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Author Topic:   Do you really understand the mathematics of evolution?
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 106 of 239 (877489)
06-16-2020 6:49 PM
Reply to: Message 105 by Kleinman
06-16-2020 6:18 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
If it takes 2 (and they don't need to be simultaneous) mutations to improve fitness, the number of replications goes into the trillions for there to be a reasonable probability of that happening.
Let's see your math.
There is no such thing as a detrimental (fatal) mutation unless there is competition?
Correct. It seems you are starting to catch on.
What happens if there is a mutation that causes the failure of some vital metabolic pathway?
That would only happen in a model where there is competition. In a model free from competition there would be no lethal mutations.
The first law of thermodynamics pertains to energy. DNA evolution is a second law of thermodynamics process.
The second law of thermodynamics also pertains to energy. It doesn't pertain to DNA evolution. Just because they use some of the same concepts does not make them the same thing.
Obviously you are ignoring the links I've given you to Markov chain DNA evolution models and Markov chain entropy.
You seem to be under the impression that Markov chain entropy is the same as thermodynamic entropy. It isn't.
I have done the math and it has been peer-reviewed and published and is also in the National Library of Medicine.
Great, then discuss it here. GET TO THE POINT!!

This message is a reply to:
 Message 105 by Kleinman, posted 06-16-2020 6:18 PM Kleinman has replied

Replies to this message:
 Message 107 by Kleinman, posted 06-16-2020 8:13 PM Taq has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 107 of 239 (877496)
06-16-2020 8:13 PM
Reply to: Message 106 by Taq
06-16-2020 6:49 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
The empirical evidence starts with the Kishony and Lenski experiments.
Taq writes:
Ok. Keep going.
Kleinman writes:
Genetic information has to be measured in the context of the environment. So, consider the Kishony experiment. What mutations give increased information (fitness) for that environment? And what is the rate of accumulation of that information? That is your Markov chain calculation. And if you know how to do that calculation, you will understand how DNA evolution works and how it relates to genetic information.
Taq writes:
Then how does DNA evolution work and how does it relate to genetic information? Spit it out.
I'll say it again and as many times as necessary for you to get it. DNA evolution is a Markov Chain process. From the way you are posting, it appears you have no idea what a Markov Chain process is. Here's a simple introductory video to learn how you do a Markov Chain calculation. This is part 1, it wouldn't hurt for you to watch all three parts.
Entropy (energy dispersal) - Wikipedia
Kleinman writes:
Obviously you are ignoring the links I've given you to Markov chain DNA evolution models and Markov chain entropy.
Taq writes:
You seem to be under the impression that Markov chain entropy is the same as thermodynamic entropy. It isn't.
Why don't you tell us all what that difference is. And make sure you show your math.
Kleinman writes:
I have done the math and it has been peer-reviewed and published and is also in the National Library of Medicine.
Taq writes:
Great, then discuss it here. GET TO THE POINT!!
How many times do you want me to post the links to the papers?
So, here's a link to the paper for the mathematics of DNA evolution to a single selection pressure:
Just a moment...
Here's the link to the paper for the mathematics of DNA evolution to multiple simultaneous selection pressures:
Just a moment...
Here's a link to the paper on the mathematics of random recombination:
Just a moment...
Sorry, that paper is behind a paywall.
Here's the paper which explains the mathematics of the Lenski experiment:
Just a moment...
Have fun learning how DNA evolution works.

This message is a reply to:
 Message 106 by Taq, posted 06-16-2020 6:49 PM Taq has replied

Replies to this message:
 Message 108 by Taq, posted 06-17-2020 12:02 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 108 of 239 (877524)
06-17-2020 12:02 PM
Reply to: Message 107 by Kleinman
06-16-2020 8:13 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
I'll say it again and as many times as necessary for you to get it. DNA evolution is a Markov Chain process.
I already knew that. Is that your grand point? This has been common knowledge for a while. Here is an excerpt from TalkOrigins:
quote:
As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as "groups within groups", otherwise known as a nested hierarchy. The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. Common descent is a genetic process in which the state of the present generation/individual is dependent only upon genetic changes that have occurred since the most recent ancestral population/individual. Therefore, gradual evolution from common ancestors must conform to the mathematics of Markov processes and Markov chains. Using Markovian mathematics, it can be rigorously proven that branching Markovian replicating systems produce nested hierarchies (Givnish and Sytsma 1997; Harris 1989; Norris 1997). For these reasons, biologists routinely use branching Markov chains to effectively model evolutionary processes, including complex genetic processes, the temporal distributions of surnames in populations (Galton and Watson 1874), and the behavior of pathogens in epidemics.
29+ Evidences for Macroevolution: Part 1
Why don't you tell us all what that difference is.
Thermodynamics deals with energy. A Markov chain model of DNA evolution does not.
How many times do you want me to post the links to the papers?
I want you to discuss them.
What point are you trying to make, and how do those papers relate to that point?
Edited by Taq, : No reason given.

