Do you really understand the mathematics of evolution?

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I thought you said they were modeling neutral evolution. That is drift, isn't it? And doesn't fixation occur with drift

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Fixation occurs within a population and populations are outside the scope of the model. It’s a model of DNA evolution, not population genetics.

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Now you really have me confused. These models as time proceeds go to a condition when "all four bases roughly equally represented". So, are you saying that the genomes in the distant relative were already at equilibrium? And, how can the site be fixed and have "all four bases roughly equally represented" at the same time?

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No, you’ve done that to yourself. I really don’t know how you make up this stuff. The equilibrium state is reached in the distant descendants who are divided amongst a number of populations. The base may be fixed in some populations but it is not fixed over all the populations combined.

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How do they tell when the genetic sequence they put into the model is fixed or at equilibrium?

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Why would they need to? That isn’t what these models are about.

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And if a base is fixed in a population, does it over time go to equilibrium and if a site is at equilibrium in a population does it go to fixation?

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For the purposes of this discussion that doesn’t matter at all. The models don’t deal with populations and don’t need to.

Population Genetics (Stanford Encyclopedia of Philosophy) Competition, drift, DNA evolution, recombination,... are all part of population genetics. You are very confused about this subject. I'm not confused about the subject of population genetics, I'm confused about your explanation of the subject. First, you claim that these Markov models are models of neutral evolution and now you are claiming something different. Don't you remember this exchange we had in Message 181? And now you are saying that in neutral evolution "The equilibrium state is reached in the distant descendants who are divided amongst a number of populations". And now you are saying "The base may be fixed in some populations but it is not fixed over all the populations combined." So, if you are going to try to apply any of these models to real genetic sequences, how do you know when the sequence you are using is from a fixed population or a population that has reached equilibrium? You would think the people who write these models are trying to predict something about population genetics. What do you think they are trying to predict with these Markov chain models? It does if you want to understand the subject of population genetics. Again, from the link I posted above:"Population geneticists pursue their goals by developing abstract mathematical models of gene frequency dynamics, trying to extract conclusions from those models about the likely patterns of genetic variation in actual populations, and testing the conclusions against empirical data."You are completely confused about this subject and have no idea how to apply these mathematical models to population genetics and probably to applying any other mathematical models to any other scientific discipline.

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Competition, drift, DNA evolution, recombination,... are all part of population genetics. You are very confused about this subject.

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If you think you can get population level information out of a model which doesn’t deal with the concept of populations at all, you are the one that is confused. Population genetics deals with the dynamics of evolution within populations, so that is obviously more appropriate,

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I'm not confused about the subject of population genetics, I'm confused about your explanation of the subject. First, you claim that these Markov models are models of neutral evolution and now you are claiming something different

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Oh dear, you are deeply confused. I‘m not claiming anything different at all. I’m just trying to interpret the probabilities produced by the models in terms of the genes we might find, taking into account simple facts like the fact that genes are inherited and that individual bases have a low mutation rate so that closely related individuals will tend to have very similar genes (especially in your favourite haploid populations)

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And now you are saying that in neutral evolution "The equilibrium state is reached in the distant descendants who are divided amongst a number of populations". And now you are saying "The base may be fixed in some populations but it is not fixed over all the populations combined." So, if you are going to try to apply any of these models to real genetic sequences, how do you know when the sequence you are using is from a fixed population or a population that has reached equilibrium?

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It don’t believe that it matters, not for the actual applications of the models. Why should it ? If you want to interpret the probabilities as frequencies among descendants, go ahead. But the model won’t give you the distribution. Even you should be able to see that.I guess I should leave the task of educating you to better teachers, with great patience (which you will no doubt sorely try).

I'm not the one who thinks you can do phylogenetic analysis with this model, especially when you think you tell how many generations separate two genetic sequences. Sure, I'm confused about your explanation, first, you say this model is about neutral evolution, but then you say it doesn't compute fixation, it's about the frequencies of bases being equally distributed and it happen long ago. What kind of information can you get out of this model? Can you put in a portion of your genome and a portion of the genome from a banana and tell how many generations back your most recent common ancestor is? You do a pretty good Professor Irwin Corey imitation.Anyone on this forum thinks they actually understand Markov chains and how to do DNA analysis with them?

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I'm not the one who thinks you can do phylogenetic analysis with this model, especially when you think you tell how many generations separate two genetic sequences.

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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.

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Sure, I'm confused about your explanation, first, you say this model is about neutral evolution, but then you say it doesn't compute fixation, it's about the frequencies of bases being equally distributed and it happen long ago. What kind of information can you get out of this model? Can you put in a portion of your genome and a portion of the genome from a banana and tell how many generations back your most recent common ancestor is?

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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.

My model explains how DNA evolution works and you could do the same with a Markov model if you understood how to write the correct transition matrix. What has your model done other than tell you that you are related to a banana? Sure, but you aren't going to do it by cherrypicking the genome for tiny homologous portions. In fact, you have to use the entire genome and account for all the differences. You can't even use the entire coding portion of the genome because even if the coding genes are similar between two species, it's the non-coding regulatory portion of the genome (what the fish evolve into mammals clique like to call junk DNA) is what makes creatures what they are and that's a much, much larger portion of the genome than the coding portion.Since you aren't going to explain how the Jukes-Cantor model is used (because you don't know how), here's a link which shows how the model is used:
Jukes Cantor Model of DNA substitution | Workshop in Applied Phylogenetics
In particular, from that page is a figure where they calculate the number of generations it takes to reach equilibrium for the one site model with a mutation rate of e-8: It only takes a mere 50 million generations to reach equilibrium. Do you want to explain that to us, Professor Corey?

