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Author | Topic: Rebuttal To Creationists - "Since We Can't Directly Observe Evolution..." | |||||||||||||||||||||||||||||||||||||||
Taq Member Posts: 10072 Joined: Member Rating: 5.2
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And 54.5 is not the correct value to use in your equation. Just because the number of mutations that occur in a replication is 54.5 doesn't mean that all 54.5 are fixed. The mutation rate in the equation is the number of mutations per person per generation.
quote: If the number of new mutations in the population is 2 times the population size then the mutation rate has to be number of mutations per person. Also, the last sentence explicitly states that the rate of fixation is simply the rate of the introduction of such mutations. Across a whole genome that would be 50 mutations. Added in edit: We can also calculate the per nucleotide fixation rate if you want. That would end up being the per nucleotide mutation rate which is 1.1E-8 per nucleotide. At a fixation rate of 1.1E-8 per nucleotide how many fixed mutations would that be across the entire human diploid genome?Edited by Taq, .
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Kleinman Member (Idle past 361 days) Posts: 2142 From: United States Joined: |
quote:You should watch this video, the derivation of your calculation begins at about the 6:00 minute mark. https://www.youtube.com/watch?v=l2Y8oC6G1us&ab_channel=Kr... You are using a definition of mutation rate based on the entire size of the genome. 2N is the total number of alleles at a given locus and 1/2N is the initial frequency of the first mutation in that allele. The neutral mutation rate being used is just for that genetic locus. If that locus has only a single base, then the neutral mutation rate will be 1.1x10-8. If that genetic locus has 1000 bases, the neutral mutation rate will be about 1.1x10-5 (actually lower if you compute the probability of a mutation occurring at least one site when multiple possible sites are considered). The number of generations to fixation for a single neutral mutation case is about 90,000 generations. Edited by Kleinman, : Correct math
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Taq Member Posts: 10072 Joined: Member Rating: 5.2 |
Kleinman writes:
You are using a definition of mutation rate based on the entire size of the genome. 2N is the total number of alleles at a given locus and 1/2N is the initial frequency of the first mutation in that allele. The neutral mutation rate being used is just for that genetic locus. If that locus has only a single base, then the neutral mutation rate will be 1.1x10-8. If that genetic locus has 1000 bases, the neutral mutation rate will be about 1.1x10-5 (actually lower if you compute the probability of a mutation occurring at least one site when multiple possible sites are considered). The number of generations to fixation for a single neutral mutation case is about 90,000 generations.
Great, let's find the per nucleotide fixation rate. Since 2N cancels out in the equation for fixation we are left with the per nucleotide mutation rate. If the fixation rate is 1.1E-8 fixed mutations per nucleotide per generation then the number of fixed mutations in a full human genome is (6E9)*(1.1E-8) which is 66 fixed mutations per generation.
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Kleinman Member (Idle past 361 days) Posts: 2142 From: United States Joined: |
Kleinman:You are making another mathematical blunder here. 1/2N is the initial frequency of the mutant allele. Only a tiny fraction of the genome has mutations. What is the initial frequency for your calculation? It certainly isn't 1/2N. This model only makes sense when considering a single genetic locus because the entire length of the genome and the total number of genetic loci in that genome does not affect the calculation. Not all the mutations in an entire genome are fixed. In fact, some mutations are lost over generations. Perhaps you think that the entire genome is fixed? You should watch the entire video. It gives a very sensible explanation of the equation you are trying to use. You cannot use the entire genome length to compute the mutation rate and do this calculation correctly. It must be done based on the mutations/locus. Mutation rate - Wikipedia quote:I put the boldfacing on the correct definition for mutation rate to be used for this calculation. 90,000 generations/fixation, Haldane's estimate of only 300 generations/fixation but that's with selection. So, when are you going to learn how to do the mathematics of adaptive DNA evolution and give a correct description of the Kishony and Lenski experiments? Don't you think a microbiologist should know how to do that math?
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Taq Member Posts: 10072 Joined: Member Rating: 5.2
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Kleinman writes:
You are making another mathematical blunder here. 1/2N is the initial frequency of the mutant allele. Only a tiny fraction of the genome has mutations.
1/2N is the fraction of the population that has the mutation when the mutation first occurs. That's what that means.
This model only makes sense when considering a single genetic locus because the entire length of the genome and the total number of genetic loci in that genome does not affect the calculation. The equation applies equally to every neutral mutation in the genome.
Not all the mutations in an entire genome are fixed. In fact, some mutations are lost over generations. Perhaps you think that the entire genome is fixed? I know all of this. If you think I am saying all mutations are fixed then you don't understand what the equation is saying. In a steady population of 100,000 and a mutation rate of 50 mutations per individual you will have 5 million mutations per generation, 50 of which will reach fixation if all 5 million mutations are neutral.