This message is a reply to:
 Message 107 by Kleinman, posted 06-16-2020 8:13 PM Kleinman has replied

Replies to this message:
 Message 109 by Kleinman, posted 06-17-2020 12:39 PM Taq has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 109 of 239 (877526)
06-17-2020 12:39 PM
Reply to: Message 108 by Taq
06-17-2020 12:02 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
I'll say it again and as many times as necessary for you to get it. DNA evolution is a Markov Chain process.
Taq writes:
I already knew that. Is that your grand point? This has been common knowledge for a while. Here is an excerpt from TalkOrigins:
As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as "groups within groups", otherwise known as a nested hierarchy. The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. Common descent is a genetic process in which the state of the present generation/individual is dependent only upon genetic changes that have occurred since the most recent ancestral population/individual. Therefore, gradual evolution from common ancestors must conform to the mathematics of Markov processes and Markov chains. Using Markovian mathematics, it can be rigorously proven that branching Markovian replicating systems produce nested hierarchies (Givnish and Sytsma 1997; Harris 1989; Norris 1997). For these reasons, biologists routinely use branching Markov chains to effectively model evolutionary processes, including complex genetic processes, the temporal distributions of surnames in populations (Galton and Watson 1874), and the behavior of pathogens in epidemics.
29+ Evidences for Macroevolution: Part 1
Their application of Markov Chain mathematics is incorrect. The rate of evolution they are calculating is based on a stationary transition matrix which assumes the evolutionary process goes to equilibrium. Try to apply their mathematics to the Kishony or Lenski experiment (or for that matter, any other real empirical example of DNA evolution). The correct Markov mathematics to predict DNA evolution requires a non-stationary transition matrix. And I highly doubt you know how to do that math.
Kleinman writes:
Why don't you tell us all what that difference is.
Taq writes:
Thermodynamics deals with energy. A Markov chain model of DNA evolution does not.
I get it. Your understanding of thermodynamics doesn't go any further than the first law. There is also a second law of thermodynamics and Markov chains are an example.
Kleinman writes:
How many times do you want me to post the links to the papers?
Taq writes:
I want you to discuss them.
What point are you trying to make, and how do those papers relate to that point?
I am discussing my papers and I'm showing you how to correctly apply mathematics to DNA evolution. And the point I'm trying to make is that your link to 29+ Evidences for Macroevolution is based on an incorrect application of the mathematics. Do you think that the Kishony and Lenski experiments go to equilibrium? Because that's what the authors in your link are assuming.

This message is a reply to:
 Message 108 by Taq, posted 06-17-2020 12:02 PM Taq has replied

Replies to this message:
 Message 110 by Taq, posted 06-17-2020 1:17 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 110 of 239 (877529)
06-17-2020 1:17 PM
Reply to: Message 109 by Kleinman
06-17-2020 12:39 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
Try to apply their mathematics to the Kishony or Lenski experiment (or for that matter, any other real empirical example of DNA evolution).
Could you show us how to properly use mathematics to model human evolution using actual sequences?
Your understanding of thermodynamics doesn't go any further than the first law.
Thermo = temperature
dynamics = movement
All the laws of thermodynamics involve energy. It's right there in the name.
And the point I'm trying to make is that your link to 29+ Evidences for Macroevolution is based on an incorrect application of the mathematics.
Ok. They use an incorrect model. Now what?

