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Author | Topic: Do you really understand the mathematics of evolution? | |||||||||||||||||||
PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: Since your preferred model would be worse for that, then your opinion doesn’t count for much. You can’t get a decent model unless you understand what you are modelling.
quote: Yes, you are indeed confused due to your failure to understand what you are talking about. With a sufficiently large portion of the genome - and with decent measures of the rate of change for those portions it should certainly be possible to come up with a rough estimate.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: You say that it does, but the basis of the claim is that it handles an extremely atypical case. You claim to have been an engineer so you must understand how wrong that is.
quote: Sure, the strawman you invented isn’t going to work.
quote: Statisticians would disagree. Proper sampling should be quite adequate.
quote: While there is more non-coding DNA than coding DNA the regulatory portion is only a small part of that. And I don’t like to call regulatory DNA junk. You do like making things up.Genuine junk - which excludes regulatory regions - is worth looking at because it is not under any selective constraint, quote: What’s to explain? 50,000,000 generations is a long time in most vertebrates. Since you have an interest in bird evolution the fact that most of the birds I am familiar with have only one generation a year would seem to be relevant
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
I think that replying to this part is all that needs to be said:
quote: You call me a liar but you don’t say anything that backs up your accusation. Show us evidence of actual cherry picking or admit that you haven’t got any.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: I’d refuse to play in any team that had you as the captain.
quote: The obvious problem with the quotes is that the sequences are picked before the alignment. So, the choice of sequences isn’t cherry picked. The alignment is constrained by that choice, and I doubt you’d get a good match by pure chance. Even with only two sequences. It seems to me that alignment is needed to handle insertions and deletions. If you just try matching bases to bases without taking that into account you’ll hit problems.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: That’s the contact information for the publishers, not the author. Unlike you, I’m not too lazy to find out that much.
quote: Since the author insists on alignment which does take account of frame shifting, they hardly need to be told. It’s only the guy who think that aligning the sequences that have already been chosen is cherry picking the sequence that needs telling. And I already told him. So chalk up yet another Kleinman blunder.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: I could, but I don’t need it. She didn’t support your claim of cherry-picking and that’s all that needs to be said.
quote: Poor Kleinman. He thinks that if we acknowledge that frameshift mutations - and indels that don’t shift the frame - we must assume that all evolutionary change is explained by frameshift mutations.
quote: Well there’s your imagination running away with you again. I’ve never claimed any qualifications in biology and I’ve never worked as a teacher.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: Oh, you have plenty of problems, but that’s not one on my list.
quote: Obviously you have to compare the same gene. Do you really think you can compare a gene taken from one species with a random chunk of DNA taken from another and get a decent phylogeny? You must be hoping that I am stupid enough to fall for these silly deceptions.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: No. According to the Jukes-Cantor calculation 3/4 of the bases should have changed in 50,000,000 generations. That’s going to be more than one. A lot more.
quote: Assuming that the genes were of roughly equal length it would mean that they agreed on the divergence time. Which would be well under. 50,000,000 generations. If you can handle the math, or even read the pages you cite you should know that much.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: I don’t claim any biology qualifications. But this is mathematics. And no, Jukes-Cantor won’t tell you which bases change as you ought to know.
quote: Wrong again. The divergence time is lower than your estimate because your estimate is hopelessly wrong. And since the divergence is based on the proportion of changed bases, it won’t change unless that proportion is changed.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: No sensible person would use only two sites. You couldn’t get a usable estimate that way.
quote: I said that they would agree on the divergence time. I.e. each considered individually would give about the same divergence time. I also said that the divergence time would be well under 50,000,000 generations because only a small proportion of the bases has changed. In 50,000,000 generations 0.75 of the bases would be changed according to Jukes-Cantor with the given parameters.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: Let’s start with some simpler math. When the Jukes-Cantor model reaches equilibrium, 3 quarters of the bases should have changed. If at that point only one base in the gene has changed, how many bases would you expect to be in the gene? And for a bonus biology question: could a gene be that length?
quote: Well let’s try some more simple mathematics. If one base in a gene 10,000 bases long has changed what proportion of bases has changed ? If you have two genes, each 10,000 bases long and one base in each has changed, what proportion of bases has changed? Are the two proportions different ?
quote: Because you aren’t just counting the sites that have changed, you’re also counting all the sites that haven’t. Which comes to a lot more than just two.
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PaulK Member Posts: 17827 Joined: Member Rating: 2.3 |
quote: Feel free to calculate the probability of that happening. 0.75^n where n is the number of bases.
quote: I’m sure you know that you claimed that only one base would change in a gene in 50,000,000 generations. So the expected length of the gene would be 1/0.75 bases. Let’s generously round up and say two. Not exactly plausible is it? And of course, if you really understood the mathematics you would know that already. So obviously you are either a fraud or a troll. And either way you need help.
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