may or may not include mutations although you would claim they are all mutations, but it doesn't matter for the sake of the argument at this point what they are -- they are whatever makes up the gene pool which is composed of a new set of gene frequencies in relation to the parent population -- at this point in the argument I don't consider it important whether they are mutations or not, because the point I'm trying to make is that this new gene pool brings out new phenotypes that didn't exist in the parent population, and they are brought out due to the recombination of the new set of gene frequencies.
This would happen whether those new gene frequencies were mutations or built in. I have TRIED to say this a million times. I try to allow mutations for the sake of argument just to get the point across that it makes no difference to my argument what they are, but since I believe mutations really don't contribute anything beneficial to the organism I have to bring in the other alternative at the same time.
I'm focused on the reduction of genetic diversity through the mere reduction in numbers of individuals that founded the new population, which works best in reproductive isolation. I'm claiming that recombination of existing alleles alone produces the new phenotypes, you don't need mutations and for the most part depending on when they occur they interfere with the formation of the new species or breed anyway.
And yes I know a breed is not a species, but insofar as it is a new population with a different phenotypic presentation from other populations, and was formed by isolation of a smallish number of individuals from those other populations, it demonstrates the same process.
I don't CARE if Runx-2 is one of the few mutations that doesn't do anything overtly deleterious.
I'm actually trying to stop arguing about this because after saying it over and over for years nobody gets it anyway. Believe what you want, evolution is a lie but I'm tired of the whole debate.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 351 by Taq, posted 06-14-2016 6:55 PM Taq has replied

Replies to this message:
 Message 354 by Dr Adequate, posted 06-14-2016 9:06 PM Faith has replied
 Message 393 by Taq, posted 06-17-2016 12:47 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 355 of 455 (786026)
06-14-2016 9:14 PM
Reply to: Message 354 by Dr Adequate
06-14-2016 9:06 PM


Re: Mutations are not alleles
Aren't you supposed to be a genius? You are certainly obtuse for a genius. The mutations don't count because they would only function as normal alleles anyway, which I'm arguing have to be reduced in the formation of a new species or breed. It's the reduction of the genetic material, whether that material is made up of mutations or built-in alleles, that is the point. Mutations can not change the fact that to get a new species REQUIRES reduction of genetic diversity. You have to LOSE them to get a new species or breed, you HAVE to, Adding anything at this point is redundant or destructive.
But I know I'm talking to a box of rocks. This has been explained at least a hundred times and you continue to have your obtuse silly straw man you made up yourself without ever getting for half a second what I'm talking about. Then you have the gall to call me names.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 354 by Dr Adequate, posted 06-14-2016 9:06 PM Dr Adequate has replied

Replies to this message:
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 Message 360 by Dr Adequate, posted 06-14-2016 9:59 PM Faith has replied
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Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 357 of 455 (786028)
06-14-2016 9:43 PM
Reply to: Message 352 by Tangle
06-14-2016 7:20 PM


Re: Mutations are not alleles
Does it ever occur to you that you really might be enslaved to a false worldview?
Sure. Or at least it did when I was a Christian - but I grew out of that at about 14.
My conversion from "Christian" to atheist occurred at age 15 under the tutelage of atheist friends and a charmingly funny and brilliant atheist propagandist math teacher. Something over thirty years later I learned that Christianity is a lot more than what I barely absorbed in church as a child anyway.
I accepted science because it was taught in school and I trusted school to teach me stuff.
So did I.
It also taught me religion which was a bit confusing because when it said I could make potassium tri-iodide (a really cool explosive) by mixing ammonia with iodine I could test it myself, but when it said I was going to hell for wanking, it felt like a wanker had made it up and I couldn't test it.
School taught me no religion, and the religion I got in church didn't include any knowledge of salvation and didn't stick for long when I encountered atheists. I don't remember being told anything about hell or about evolution in church, it seemed to be the atheists who cared about all that.
It turns out that everything religions say that can be tested is in error but when science says something it can be tested and if it's wrong it gets fixed. So on the balance of probabilities I go with science and rationality in the knowledge that the bits that are wrong will be corrected.
Of course if there are areas of reality that aren't subject to scientific testing because they have nothing to do with the physical world but another realm of reality altogether, and you've arbitrarily rejected them for simply being a different kind of reality, that's pretty irrational of you isn't it?
Your problem is that for what you believe to be true - the earth is 6,000 years old, there was a global flood and evolution didn't happen - you have to throw away 200 years of science in practically all of it's disciplines from biology, physics, geology, palaeontology, astronomy and even mathematics.
That's not a problem if science has gone off the rails, and it went way off with Hutton and Lyell and Darwin for starters. I have to throw away everything that has to do with presumptuously declaring as fact mere hypotheses about what in true fact cannot be observed or tested, events in the remote past, and unfortunately there's a lot of that irrational nonsense in those sciences. But despite that there's also objective reality in all of them that I consider to be true science. Remove the evolutionary hypothesis from all of them and they'd be a lot better able to do their work as sciences.
And you, Faith, personally, with no education or training in any of these disciplines have to invent substitutes for millions upon millions of scientific papers on the fly. No wonder you get stressed.
I inhabit an entirely different paradigm than the one that corrupts the minds that write those papers, so that whatever is true in them is always being subsumed under a Big Fat Lie that skews it all beyond any real scientific usefulness. The science in them would stand without the lie, but that would require some intricate epistemological surgery.
Anyway, there's no excuse in any of that for the attitude creationists have to put up with here. I've often given as good as I get but I've been knocking myself out to avoid metaphorically punching you all in the teeth for weeks now. God loves you all so I have to learn how to no matter what you throw at me, even when it's really too much to take.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : correct spelling

This message is a reply to:
 Message 352 by Tangle, posted 06-14-2016 7:20 PM Tangle has replied

Replies to this message:
 Message 371 by Tangle, posted 06-15-2016 3:40 AM Faith has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 359 of 455 (786030)
06-14-2016 9:56 PM
Reply to: Message 358 by Dr Adequate
06-14-2016 9:49 PM


Re: Mutations are not alleles
You are seriously delusional if you think you understand anything of what I've been arguing.

This message is a reply to:
 Message 358 by Dr Adequate, posted 06-14-2016 9:49 PM Dr Adequate has replied

Replies to this message:
 Message 362 by Dr Adequate, posted 06-14-2016 10:05 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 361 of 455 (786032)
06-14-2016 10:00 PM
Reply to: Message 360 by Dr Adequate
06-14-2016 9:59 PM


Re: Mutations are not alleles
You are seriously delusional if you think your little formula is any kind of answer to what I've been arguing.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 360 by Dr Adequate, posted 06-14-2016 9:59 PM Dr Adequate has replied

Replies to this message:
 Message 363 by Dr Adequate, posted 06-14-2016 10:07 PM Faith has replied

  
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