This message is a reply to:
 Message 109 by Kleinman, posted 06-17-2020 12:39 PM Kleinman has replied

Replies to this message:
 Message 111 by Kleinman, posted 06-17-2020 1:55 PM Taq has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 111 of 239 (877531)
06-17-2020 1:55 PM
Reply to: Message 110 by Taq
06-17-2020 1:17 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
Try to apply their mathematics to the Kishony or Lenski experiment (or for that matter, any other real empirical example of DNA evolution).
Taq writes:
Could you show us how to properly use mathematics to model human evolution using actual sequences?
Sure! DNA evolution doesn't work any different for humans as it does for any other replicator. Identify a selection pressure, a mutation rate and you can predict the number of generations necessary for that genetic transformation to occur. But note, only about 1e11 people have live in our entire history. That doesn't give many beneficial mutations to work with when it takes 3e9 replications for each of those mutations.
Kleinman writes:
Your understanding of thermodynamics doesn't go any further than the first law.
Taq writes:
Thermo = temperature
dynamics = movement
All the laws of thermodynamics involve energy. It's right there in the name.
The second law explains how energy is dispersed. If you are going to relate this to DNA evolution, it takes energy to replicate, replication is the random trial for a beneficial mutation, only those lineages which replicate sufficiently have a reasonable probability of increasing their information to the environmental selection conditions.
Kleinman writes:
And the point I'm trying to make is that your link to 29+ Evidences for Macroevolution is based on an incorrect application of the mathematics.
Taq writes:
Ok. They use an incorrect model. Now what?
Correct the model and explain DNA evolution correctly.

This message is a reply to:
 Message 110 by Taq, posted 06-17-2020 1:17 PM Taq has replied

Replies to this message:
 Message 112 by Taq, posted 06-17-2020 3:07 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 112 of 239 (877532)
06-17-2020 3:07 PM
Reply to: Message 111 by Kleinman
06-17-2020 1:55 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
But note, only about 1e11 people have live in our entire history. That doesn't give many beneficial mutations to work with when it takes 3e9 replications for each of those mutations.
Let's do some back of the envelope calculations. The human mutation rate is about 50 point mutations per person per generation. Let's be conservative and use a 25 year generation time, a constant 100,000 person population, and 5 million years since diverging from chimps. That would be 5 million mutations per generation spread across the entire population. In 5 million years we would have 200,000 generations. 5 million mutations per generation over 200,000 generations is 1E12 mutations that have happened over the history of human evolution.
So how many point mutations separate humans and chimps? 35 million. Let's say half of those mutations occurred in each lineage, so 17.5 million mutations in the human lineage. This means that we needed to keep just 0.00175% of the total mutations that did happen.
Does that math seem right to you?
If you are going to relate this to DNA evolution, it takes energy to replicate, replication is the random trial for a beneficial mutation, only those lineages which replicate sufficiently have a reasonable probability of increasing their information to the environmental selection conditions.
The energy needed to replicate DNA is a function of its length, not its sequence.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 111 by Kleinman, posted 06-17-2020 1:55 PM Kleinman has replied

Replies to this message:
 Message 113 by Kleinman, posted 06-17-2020 3:41 PM Taq has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 113 of 239 (877533)
06-17-2020 3:41 PM
Reply to: Message 112 by Taq
06-17-2020 3:07 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
But note, only about 1e11 people have live in our entire history. That doesn't give many beneficial mutations to work with when it takes 3e9 replications for each of those mutations.
Taq writes:
Let's do some back of the envelope calculations. The human mutation rate is about 50 point mutations per person per generation. Let's be conservative and use a 25 year generation time, a constant 100,000 person population, and 5 million years since diverging from chimps. That would be 5 million mutations per generation spread across the entire population. In 5 million years we would have 200,000 generations. 5 million mutations per generation over 200,000 generations is 1E12 mutations that have happened over the history of human evolution.
So how many point mutations separate humans and chimps? 35 million. Let's say half of those mutations occurred in each lineage, so 17.5 million mutations in the human lineage. This means that we needed to keep just 0.00175% of the total mutations that did happen.
Does that math seem right to you?
That math works ok if all you want to do is compute mutational divergence. But that has virtually nothing to do with DNA evolution. To put that into the context of the Kishony experiment, in the 3e9 replications, you have about 14 million mutations which represent the divergence from the wild-type. Only a tiny fraction of those mutations give improved fitness. When you are talking about adaptation, you have to get a specific set of mutations into a particular lineage. Try doing the same math for the Lenski experiment. The vast majority of mutations occurring in those lineages do not give improved fitness to those variants that get those mutations.
Kleinman writes:
If you are going to relate this to DNA evolution, it takes energy to replicate, replication is the random trial for a beneficial mutation, only those lineages which replicate sufficiently have a reasonable probability of increasing their information to the environmental selection conditions.
Taq writes:
The energy needed to replicate DNA is a function of its length, not its sequence.
That is a minuscule amount of the energy needed to replicate. The member that replicates needs the energy to grow and mature before it ever expends the much smaller amount of energy necessary to duplicate the DNA molecule. Think of it in terms of the Lenski experiment. A bacterium is about to replicate. When it does, the resulting fission of the single bacterium into 2 bacteria each with about half the mass of the parent cell. Those 2 bacteria need to grow to full size before able to replicate again. That's where most of the energy (glucose) is going to in that experiment.

