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Author Topic:   What have we accomplished?
Kleinman
Member (Idle past 336 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 106 of 263 (879112)
07-11-2020 4:21 PM
Reply to: Message 105 by PaulK
07-11-2020 2:48 PM


Re: Self Serving Beliefs
PaulK writes:
For the benefit of anyone actually interested in understanding the model. I’ll answer. But thanks for proving your incompetence.
The only thing you have proven is that you are a direct descendant from bananas. And I suggest you submit your work for publication, in Mad magazine.
Kleinman writes:
I've posted the links multiple times which explain the Jukes-Cantor model. Here's the one which explains how you derive the Jukes-Cantor model and that for a mutation rate of e-8, it takes 50,000,000 generations for just a single base in a single gene
PaulK writes:
Wrong. It takes 50,000,000 generations to get to the equilibrium state, which is not a single mutations. To quote from the article:
What a surprise, a fish-to-mammals aficionado thinks that DNA evolution is an equilibrium process. Just one more reason that shows you are a mathematically incompetent bungler.
Kleinman writes:
That is the probability of the particular mutation occurring as a function of the number of generations.
PaulK writes:
Wrong. That is the probability of a base being different from the original state, accounting for the fact that it could mutate back. And it applies to all bases, not just one.
Are you sure you want to do this PaulK. I mean you are making one mathematical blunder after another. The Juke-Cantor describes DNA evolution at just a single site, not to all bases.
Models of DNA evolution - Wikipedia
Wikipedia writes:
The models described on this page describe the evolution of a single site within a set of sequences.
Another blunder on your part.
Kleinman writes:
Actually, if you understood this math, you would understand that is wrong. It is not the number of generations that should be plotted but the number of replications.
PaulK writes:
No, it isn’t wrong in that either. If you understood the model you would know that,
Oh my, do you think the generation is the random trial for DNA evolution and not the replication? In your limited understanding of population genetics, do you think there are no instances where there are more than single offspring in a given generation? Another blunder on your part.
Kleinman writes:
That probability will be close to 1 at about 1e8 replication
PaulK writes:
No, the probability never rises above 0.75, as can be clearly seen if you look at the graph. See the quote from the article above.
That's because at equilibrium the probability that the base at that site will be different than the base was originally will be 0.75 and the probability the base will be the original base is 0.25. These are the two probability equations from that link:
P(A|A,,t)=1/4(1-e^{-8t})
and
P(different|A,,t)=3/4(1-e^{-8t})
That graph is a plot of the second probability curve. You are correct on this point (mark this day on your calendar). That curve approaches an asymptote of 0.75, not 1, and that is the equilibrium point for that site. Too bad that DNA evolution is not an equilibrium process. What that equilibrium point represents is the point where each possible substitution has occurred at least once at that site. Go back and read this paragraph from the link:
Floyd Reed writes:
By definition, the total probability of all possible outcomes must sum to one, something has to happen, even if it is nothing. So the probability of one or more events (at least one event) is one minus the probability that it did not mutate, which is the probability complement of P(0|\lambda) , which can be written as P(\neg0|\lambda) (the probability that there are not zero events given the expected number of events):
Kleinman writes:
But this model is only valid for an evolutionary process of one mutation at a time in a sequential evolutionary process
PaulK writes:
By which you mean that your assertions are only valid in such a case. But that is obviously not what Jukes-Cantor is modelling.
So, show us how to apply the Jukes-Cantor model to the Kishony experiment. You won't. I've shown you how to use that model to predict the Kishony experiment because when the Jukes-Cantor model reaches equilibrium, all it shows you is the number of replication necessary to reach that equilibrium and that number is simply 1/(mutation rate). But feel free to use this model to demonstrate how you are descended from bananas.
PaulK writes:
Failing to understand what the Jukes-Cantor model is actually modelling is bad enough. But the mathematical errors are also severe and fatal. Too bad you don’t understand the mathematics of Markov chains.
I'll wager I'll get a paper peer-reviewed and published on Markov chains and DNA evolution before you do. Why don't you write a paper using the Jukes-Cantor model showing that you are a direct descendent from bananas?