You cannot use the entire genome length to compute the mutation rate and do this calculation correctly. It must be done based on the mutations/locus. Neutral mutations don't have to be in genes in order to reach fixation. That's just silly. Do you really think all of the sequence outside of genes never mutates? The rate of fixation can be calculated for the whole genome, and there is no reason why it can't be. You seem to be hung up on the idea that alleles are only single chunks of sequence within genes. That simply isn't true. An allele can be any base that differs between two organisms within a population, and that's inside or outside of coding regions or genes.
90,000 generations/fixation, Haldane's estimate of only 300 generations/fixation but that's with selection. The size of the effective population numbers I have seen for populations in the human lineage usually don't go above 10,000 which would require 40,000 generations for a neutral mutation to fix. At 25 years per generation, that would be 1 million years. This means the mutations reaching fixation first entered the genome 1 million years before they fix. This would also mean that the initial population that first split off from the chimp branch would be fixing neutral mutations that first appeared 1 million years before the split. Still, in each generation you will still be fixing a number of neutral mutations that is close to the per genome mutation rate. For beneficial mutations, this only puts a 300 generation delay on fixation. If there are 5 beneficial mutations in generation 1 then they reach fixation at generation 301. Beneficial mutations that happen in generation 2 reach fixation in generation 302. Beneficial mutations that happen in generation 3 reach fixation in generation 303. See a pattern? It's not as if all mutations stop until the first mutation reaches fixation. Every generation has mutations which start their march towards extinction or fixation starting at that generation.
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Kleinman Member (Idle past 361 days) Posts: 2142 From: United States Joined: |
Kleinman:Why are you doing this to yourself? 1/2N is the frequency of the mutant allele. For a diploid population, there are 2N copies of the allele at the particular genetic locus. One of those 2N copies is the first mutant allele. Only 1 member of that population has that mutant allele. The fraction of the population with a mutant allele initially is 1/N. Kleinman:It applies to any mutant allele but only for a single genetic locus. Kleinman:You don't understand this equation. You have even confused the number of copies of alleles with population size. There are 2N copies of an allele in a diploid population size N. And if you somehow want to extrapolate this model to the entire genome means that the entire genome is being fixed. ringo, if you are reading this post, this is GIGO. Kleinman:If you want to do the math for a mutation not in a coding portion of the genome, then the number of bases in that sequence is one and the mutation rate you need to use is 1.1x10-8. That's about 9,000,000 generations to fixation. Post a link to a paper or biology lecture where they do a neutral mutation fixation calculation the way you want to do it. You are just blowing smoke. Nobody does the calculation the way you want because it is nonsense. Kleinman:Fixations aren't adaptation you should understand this by now from the results of the Lenski experiment. Large numbers of replications are what is required for DNA adaptive evolution. Certainly, small populations can have mutations fix more rapidly than large populations. You get all the mutations your parents have plus a few new ones for your own. Populations do exhaustive searches of all possible mutations in order to get just one member with an adaptive mutation. That's why it takes a billion replications for each adaptive mutation in the Kishony and Lenski experiments for a mutation rate of 1e-9. The reason is that "at least one" calculation applies to every site in the genome. The reason why humans have much larger populations than chimps is that humans can do farming on an industrial scale. It is clear that humans had this capability 10,000 years ago. They understood how to irrigate and use animals for labor. You have a population of about 1 billion population with 2 billion chromosome sets replications and use your mutation rate of 1.1x10-8. That doesn't give you many genome replications to work with for adaptive evolution to operate, even if you want to include recombination. Taq:Taq, the math gets orders of magnitude worse if it takes 2 or more mutations to give an improvement in fitness. It introduces another instance of the multiplication rule for each selection condition the population must adapt to. That's really bad for your belief in universal common descent but really good for the fields of medicine and agriculture. It gives a successful treatment of HIV and inhibition of the evolution of herbicide-resistant weeds and pesticide-resistant insects. I don't know if you are ready for that math yet but if you or any other readers of this thread are interested, you can find that paper here: The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance Don't worry Percy, I'll post equations and quotes in my next few posts if Taq is finished with his neutral fixation model.
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Taq Member Posts: 10072 Joined: Member Rating: 5.2 |
Kleinman writes:
1/2N is the frequency of the mutant allele.
Yes. That is true for every mutation throughout the genome, not just in genes.
It applies to any mutant allele but only for a single genetic locus. It applies to all bases in the genome.
You don't understand this equation. You have even confused the number of copies of alleles with population size. There are 2N copies of an allele in a diploid population size N. And if you somehow want to extrapolate this model to the entire genome means that the entire genome is being fixed. Please learn what chromosomes are, what cross-overs are, and how meiosis works. The entire genome is not passed on as a unit. Recombination happens within a chromosome. The copies of different chromosomes are passed on independently of each other. Just as mutations in genes are evolving independently, so too are the mutations outside of genes. In a population of 100,000 and a mutation rate of 50 mutations per genome per generation you will get 5 million mutations. The equation for neutral fixation states that 50 of those mutations will reach fixation if all 5 million mutations are neutral.