This message is a reply to:
 Message 112 by Taq, posted 06-17-2020 3:07 PM Taq has replied

Replies to this message:
 Message 114 by Taq, posted 06-17-2020 6:19 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 114 of 239 (877544)
06-17-2020 6:19 PM
Reply to: Message 113 by Kleinman
06-17-2020 3:41 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
That math works ok if all you want to do is compute mutational divergence. But that has virtually nothing to do with DNA evolution.
You are changing your tune. This is what you said before:
But note, only about 1e11 people have live in our entire history. That doesn't give many beneficial mutations to work with when it takes 3e9 replications for each of those mutations.
That's wrong. As shown above, there were about 1E12 mutations that happened in the human lineage after it split from the chimp lineage. The human haploid genome is only 3E9 bases long. That's enough mutations to change each base 300 times over. Your numbers are way off.
Let's look at it a different way. There are 3E9 bases in the human haploid genome, so we would need 9E9 point mutations to get all possible substitutions. At 50 mutations per person, that would be 180 million births to get all mutations. Right now, there are 130 million births each year. It would take less than two years for the current population to get all of those mutations, assuming the chances of all mutations is equal.
Try doing the same math for the Lenski experiment.
I am starting to get the feeling that the only things that exist in your universe is the Lenski and Kishony experiments.
That is a minuscule amount of the energy needed to replicate.
The energy difference between two DNA sequences is even less. So why do you keep trying to relate DNA sequence to thermodynamics?
Edited by Taq, : No reason given.

This message is a reply to:
 Message 113 by Kleinman, posted 06-17-2020 3:41 PM Kleinman has replied

Replies to this message:
 Message 115 by Kleinman, posted 06-17-2020 7:49 PM Taq has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 115 of 239 (877547)
06-17-2020 7:49 PM
Reply to: Message 114 by Taq
06-17-2020 6:19 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
That math works ok if all you want to do is compute mutational divergence. But that has virtually nothing to do with DNA evolution.
Taq writes:
You are changing your tune. This is what you said before:
Kleinman writes:
But note, only about 1e11 people have live in our entire history. That doesn't give many beneficial mutations to work with when it takes 3e9 replications for each of those mutations.
Taq writes:
That's wrong. As shown above, there were about 1E12 mutations that happened in the human lineage after it split from the chimp lineage. The human haploid genome is only 3E9 bases long. That's enough mutations to change each base 300 times over. Your numbers are way off.
It's not enough to change each base 300 times over. DNA evolution requires a lineage to accumulate specific mutations. If adaptation requires the lineage to accumulate mutations A and B, it's going to take 3e9 replications for a variant to get mutation A and that variant with mutation A will need to do 3e9 replications to get mutation B regardless of how long the genome is.
Taq writes:
Let's look at it a different way. There are 3E9 bases in the human haploid genome, so we would need 9E9 point mutations to get all possible substitutions. At 50 mutations per person, that would be 180 million births to get all mutations. Right now, there are 130 million births each year. It would take less than two years for the current population to get all of those mutations, assuming the chances of all mutations is equal.
All you are describing here is genetic diversification. Or perhaps you think every one is getting identical mutations.
Kleinman writes:
Try doing the same math for the Lenski experiment.
Taq writes:
I am starting to get the feeling that the only things that exist in your universe are the Lenski and Kishony experiments.
In my universe, I have to deal with drug-resistant infections. Your problem is that you think that DNA evolution works different for different length genomes. It doesn't.
Kleinman writes:
That is a minuscule amount of the energy needed to replicate.
Taq writes:
The energy difference between two DNA sequences is even less. So why do you keep trying to relate DNA sequence to thermodynamics?
It's the information in the DNA sequence that is related to thermodynamics, specifically the second law. Perhaps it would be easier for you to understand if instead of using the terms information and entropy to describe this by using the terms order and disorder. Genetic adaptation to selection conditions is done by increasing the order of the genome. In the context of the Kishony experiment, the mutations are being selected for to increase the order in the genome to grow in the higher drug-concentration regions. It works the same way for any DNA evolution situation. Random mutations without selection increase the disorder in the genome. If it was possible, over time, the genome would become random sequences of bases as these random mutations without selection are accumulated.

