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Author Topic:   Do you really understand the mathematics of evolution?
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 196 of 239 (878411)
06-29-2020 6:22 PM
Reply to: Message 194 by PaulK
06-29-2020 5:40 PM


Re: An important note regarding models of evolution
Kleinman writes:
I know exactly how fish evolve into mammals clique use these models.
PaulK writes:
Then why are you misrepresenting it?
I'm not. I'm trying to point to the error in the assumptions and you see that error as a feature. That's why you get garbage out of the predictions you make based on these models. If you had any skill at mathematical modeling, you could modify the Jukes-Cantor model (or the Felsenstein variant) and predict the behavior of the Kishony and Lenski experiments. But, you don't have either the training or the skill.
Kleinman writes:
I know exactly where they make their error in their assumptions and I know exactly how to correct the error so that the model works correctly to predict the behavior of experiments such as the Kishony and Lenski experiments
PaulK writes:
The models aren’t meant to predict the results of those experiments.
So the mistake is all yours.
Those models don't predict anything correctly. If I put a small piece of DNA from a banana that happens to be homologous with a small piece of your DNA, into these models, they are going to say you are closely related to a banana. If you think there is some valid prediction of DNA evolution from any of these models as written, present it. You won't because there is none. All you can do is blow smoke. You don't even understand that microevolutionary transitions are random events and because of this you have to multiply the individual probabilities to compute the joint probabilities of these events happening. You don't have any capability to do these simple probability problems. You are the one who makes one blunder after another.

This message is a reply to:
 Message 194 by PaulK, posted 06-29-2020 5:40 PM PaulK has replied

Replies to this message:
 Message 198 by PaulK, posted 06-30-2020 12:16 AM Kleinman has replied

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


Message 197 of 239 (878412)
06-29-2020 6:58 PM
Reply to: Message 195 by Straggler
06-29-2020 6:19 PM


Re: An important note regarding models of evolution
Straggler writes:
Are you still here?
Shouldn’t you be lapping up the adulation of the scientific community and preparing your Nobel acceptance speech?
I don't expect adulation from the fish evolve into mammals clique. In fact, when I shed some light on this topic, this clique acts like I'm opening Dracula's coffin after sunrise. If I get adulation from anyone, it will be the people who have to deal with drug-resistant infections and failed cancer treatments.
Straggler writes:
I mean you have single handedly and indisputably falsified one of the most accepted and respected scientific theories of all time. The underpinning concept of all biology. You. Standing on the shoulders of giants. The Newton of biology. The Newton of our time.
You just run in the wrong circles. There are plenty of people who can do this math, they just don't happen to be in the fish evolve into mammals clique.
Straggler writes:
As much as I enjoy basking in your gloriousness and as honoured as we all are by your benevolent presence oh great one, I have to ask - Why are you posting here rather than revoloutionising the whole of biology with your flawless and paradigm-shifting proof that descent from common ancestry is a physical impossibility?
If you mean by descent from some common ancestor in the primordial soup, even the mathematically incompetent should see the lunacy in that. It's that human and chimp from a common ancestor which requires a little math to show the irrationality of that concept. Of course, you could send some of your DNA and chimpanzee DNA into ancestory.com and see if you get a hit. If you do get a hit, don't forget to take into account all the misses.
Straggler writes:
Why have you chosen us to spread the word rather than - oh I dunno - The biological research community (for example)?
I publish my papers and occasionally I have done conferences. But I'm a clinical physician in private practice so everything I do, I pay out of my own pocket. My work is getting more and more attention and I have enough training and skill at doing mathematical modeling that I know this is correct. But when you tell people who believe that the earth is flat that it isn't, I don't expect an easy time convincing them. It's the people with skin in the game where I expect the breakthrough to occur. What I mean by that, those people who are trying to deal with drug-resistant infections, failed cancer treatments, herbicide, and pesticide resistance. These are the people who really need to have a correct understanding of DNA evolution, not some vague understanding of the process. On the other hand, this is a major embarrassment to those in the fish evolve into mammals clique in academia who can't even explain the simplest evolutionary experiments such as the Kishony and Lenski experiments. That would be like someone in engineering claiming they can explain the motion of a building or bridge in an earthquake but can't explain the mathematics of a mass and spring or a swinging pendulum. Where I got my engineering training, they wouldn't put up with that kind of crap for a minute. So straggle back to your hole or wherever you dwell and learn something about the physics and mathematics of evolution.

This message is a reply to:
 Message 195 by Straggler, posted 06-29-2020 6:19 PM Straggler has not replied

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


Message 199 of 239 (878436)
06-30-2020 4:26 AM
Reply to: Message 198 by PaulK
06-30-2020 12:16 AM


Re: An important note regarding models of evolution
Kleinman writes:
I'm not.
PaulK writes:
Yes you did. You tried to pretend that phylogenetic analysis was derived from the figures for a single base. Either you know that’s not true or you don’t know how the models are used.
Let's see if you have stopped thinking about the mathematics DNA evolution and how it applies to phylogenic analysis. How many bases do you have to compare and be identical in order to say these two replicators are related. And relate this to the bacteria in the Kishony experiment. And by the way, I showed you how to draw the Markov Chain transition diagram for a second-order transition and you have no idea how to write the correct transition matrix for that case. Each increase in order of the Markov chain for DNA analysis introduces another instance of the multiplication rule but you need to understand introductory probability theory to recognize this and you don't. Are all of you in the fish evolve into mammals clique this poorly trained in mathematics? It certainly seems so.
Kleinman writes:
I'm trying to point to the error in the assumptions and you see that error as a feature
PaulK writes:
It is not an error, but since you don’t understand DNA evolution or how the models are used you can’t see that. Too bad for you.
When you tell us how many bases need to match and how to account for the differences over time to determine relatedness such as in the Kishony experiment then we will know who understands DNA evolution and who does not. Oh, that's right, you think these Markov equations models drift. And you think that fish drift into mammals. You cherry-pick a few minuscule portions of a couple of genomes, find a few matches and say the species are related and this is too bad for those suffering from drug-resistant infections and failed cancer treatments.