This message is a reply to:
 Message 105 by PaulK, posted 07-11-2020 2:48 PM PaulK has replied

Replies to this message:
 Message 107 by PaulK, posted 07-11-2020 4:58 PM Kleinman has replied

PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 107 of 263 (879118)
07-11-2020 4:58 PM
Reply to: Message 106 by Kleinman
07-11-2020 4:21 PM


Re: Self Serving Beliefs
quote:
What a surprise, a fish-to-mammals aficionado thinks that DNA evolution is an equilibrium process. Just one more reason that shows you are a mathematically incompetent bungler.
We are discussing the implications of the model which does reach an equilibrium. If you have to deviate from the model to make your point then you’re wrong.
And that would be true even if your objection had merit.
quote:
Are you sure you want to do this PaulK. I mean you are making one mathematical blunder after another. The Juke-Cantor describes DNA evolution at just a single site, not to all bases.
Models of DNA evolution - Wikipedia
Only if a blunder is being right when Kleinman is stupidly wrong. The mathematical model describes how a single site evolves - and it is applied to all sites. The idea that only one site can mutate while all the others cannot change is not part of the model and has no basis in biology.
quote:
Oh my, do you think the generation is the random trial for DNA evolution and not the replication? In your limited understanding of population genetics, do you think there are no instances where there are more than single offspring in a given generation? Another blunder on your part.
Of course I realise that there can be multiple offspring, but that really doesn’t affect the point. For instance the number of siblings your father had makes no difference to your DNA.
quote:
That's because at equilibrium the probability that the base at that site will be different than the base was originally will be 0.75 and the probability the base will be the original base is 0.25.
I’m glad I managed to set you right on this.
quote:
What that equilibrium point represents is the point where each possible substitution has occurred at least once at that site. Go back and read this paragraph from the link
What that equilibrium point represents is the point where the initial state has no influence on the final state, and that is rather important for understanding why 50,000,000 generations is the longest time the model could show. There is no way it could give a time of 500,000,000 generations as you claimed. Indeed, without other evidence you couldn’t conclude any relationship at all if the genomes had diverged so far.
quote:
So, show us how to apply the Jukes-Cantor model to the Kishony experiment. You won't
There would be ways to apply it, but certainly it should not be applied to the particular mutations that grant resistance because the model is not about selection at all. It could, however be applied to other changes in the DNA - which will occur (yes, even in the Kishony experiment there will be other mutations).
Your failure to understand what the model represents is your error, not a fault in the model.

This message is a reply to:
 Message 106 by Kleinman, posted 07-11-2020 4:21 PM Kleinman has replied

Replies to this message:
 Message 108 by Kleinman, posted 07-11-2020 5:33 PM PaulK has replied

Kleinman
Member (Idle past 336 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 108 of 263 (879119)
07-11-2020 5:33 PM
Reply to: Message 107 by PaulK
07-11-2020 4:58 PM


