Molecular Population Genetics and Diversity through Mutation

Then which step are you saying that evolution can't do? Barrier to gene flow? Mutation? Selection?

You keep insisting that you can't change the human genome by one base without it causing all this harm, and yet there are chimps with 40 million changes and they are doing just fine. How do you explain that?You claim that mutations can't produce the differences seen between species, so I am asking you to prove it. Those are the differences between humans and chimps. Please show how mutations couldn't produce those differences.Edited by Taq, : No reason given.

Yes they are. For example, if I want to say that an allele is deleterious, I use the adjective "deleterious". If I want to say that an allele is beneficial, I use the adjective "beneficial". Yes. This is how nouns work. In the same way, though we can speak of "a red boat" or "a blue boat", the word "boats" is used alone to designate every boat.This is how the English language works, Faith.Edited by Dr Adequate, : No reason given.

If that is not in fact your argument, then all the words you have spent on expounding that point of view would seem to have been wasted.

You're not going to get Faith to compare chimps and humans. To her, humans were a special creation separate from the creation of ape kind.Do we have comparisons between apes such as chimps, bonobos, gorillas, etc. Since they are ape kind, their ancestor should have carried the ape super genes that all apes are derived from.

If by "stranglehold" you mean that we understand that disease alleles are... alleles, since they actually are alleles. If you are trying to say that we think that "disease alleles" increase diversity and lead to evolutionary progress, well then, that is YOUR strawman representation of what we have been saying.Again, the example I gave you of Runx-2 has no "disease alleles" and you couldn't point to one of them that was... or did you?? LOL. That doesn't address my question at all. Do you know what that reference is for?First of all, it is for a mouse gene, not for a dog gene. This would be an example of a homolog, not a dog allele. I presented a paper on dog alleles.Second, it is a knockout mouse line. (Jargon: knockout means a genetic modification that deletes or otherwise inactivates a specific gene). This is not a natural mutation but a research tool.From the "Mutation description" section:

quote:

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Allele Type:Targeted (Null/knockout)

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Mutations: Insertion, Intragenic deletion

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Mutation details: The P1 promoter and exon 1 were replaced with a neo cassette via homologous recombination. This specifically deleted the Runx2-II isoform and not the Runx2-I isoform. Rt-PCR confirmed the absence of Runx2-II RNA and the presence of Runx2-I RNA.

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So... my question was NOT is there any kind of mutation that could occur in the gene that would cause disease, it was which of the dog alleles was diseased?HBD

A misrepresentation? Or is it your actual argument? I'll admit to making posts lampooning your arguments, but I think I get them right a higher percentage of the time than you might want to acknowledge. I'm not perfect of course,and of course you'll take any error as proof that folks don't understand you. So I try to be extra careful before I post here. Often, all I need to do to poke fun is to quote you without comment.Poking fun is easy because your own posts seem to include what you claim is straw manning of your argument.Examples below:Here is why Dr. Adequate and others might say the kind of things quoted above. or Here is why people repeatedly point out that species really are not homogeneous collections of people/animals/plants, often using things like dogs or even races of humans as an example. Finally, if you cannot keep points about your argument straight, what chance to we have:Here is you talking about whether species consists of distinct genotypes and accusing me of missing the point. You later confirming my point... Of course you've also since then backed off and reversed course on this particular point, and then pretended that your new position was of no consequence to your argument. As if.Edited by NoNukes, : No reason given.

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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.

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. Breathing problems, mating problems, birth problems. Are these products of your normal Runx-2 gene? Edited by Faith, : No reason given.

I did not claim that there were contradictions in your other quotes. I provided notes in each section explaining exactly why material was quoted. The first section showed where your own comments justified the summary Dr. Adequate provided. The second section illustrated your ridiculous statements that species were composed of homogeneous individuals, when observation of dogs and humans, no matter how sub divided, show that individuals clearly are not homogeneous. Yet being homogeneous is essential to your "mutations ruins the species" litany. At least it did until you basically bailed on your argument and went for the all allele mutations are disease path.The third section only shows contradictions involved both you claiming I misunderstood you, you later, and on more than one occasion demonstrating that I was correct, and then you finally changing your mind about all of that. It did not describe simply one mistake on the topic but a waffling back and forth. The result of your backing away afterwards is that you are left in the position of misinterpreting references about mutation to find at least some support for your ideas. Small wonder that the next few posts by others were full of ridicule.If you want to deny repeatedly made errors, how about if we just refer to your misstating of the theory of evolution in the face of repeated citings of references to the contrary. Yeah, we've noticed how you finally stopped pretending that the theory of evolution does not include variation after adamantly insisting otherwise.Edited by NoNukes, : No reason given.