If you want to do the math for a mutation not in a coding portion of the genome, then the number of bases in that sequence is one and the mutation rate you need to use is 1.1x10-8. Coding portions of the genome make up just 1-2%. Sorry, but there is more than one base outside of coding regions. In fact, there are billions. You also never put any units on your 1.1E10-8 figure. Why is that? Is it because it is the per base mutation rate across the entire genome? When they measured the mutation rate in humans do you think they only looked at coding regions?
That's about 9,000,000 generations to fixation.
Mutations don't fix one at a time. They fix in parallel.
ou have a population of about 1 billion population with 2 billion chromosome sets replications and use your mutation rate of 1.1x10-8. 1 billion births with 1.1E-8 mutations per nucleotide per birth in a 6 billion base diploid genome is 1E9*1.1E-8*6E9 = 66 billion mutations. In a 6 billion base genome there are 18 billion possible SNP's. 1 billion births is more than enough to get every possible non-lethal mutation kicking around on the globe somewhere if all mutations are equally probable.
That's about 9,000,000 generations to fixation.
Mutations fix in parallel, not sequentially.
hat's why it takes a billion replications for each adaptive mutation in the Kishony and Lenski experiments for a mutation rate of 1e-9. Again, where are the units on your mutation rate?
Taq, the math gets orders of magnitude worse if it takes 2 or more mutations to give an improvement in fitness. It introduces another instance of the multiplication rule for each selection condition the population must adapt to. For such a claim you would first need to calculate all of the possible combinations of 2 mutations that would be beneficial. If there are billions and billions of possible beneficial combinations then they wouldn't be hard to find.
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Theodoric Member Posts: 9197 From: Northwest, WI, USA Joined: Member Rating: 3.2
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Kind of funny when cranks and trolls think they a smarter than everyone else. You gave him the rope, he hung himself but he is still going. When I am shown I have no idea what I am talking about I shut up and slink away. Not this guy.
What can be asserted without evidence can also be dismissed without evidence. -Christopher Hitchens Facts don't lie or have an agenda. Facts are just facts "God did it" is not an argument. It is an excuse for intellectual laziness. If your viewpoint has merits and facts to back it up why would you have to lie?
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Kleinman Member (Idle past 361 days) Posts: 2142 From: United States Joined: |
Kleinman:You are having trouble doing undergraduate lower division work so I don't know whether I should give you this paper but why not? THE AVERAGE NUMBER OF GENERATIONS UNTIL FIXATION OF A MUTANT GENE IN A FINITE POPULATION Kimura carries out the computation of the fixation of a mutant gene. His calculation doesn't depend on the mutation rate. quote:Now the effective population size can be slightly smaller than the actual population size under certain circumstances that I'm sure you know what they are. Remind me again what the population size you use is. Wasn't it 100,000? That gives the generations to fixation of that mutant gene of 4*100,000=400,000 generations. That really helps. Your lower division equation gave an estimate of 900,000 generations for the fixation of a neutral mutation. How many generations since the divergence of humans and chimps from the common ancestor? Kleinman:You still haven't figured out that different combinations of adaptive mutations give different lineages on different evolutionary trajectories. That math is way over your head. You should stick to trying to figure out an undergraduate lower division equation of neutral fixation.
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AZPaul3 Member Posts: 8549 From: Phoenix Joined: Member Rating: 4.9
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Taq has his fish and he's playing with it.
Stop Tzar Vladimir the Condemned!
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Kleinman Member (Idle past 361 days) Posts: 2142 From: United States Joined: |
AZPaul3:Taq likes to tell fish stories. Did you hear the one about the one-armed fisherman? He was telling his friend about one of the fish he caught. He held up his arm and said, "It was that long"!
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AZPaul3 Member Posts: 8549 From: Phoenix Joined: Member Rating: 4.9
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Sounds a lot like the math you use.
Stop Tzar Vladimir the Condemned!
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Kleinman Member (Idle past 361 days) Posts: 2142 From: United States Joined: |
AZPaul3:AZPaul3 will now explain the physics and mathematics of the Kishony and Lenski biological evolutionary experiments. He won't because unlike the one-armed fisherman, AZPaul3 doesn't have a leg to stand on.
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Percy Member Posts: 22490 From: New Hampshire Joined: Member Rating: 5.0 |
Kleinman writes: Percy:I already have but I'll do it again. There was no equation in what followed. Please present the Haldane equation you're talking about, then convert it to Joules. Using math equations. --Percy
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Percy Member Posts: 22490 From: New Hampshire Joined: Member Rating: 5.0 |
Kleinman writes: You will have to forgive me if I have difficulty distinguishing mockery from a serious argument when carrying on a discussion with people that think that blizzards turn lizards into buzzards with gizzards. It might help if you ceased placing a higher priority on being obnoxious than on constructive discussion. --Percy
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