Re: Self Serving Beliefs
Kleinman writes:
What a surprise, a fish-to-mammals aficionado thinks that DNA evolution is an equilibrium process. Just one more reason that shows you are a mathematically incompetent bungler.
PaulK writes:
We are discussing the implications of the model which does reach an equilibrium. If you have to deviate from the model to make your point then you’re wrong.
And that would be true even if your objection had merit.
Go for it PaulK, show us how to use the Jukes-Cantor model and that you are a direct descendent to bananas.
quote:
Kleinman writes:
Are you sure you want to do this PaulK. I mean you are making one mathematical blunder after another. The Juke-Cantor describes DNA evolution at just a single site, not to all bases.
Models of DNA evolution - Wikipedia
PaulK writes:
Only if a blunder is being right when Kleinman is stupidly wrong. The mathematical model describes how a single site evolves - and it is applied to all sites. The idea that only one site can mutate while all the others cannot change is not part of the model and has no basis in biology.
Even to the non-homologous portions of the genome? So that's why you think you are a direct descendent to bananas.
Kleinman writes:
Oh my, do you think the generation is the random trial for DNA evolution and not the replication? In your limited understanding of population genetics, do you think there are no instances where there are more than single offspring in a given generation? Another blunder on your part.
PaulK writes:
Of course I realise that there can be multiple offspring, but that really doesn’t affect the point. For instance the number of siblings your father had makes no difference to your DNA.
Oh? So the Jukes-Cantor model only applies to a single individual? I'm beginning to believe that you are a direct descendant of bananas.
Kleinman writes:
That's because at equilibrium the probability that the base at that site will be different than the base was originally will be 0.75 and the probability the base will be the original base is 0.25.
PaulK writes:
I’m glad I managed to set you right on this.
Do you know how to solve the Jukes-Cantor model without assuming a Poisson distribution? I bet you don't.
Kleinman writes:
What that equilibrium point represents is the point where the initial state has no influence on the final state, and that is rather important for understanding why 50,000,000 generations is the longest time the model could show. There is no way it could give a time of 500,000,000 generations as you claimed. Indeed, without other evidence you couldn’t conclude any relationship at all if the genomes had diverged so far.
PaulK writes:
What that equilibrium point represents is the point where the initial state has no influence on the final state, and that is rather important for understanding why 50,000,000 generations is the longest time the model could show. There is no way it could give a time of 500,000,000 generations as you claimed. Indeed, without other evidence you couldn’t conclude any relationship at all if the genomes had diverged so far
This is really pathetic. Each state of a Markov chain process only depend on the previous state of the system, all other states have no effect.
Kleinman writes:
So, show us how to apply the Jukes-Cantor model to the Kishony experiment. You won't
PaulK writes:
There would be ways to apply it, but certainly it should not be applied to the particular mutations that grant resistance because the model is not about selection at all. It could, however be applied to other changes in the DNA - which will occur (yes, even in the Kishony experiment there will be other mutations).
Your failure to understand what the model represents is your error, not a fault in the model.
So when are you going to submit your paper for publication that shows that the Jukes-Cantor model says you are directly related to bananas?

This message is a reply to:
 Message 107 by PaulK, posted 07-11-2020 4:58 PM PaulK has replied

Replies to this message:
 Message 109 by PaulK, posted 07-12-2020 1:02 AM Kleinman has replied

PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 109 of 263 (879132)
07-12-2020 1:02 AM
Reply to: Message 108 by Kleinman
07-11-2020 5:33 PM


Re: Self Serving Beliefs
quote:
Only if a blunder is being right when Kleinman is stupidly wrong. The mathematical model describes how a single site evolves - and it is applied to all sites. The idea that only one site can mutate while all the others cannot change is not part of the model and has no basis in biology.
Even to the non-homologous portions of the genome?
The non-homologous parts - if there are any - are as free to mutateAs any other parts. What that has to do with the discussion I can’t say,
quote:
Oh? So the Jukes-Cantor model only applies to a single individual?
The Jukes-Cantor method is used to compare the genomes of individuals, as well as to consensus genomes constructed from multiple individuals.
In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material; a substantial sample of individuals of the target species or other taxon is used; however, many current studies are based on single individuals
Molecular Phylogentics
quote:
This is really pathetic. Each state of a Markov chain process only depend on the previous state of the system, all other states have no effect.
You can’t even get the maths right. Before the equilibrium state the probability that the base has not changed from the original is > 0.25. That is a bias in favour of the original state.
The rest of the consequences are also correct. You cannot derive any number of generations > 50,000,000 from the method, with the chosen parameter. And certainly not 500,000,000 however many changes there are in the genome.
That you claim otherwise is just your ignorance.

This message is a reply to:
 Message 108 by Kleinman, posted 07-11-2020 5:33 PM Kleinman has replied

Replies to this message:
 Message 110 by Kleinman, posted 07-12-2020 6:47 AM PaulK has replied

Kleinman
Member (Idle past 336 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 110 of 263 (879139)
07-12-2020 6:47 AM
Reply to: Message 109 by PaulK
07-12-2020 1:02 AM


Re: Self Serving Beliefs
PaulK writes:
Only if a blunder is being right when Kleinman is stupidly wrong. The mathematical model describes how a single site evolves - and it is applied to all sites. The idea that only one site can mutate while all the others cannot change is not part of the model and has no basis in biology.
Kleinman writes:
Even to the non-homologous portions of the genome?
PaulK writes:
The non-homologous parts - if there are any - are as free to mutateAs any other parts. What that has to do with the discussion I can’t say,
Nothing if you want to claim that you are related to bananas.