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My model explains how DNA evolution works and you could do the same with a Markov model if you understood how to write the correct transition matrix.

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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.

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Sure, but you aren't going to do it by cherrypicking the genome for tiny homologous portions.

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Sure, the strawman you invented isn’t going to work.

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In fact, you have to use the entire genome and account for all the differences

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Statisticians would disagree. Proper sampling should be quite adequate.

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You can't even use the entire coding portion of the genome because even if the coding genes are similar between two species, it's the non-coding regulatory portion of the genome (what the fish evolve into mammals clique like to call junk DNA) is what makes creatures what they are and that's a much, much larger portion of the genome than the coding portion.

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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,

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It only takes a mere 50 million generations to reach equilibrium. Do you want to explain that to us, Professor Corey?

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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

I still am an engineer with an active state license in the profession and have taught the subject at the undergraduate and graduate university level. I also happen to be a licensed physician. And the Kishony and Lenski experiments are completely typical examples of DNA evolution in two different types of environments. The Kishony experiment is more typical of DNA evolution of bacterial drug-resistance in humans not because they happen to be using antibiotics as the selection pressures but because the carrying capacity of the human body for bacterial populations is much larger than that of the competitive low carrying capacity Lenski experiment. Engineers are trained to use mathematics to relate the variables in physical (and biological) systems. You don't have that kind of training and experience. That's why you are
so confused by these problems. You are a liar PaulK, this is exactly how the fish evolves into mammals clique uses these Markov models. That's why you won't present any real examples of how these models are used. With "proper" sampling we can show your parents were bananas. Why don't you present papers to us and explain how this "proper" sampling is done? That should be easy since you claim to understand this subject so well. Why don't you do the math?
Regulatory DNA sequences, human genome
Anything you don't understand, you in the fish evolve into mammals clique call junk. In your mathematically incompetent mind, 20-40% of the genome as regulatory is a small part of the genome while 1.5% of the genome that codes for proteins is a large part of the genome. And you dumb clucks think I have a mental problem. You really are delusional.Why don't you use some of your fish evolves into mammals logic and claim that there is no junk DNA because useless junk DNA is wasted energy for the replicator to carry around and natural selection would remove those variants from the population? 50,000,000 generations is 50,000,000 generations for any replicator. That's why the Kishony and Lenski experiments are totally typical examples of DNA evolution and these are examples of Markov chain DNA evolution, one site at a time. You should learn something about the subject.

I think that replying to this part is all that needs to be said:

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Kleinman writes:

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Sure, but you aren't going to do it by cherrypicking the genome for tiny homologous portions.

PaulK writes:

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Sure, the strawman you invented isn’t going to work.

You are a liar PaulK, this is exactly how the fish evolves into mammals clique uses these Markov models. That's why you won't present any real examples of how these models are used.

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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.

If there was a league of lazy dumb asses, you would be on the all-star team. So, if I have to present this evidence to you, I better find a link aimed at someone with your level of intellect. Oh, here's one from the Department of Genetics, Stanford School of Medicine, where they answer this question from a high school student.
How do scientists build phylogenetic trees? | The Tech Interactive And the answer is... You definitely don't want to pick any sour cherries. So, son of banana parents, that's how the cherry-picking should be done if you want to show that your parents are bananas.And you still don't have any idea how the math is done.

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If there was a league of lazy dumb asses, you would be on the all-star team

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I’d refuse to play in any team that had you as the captain.

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You definitely don't want to pick any sour cherries. So, son of banana parents, that's how the cherry-picking should be done if you want to show that your parents are bananas.

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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.

Well, you are the king, take that. Here's the contact information for the authors of the page, take it up with them:
The Tech Interactive
201 S. Market St.
San Jose, CA 95113
1-408-294-8324
I'm sure they are sitting by the phone right now waiting for a call from the king explaining how frameshift mutations have to be taken into account in their phylogenic analysis.

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Here's the contact information for the authors of the page, take it up with them:
The Tech Interactive
201 S. Market St.
San Jose, CA 95113
1-408-294-8324

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That’s the contact information for the publishers, not the author. Unlike you, I’m not too lazy to find out that much.

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I'm sure they are sitting by the phone right now waiting for a call from the king explaining how frameshift mutations have to be taken into account in their phylogenic analysis

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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.

Maybe the king can find the contact information by reading some fossil tea-leaves. The king will now explain how fish evolve into mammals with frameshift mutations. All bow to the king. Is this the best that the fish evolves to mammals clique has to offer? What really scares me is that I think PaulK actually was a biology teacher.

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Maybe the king can find the contact information by reading some fossil tea-leaves.

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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.

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The king will now explain how fish evolve into mammals with frameshift mutations.

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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.

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What really scares me is that I think PaulK actually was a biology teacher.

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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.