This message is a reply to:
 Message 114 by Taq, posted 06-17-2020 6:19 PM Taq has replied

Replies to this message:
 Message 116 by Taq, posted 06-18-2020 12:00 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 116 of 239 (877563)
06-18-2020 12:00 PM
Reply to: Message 115 by Kleinman
06-17-2020 7:49 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
If adaptation requires the lineage to accumulate mutations A and B, it's going to take 3e9 replications for a variant to get mutation A and that variant with mutation A will need to do 3e9 replications to get mutation B regardless of how long the genome is.
As I feared, E. coli and the two oft mentioned experiments are all that exists in your universe.
You appear to be using the mutation rate from E. coli in human genetics. That is obviously wrong. In E. coli there is just one mutation in every few hundred replications. In humans, there are about 50 mutations in a single replication. You need to account for this.
You also need to account for diploid genomes and sexual reproduction. If mutation A happens in one individual and mutation B happens in another individual then their descendants can mate and have offspring with both mutations.
All you are describing here is genetic diversification. Or perhaps you think every one is getting identical mutations.
Do you agree that it takes less than two years for every possible point mutation to occur in at least one individual within the modern human population? Yes or no?
It's the information in the DNA sequence that is related to thermodynamics, specifically the second law.
They are only related in the sense that they use some of the same equations.

This message is a reply to:
 Message 115 by Kleinman, posted 06-17-2020 7:49 PM Kleinman has replied

Replies to this message:
 Message 117 by Kleinman, posted 06-18-2020 1:03 PM Taq has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 117 of 239 (877564)
06-18-2020 1:03 PM
Reply to: Message 116 by Taq
06-18-2020 12:00 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
If adaptation requires the lineage to accumulate mutations A and B, it's going to take 3e9 replications for a variant to get mutation A and that variant with mutation A will need to do 3e9 replications to get mutation B regardless of how long the genome is.
Taq writes:
As I feared, E. coli and the two oft mentioned experiments are all that exists in your universe.
If you think that DNA evolution works differently in bacteria than any other replicator, produce your mathematical and empirical evidence to prove this. Bare assertions may work in your universe, but they don't work well in science.
Taq writes:
You appear to be using the mutation rate from E. coli in human genetics. That is obviously wrong. In E. coli there is just one mutation in every few hundred replications. In humans, there are about 50 mutations in a single replication. You need to account for this.
You also need to account for diploid genomes and sexual reproduction. If mutation A happens in one individual and mutation B happens in another individual then their descendants can mate and have offspring with both mutations.
If you understood DNA evolution, you would understand that the mutation rate doesn't dominate the process. It is the multiplication rule of probabilities which dominates the DNA evolution process. This is why the Kishony experiment, as designed, will not work with 2 or more drugs. Just make his mega-plate vastly larger then you can achieve the population sizes need for this DNA evolutionary process to work.
As for recombination giving an offspring with the two beneficial mutations occurring, are you ready to do that math? Don't be surprised if you see the multiplication rule showing up in the mathematics of that evolutionary process as well.
Kleinman writes:
All you are describing here is genetic diversification. Or perhaps you think every one is getting identical mutations
Taq writes:
Do you agree that it takes less than two years for every possible point mutation to occur in at least one individual within the modern human population? Yes or no?
So what? All you have shown is diversification, not DNA evolution. What's the probability of any one of those individuals getting two beneficial mutations. Maybe you think that someone in Australia with a beneficial mutation will meet someone online from Finland with a different beneficial mutation, get married and have a child with both beneficial mutations. Is that how things work in your universe?
All it takes, for a mutation rate of 1e9, for there to be 3e9 replications for you to get on average some member of the population with one of every possible point mutation. You did that math! And it doesn't matter what the length of the genome is. Now, what does that do to the use of targeted therapy for a cancerous tumor that has 3e9 cells?
Kleinman writes:
It's the information in the DNA sequence that is related to thermodynamics, specifically the second law.
Taq writes:
They are only related in the sense that they use some of the same equations.
Same physics, same math.