Will it do the same thing no matter what the DNA sequence of the gene is? You seem to be veering away from your breeder's mentality. If the breeder wants a specific face type, wouldn't that be an example of a beneficial mutation?Edited by Taq, : No reason given.

Indeed it probably does regulate the same developmental pathway. BUT... we were not talking about mouse alleles, we were talking about dog alleles. Perhaps you lost track of the line of discussion, which would be understandable... Here is the basic outline of how I remember the discussion going:Faith: claimed that mutation can't add genetic diversity and if it did, it would mess up the breed.HBD: submitted an article describing the Runx-2 gene which has added diversity to the dog "kind" AND has not messed up the breed. In fact, breeders began selecting for the new alleles which changed the look of the breed over the yearsFaith: read an article on Wikipedia that she interpreted as saying ALL polymorphic alleles were disease allelesHBD: asked which of the dog alleles presented in the paper were "disease alleles"Faith: replied with an example of a genetically engineered mouse line where a portion of the Runx-2 gene was knocked out as evidence that all mutations cause "disease alleles":blink:You don't think mice and dogs are in the same kind do you? So why would you present mouse alleles as evidence in a discussion about diversity of dogs? Yes, Runx-2 is involved in the development of canio-facial features. Again, it is a transcription factor (Jargon: a transcription factor is a protein that binds to specific DNA sequences and regulates transcription)(Jargon: transcription is the conversion of DNA to messenger RNA - mRNA) and the mutations described in the paper affect the protein's binding affinity to it's target sequence and thus affects transcription rates. "That gene" is not presented as creating abnormalities, the specific mutation that the researchers put into the gene caused those abnormalities. They deleted an exon, the protein was severely damaged, possibly non-functional - it is called a "knockout mouse" (already explained this jargon term). Researchers uses this technology all the time, it helps identify the function of particular genes and how they interact with other genes.The dog alleles do NOT have the same mutation - not all mutations are created equal. The dog variations are in the microsatellites, the tandem repeats. The number and ratio of repeats varies and affects binding affinity and therefore transcription rates. There probably is a connection. If you look at the bulldog skull, it seems clear that the changes are related to the bulldogs breathing problems. Breeders selected for those traits, didn't they. Thus why breeding is referred to as ARTIFICIAL SELECTION. Traits that in the wild would be detrimental actually give the individuals greater reproductive success - which would mean that the traits in question, despite their seemingly harmful effects, have improved fitness - that is, individuals are selected FOR those traits.The conversation about "what is disease?" actually comes up quite frequently. While it seems as if it should be a straight-forward, easy definition, it turns out to be a bit elusive at times. For example, there is a fungus called Ustilago maydis that causes a "disease" called corn smut. pretty gross, huh? So it would clearly be a disease right? Well it turns out that this corn smut is also a delicacy in some parts. So... is it a disease or a delicacy? I guess it depends on who you ask. If you ask a farmer who is trying to sell corn, it is a disease. If you ask a corn smut canner, it is a delicacy.Same way with the bulldog. I have a friend who has bulldogs and she just loves them, thinks they are so cute. They drove like 200 miles to buy their dogs and paid like $1000 for them. They like the flattened nose. I bet you won't get them to say that their breed is "diseased" or malformed. It is exactly what they want in a breed.So your use of the word "normal" in this context is rather odd. What is "normal?" I guess you should say that only the original "kind" was normal and all other sub-species, breeds, or whatever are degraded somehow. But most people don't see it that way.So bottom line... different is not defective. Genetic diversity has increased in dogs. Humans selected traits they found appealing. Faith doesn't get to define normal when it comes to nature.HBD

This would not be the first instance, nor will it be the last one, in which breeders deliberately go for some specific traits and end up producing breeds with health issues. And not all, or even most of those compromised health results are the result of mutation. Yes there are lots of great dogs out there, but humans insist on, and get some pretty messed up dogs on purpose.If the idea is to blame the mutations for the dogs health, let's be clear that the breeders in this case selected for extreme cranial changes and got the result they wanted. They probably could have gone for a better health/shape mix.

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.