This message is a reply to:
 Message 109 by PaulK, posted 07-12-2020 1:02 AM PaulK has replied

Replies to this message:
 Message 111 by PaulK, posted 07-12-2020 2:08 PM Kleinman has replied

PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 111 of 263 (879149)
07-12-2020 2:08 PM
Reply to: Message 110 by Kleinman
07-12-2020 6:47 AM


Re: Self Serving Beliefs
So no substantive reply. What a surprise. Not.

This message is a reply to:
 Message 110 by Kleinman, posted 07-12-2020 6:47 AM Kleinman has replied

Replies to this message:
 Message 112 by Kleinman, posted 07-12-2020 5:09 PM PaulK has replied

Kleinman
Member (Idle past 336 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 112 of 263 (879184)
07-12-2020 5:09 PM
Reply to: Message 111 by PaulK
07-12-2020 2:08 PM


Re: Self Serving Beliefs
PaulK writes:
Only if a blunder is being right when Kleinman is stupidly wrong. The mathematical model describes how a single site evolves - and it is applied to all sites. The idea that only one site can mutate while all the others cannot change is not part of the model and has no basis in biology.
Kleinman writes:
Even to the non-homologous portions of the genome?
PaulK writes:
The non-homologous parts - if there are any - are as free to mutateAs any other parts. What that has to do with the discussion I can’t say,
Kleinman writes:
Nothing if you want to claim that you are related to bananas.
PaulK writes:
So no substantive reply. What a surprise. Not.
If you are dumb enough to believe that you can ignore the non-homologous portions of genomes to do DNA phylogenetics, that's the only reply you deserve. Go publish a paper showing you are a direct descendent of bananas.

This message is a reply to:
 Message 111 by PaulK, posted 07-12-2020 2:08 PM PaulK has replied

Replies to this message:
 Message 113 by jar, posted 07-12-2020 5:17 PM Kleinman has replied
 Message 114 by PaulK, posted 07-12-2020 5:23 PM Kleinman has replied
 Message 126 by ringo, posted 07-13-2020 12:33 PM Kleinman has replied

jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 113 of 263 (879185)
07-12-2020 5:17 PM
Reply to: Message 112 by Kleinman
07-12-2020 5:09 PM


Kleinman continues the dishonest we expect from him.
Kleinman writes:
Go publish a paper showing you are a direct descendent of bananas.
And so you continue to post utter nonsense and misrepresent all that folk have attempted to teach you.
That is classic Christian Cult of Ignorance behavior.

My Sister's Website: Rose Hill StudiosMy Website: My Website

This message is a reply to:
 Message 112 by Kleinman, posted 07-12-2020 5:09 PM Kleinman has replied

Replies to this message:
 Message 115 by Kleinman, posted 07-12-2020 5:41 PM jar has replied

PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 114 of 263 (879187)
07-12-2020 5:23 PM
Reply to: Message 112 by Kleinman
07-12-2020 5:09 PM


Re: Self Serving Beliefs
And still no substantive answer.

This message is a reply to:
 Message 112 by Kleinman, posted 07-12-2020 5:09 PM Kleinman has replied

Replies to this message:
 Message 116 by Kleinman, posted 07-12-2020 5:51 PM PaulK has replied

Kleinman
Member (Idle past 336 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 115 of 263 (879188)
07-12-2020 5:41 PM
Reply to: Message 113 by jar
07-12-2020 5:17 PM


Re: Kleinman continues the dishonest we expect from him.
Kleinman writes:
Go publish a paper showing you are a direct descendent of bananas.
jar writes:
And so you continue to post utter nonsense and misrepresent all that folk have attempted to teach you.
That is classic Christian Cult of ********* behavior.
Have you sobered up yet? All you have to do is cherry-pick the correct homologous gene from a banana, plug it into the Jukes-Cantor model, and voil, you have bananas in your family tree. Who knew that bananas grow on a tree?