This message is a reply to:
 Message 116 by Taq, posted 06-18-2020 12:00 PM Taq has replied

Replies to this message:
 Message 118 by Taq, posted 06-18-2020 1:29 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 118 of 239 (877565)
06-18-2020 1:29 PM
Reply to: Message 117 by Kleinman
06-18-2020 1:03 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
If you think that DNA evolution works differently in bacteria than any other replicator, produce your mathematical and empirical evidence to prove this.
You seriously have to ask how asexual and sexual reproduction differs mathematically?
If you understood DNA evolution, you would understand that the mutation rate doesn't dominate the process. It is the multiplication rule of probabilities which dominates the DNA evolution process. This is why the Kishony experiment, as designed, will not work with 2 or more drugs. Just make his mega-plate vastly larger then you can achieve the population sizes need for this DNA evolutionary process to work.
You once again fail to understand the impact of sexual reproduction.
So what? All you have shown is diversification, not DNA evolution.
It's a yes or no question.
Do you agree that it takes less than two years for every possible point mutation to occur in at least one individual within the modern human population? Yes or no?
All it takes, for a mutation rate of 1e9, for there to be 3e9 replications for you to get on average some member of the population with one of every possible point mutation.
That number is 0.18E9 for humans. I did the math. Did you look at it?
You did that math! And it doesn't matter what the length of the genome is.
Want to try that one again? Let's use your figure of one mutation per 1E9 bases.
E. coli have a 4 million base genome. This means 1 mutation per 250 replications, or 0.004 mutations per replication.
Humans have a 6 billion base diploid genome. This means 6 mutations per replication. This also doesn't factor in the fact that the per base mutation rate is higher in humans.
quote:
Through extensive validation, we identified 49 and 35 germline de novo mutations (DNMs) in two trio offspring, as well as 1,586 non-germline DNMs arising either somatically or in the cell-lines from which DNA was derived
https://www.coriell.org/...ationrateswithinhumanfamilies.pdf
So the human mutation rate is 10 fold higher than in E. coli, which is in keeping with the 50 or so mutations per replication in humans that I keep telling you about.
Genome size does affect how many mutations there will be per replication, as does mutation rate.
Same physics, same math.
Category error.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 117 by Kleinman, posted 06-18-2020 1:03 PM Kleinman has replied