This message is a reply to:
 Message 113 by jar, posted 07-12-2020 5:17 PM jar has replied

Replies to this message:
 Message 117 by jar, posted 07-12-2020 7:33 PM Kleinman has replied

Kleinman
Member (Idle past 336 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 116 of 263 (879190)
07-12-2020 5:51 PM
Reply to: Message 114 by PaulK
07-12-2020 5:23 PM


Re: Self Serving Beliefs
PaulK writes:
And still no substantive answer.
jar will help you on you bananas-to-humans family tree. And you aren't the only one who thinks he's a banana!
https://www.youtube.com/watch?v=hmmi7QB33qk

This message is a reply to:
 Message 114 by PaulK, posted 07-12-2020 5:23 PM PaulK has replied

Replies to this message:
 Message 124 by PaulK, posted 07-13-2020 12:32 AM Kleinman has replied

jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 117 of 263 (879195)
07-12-2020 7:33 PM
Reply to: Message 115 by Kleinman
07-12-2020 5:41 PM


Re: Kleinman continues the dishonesty we expect from him.
And yet again, all you can do is misrepresent what people have been trying to teach you.

My Sister's Website: Rose Hill StudiosMy Website: My Website

This message is a reply to:
 Message 115 by Kleinman, posted 07-12-2020 5:41 PM Kleinman has replied

Replies to this message:
 Message 119 by Kleinman, posted 07-12-2020 8:37 PM jar has not replied

Trump won 
Suspended Member (Idle past 1240 days)
Posts: 1928
Joined: 01-12-2004


Message 118 of 263 (879197)
07-12-2020 8:29 PM


ironically this dust-up with kleinman and the evolutionists underline my point exactly
not only does the casual not understand what the heck any of you are saying
you're literally vapidly chattering nonsense at each other
you've outjuked the juke's-cantor cantor and it's bananas
this site has become an absurdity
i guess it always was, but when i joined in 03 as a teen, i was more naive to the psychopathetic nature of the s@#$-libs and fringe creationists
Edited by a servant of Christ, : profanity
Edited by a servant of Christ, : No reason given.

Replies to this message:
 Message 120 by Kleinman, posted 07-12-2020 8:45 PM Trump won has replied

Kleinman
Member (Idle past 336 days)
Posts: 2142
From: United States
Joined: 10-06-2016


(1)
Message 119 of 263 (879199)
07-12-2020 8:37 PM
Reply to: Message 117 by jar
07-12-2020 7:33 PM


jar is going to explain to us how fish evolve into mammals
jar writes:
And yet again, all you can do is misrepresent what people have been trying to teach you.
Is jar going to teach us how fish evolve into mammals? jar, you need to lay off the juice. You are starting to suffer from the DTs.

This message is a reply to:
 Message 117 by jar, posted 07-12-2020 7:33 PM jar has not replied

Kleinman
Member (Idle past 336 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 120 of 263 (879201)
07-12-2020 8:45 PM
Reply to: Message 118 by Trump won
07-12-2020 8:29 PM


a servant of Christ writes:
ironically this dust-up with kleinman and the evolutionists underline my point exactly
not only does the casual not understand what the heck any of you are saying
you're literally vapidly chattering nonsense at each other
you've outjuked the juke's-cantor canter and it's bananas
this site has become an absurdity
i guess it always was, but when i joined in 03 as a teen, i was more naive to the psychopathetic nature of the s@#$-libs and fringe creationists
Very few creationists understand introductory probability theory either. Don't make the mistake that something you don't understand is absurd. It makes you sound like one of those fish-to-mammals aficionados.

This message is a reply to:
 Message 118 by Trump won, posted 07-12-2020 8:29 PM Trump won has replied

Replies to this message:
 Message 121 by Trump won, posted 07-12-2020 8:58 PM Kleinman has replied
 Message 122 by AZPaul3, posted 07-12-2020 9:58 PM Kleinman has not replied

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