Replies to this message:
 Message 119 by Kleinman, posted 06-18-2020 2:18 PM Taq has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 119 of 239 (877567)
06-18-2020 2:18 PM
Reply to: Message 118 by Taq
06-18-2020 1:29 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
If you think that DNA evolution works differently in bacteria than any other replicator, produce your mathematical and empirical evidence to prove this.
Taq writes:
You seriously have to ask how asexual and sexual reproduction differs mathematically?
If you think that DNA evolution works differently in bacteria than any other replicator, produce your mathematical and empirical evidence to prove this. You don't understand the mathematics of DNA evolution, you don't understand the mathematics of recombination. If you think that DNA evolution works differently for mitosis, meiosis, or fission, explain it. Bare assertions may work in your universe, but they don't work well in science.
Kleinman writes:
If you understood DNA evolution, you would understand that the mutation rate doesn't dominate the process. It is the multiplication rule of probabilities which dominates the DNA evolution process. This is why the Kishony experiment, as designed, will not work with 2 or more drugs. Just make his mega-plate vastly larger then you can achieve the population sizes need for this DNA evolutionary process to work.
Taq writes:
You once again fail to understand the impact of sexual reproduction.
Are you ready to show us the mathematics of recombination and how it affects DNA evolution? Please show your math (that is if you know how to do the math). Just say you don't know how to do the math and I'll show you how to do the math of random recombination. I've given you so many hints already, it should be easy for you.
Kleinman writes:
All it takes, for a mutation rate of 1e9, for there to be 3e9 replications for you to get on average some member of the population with one of every possible point mutation.
Taq writes:
That number is 0.18E9 for humans. I did the math. Did you look at it?
Try again. The only correction you need to do to your previous math is that humans are diploid so it only takes 1.5e9 member replications to get the 3e9 genome replications. It is clear that math is not your strong suit so let's make this as easy as possible. Imagine that you have a haploid genome of length one single base. For a mutation rate of 1e-9, how many replications of that base for there to be an average of 1 of each of the possible 3 substitutions? Then do the math for a genome length of 2 bases and tell us how the number of replications change based on genome length.
Kleinman writes:
You did that math! And it doesn't matter what the length of the genome is.
Taq writes:
Want to try that one again? Let's use your figure of one mutation per 1E9 bases.
E. coli have a 4 million base genome. This means 1 mutation per 250 replications, or 0.004 mutations per replication.
Humans have a 6 billion base diploid genome. This means 6 mutations per replication. This also doesn't factor in the fact that the per base mutation rate is higher in humans.
You do understand that for a diploid replicator, a single-member replicating gives two genome replications. And another point you are failing to get, humans have achieved the population sizes necessary for the first mutation to occur in a DNA evolutionary process. It's the second and ensuing beneficial mutations in that lineage that have a low probability of occurring. That variant and its descendants with the first beneficial mutation must replicate 1.5e9 times (diploid) for that second beneficial mutation to occur on some member with the first beneficial mutation. What does that mean empirically? What it means is that there is a reasonable probability that somebody in the population will get a sickle cell trait mutation but a very low probability that someone will get a sickle cell trait mutation will also get a thalassemia mutation. Perhaps you want to try an do the math for someone with a sickle cell trait mutation marrying someone with a thalassemia mutation getting an offspring with both mutations?
And when are you going to learn that the mutation rate is not the dominant feature of the DNA evolution process, its the multiplication rule which drives DNA evolution. That's why hiv which has a mutation rate on the order of 1e-5 still cannot evolve efficiently to 3-drug therapy (even though the virus does recombination). If you could do the math, you would understand why this happens.
Kleinman writes:
Same physics, same math.
Taq writes:
Category error.
Bare assertions may work in your universe, but they don't work well in science. First, learn the physics and how to do the mathematics before you make your bare assertions. When are you going to show us how the mathematics of recombination works? Just tell us you don't know how to do the math. You will then understand why recombination has no effect on the treatment of hiv.

This message is a reply to:
 Message 118 by Taq, posted 06-18-2020 1:29 PM Taq has replied

Replies to this message:
 Message 120 by Taq, posted 06-18-2020 2:56 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 120 of 239 (877568)
06-18-2020 2:56 PM
Reply to: Message 119 by Kleinman
06-18-2020 2:18 PM


Re: Does competition accelerate DNA evolution?
Kleinman writes:
If you think that DNA evolution works differently in bacteria than any other replicator, produce your mathematical and empirical evidence to prove this.
Would you agree that you mutation A and mutation B can occur in different individuals and then be combined in a single descendant? If so, that differs greatly from E. coli, does it not?
The only correction you need to do to your previous math is that humans are diploid so it only takes 1.5e9 member replications to get the 3e9 genome replications.
That 3e9 number is for E. coli, not humans. You keep making this mistake. For humans, you only need 0.18e9 replications.
It's the second and ensuing beneficial mutations in that lineage that have a low probability of occurring.
You are ignoring sexual reproduction. The first mutation can happen in one individual and then spread through the population. The second mutation can happen at the same time as the first mutation and spread through the population. Descendants of both lineages can mate and produce offspring with both mutations. With sexual reproduction you can have selection for each mutation in parallel instead of in series.

This message is a reply to:
 Message 119 by Kleinman, posted 06-18-2020 2:18 PM Kleinman has replied

Replies to this message:
 Message 121 by Kleinman, posted 06-18-2020 3:37 PM Taq has replied

  
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