This message is a reply to:
 Message 198 by PaulK, posted 06-30-2020 12:16 AM PaulK has replied

Replies to this message:
 Message 200 by PaulK, posted 06-30-2020 1:02 PM Kleinman has replied

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


Message 202 of 239 (878465)
06-30-2020 2:22 PM
Reply to: Message 201 by Taq
06-30-2020 1:07 PM


Re: The mathematics of DNA evolution
Kleinman writes:
I've answered the question multiple times and even showed you how to do the mathematics for this situation.
Taq writes:
Let me do the math since you are too much of a nitwit to figure it out.
Here is the situation again:
Weed A is exposed to pesticide A in one region and develops resistance. Weed B is exposed to pesticide B in a different region and develops resistance.
We bring Weed A and Weed B into the same region. How many generations before you get resistance to pesticides A and B in a single weed?
The answer is one single generation. Doesn't take much math to figure it out. There will be at least some offspring from weed A and weed B, and some of those offspring will have the mutations for both types of resistance.
This is a far cry from what you claim with your "multiplicative rule". It doesn't take another 3 billion generations. It only takes 1 generation.
You just don't get it poor Taq. You haven't done any math you ding-a-ling. You think the world is filled with only A variant weeds and B variant weeds. And suppose you also think that both variants are homozygous at both loci for each variant. So no matter which variants mate, you will get an AB offspring. Well you would be wrong because you are a mathematically incompetent dumb-cluck because even in that circumstance the multiplication rule applies.
Let's see if I can explain it simply enough so that even a dumbbell math drop-out can understand how the multiplication rule still applies. Assume both fields have equal populations for simplicity so the frequency of A variants will be 0.5 and the frequency of B variants will be 0.5. Then, the probability of an A-B recombination event in a single recombination will be 0.5, not 1.0 because you can also have an A-A (probability 0.25) recombination event and a B-B (probability 0.25) recombination event. So your next argument is going to be, there are millions of recombination events going on here and surely, an A-B recombination event will occur in at least one of those recombination events. And you would be right. A fish evolves into mammals clique member can set up a scenario where he can breed herbicide-resistant weeds.
That's why you should never give advice to farmers how to use herbicides. And this is why you are such a slow learner about the Kishony experiment. Imagine you haven't used any herbicides on your two fields but they have their 1.5e9 (assume they are diploid) genome replication descending from some herbicide sensitive founders. In that population, you are going to have 1 A variant resistant to one herbicide and 1 B variant that is resistant to the other herbicide. The probability of the A-B recombination event is not 0.5 as in your contrived scenario, it is 2*(1/1.5e9)*(1/1.5e9) in a single recombination event. But you argue, there are millions of recombination events, at least 1 will be an A-B recombination event. Why don't you try and do that math? Recombination has very little effect on DNA evolution and if you understood the math, you would understand why. Farmers are a lot smarter than you, they don't use two different herbicides on adjacent fields, select for the herbicide-resistant variants to each herbicide, allow those herbicide-resistant variants to repopulate their fields and allow them to recombine to give multi-herbicide resistant variants.
On the other hand, maybe they would if they have the same understanding of evolutionary biology that you have. You really need to learn about the multiplication rule and how it affects not only DNA evolution but also random recombination.

This message is a reply to:
 Message 201 by Taq, posted 06-30-2020 1:07 PM Taq has replied

Replies to this message:
 Message 206 by Taq, posted 06-30-2020 4:34 PM Kleinman has not replied

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


Message 203 of 239 (878467)
06-30-2020 2:47 PM
Reply to: Message 200 by PaulK
06-30-2020 1:02 PM


Re: An important note regarding models of evolution
Kleinman writes:
And you think that fish drift into mammals.
PaulK writes:
More proof that you don’t understand DNA evolution and refuse to learn.
We keep waiting for you to show us how it works. But all you present to us is one blunder after another.
Kleinman writes:
You cherry-pick a few minuscule portions of a couple of genomes, find a few matches and say the species are related
PaulK writes:
Do you really think that making things up like this is useful or constructive?
Why don't you present us with an example where this isn't being done?
Kleinman writes:
... this is too bad for those suffering from drug-resistant infections and failed cancer treatments.
PaulK writes:
I don’t think that making a fool of yourself on an obscure Internet forum helps them much either.
So, when you said the following in Message 183 about the single site Markov Chain model you think you are a mathematical genius?
PaulK writes:
The equilibrium would be roughly equal proportions of each base in a single genome.
PaulK, I would recommend that you watch either the Harvard or MIT lectures on Markov Chain mathematics on YouTube (both are very good) except I don't think you will understand either lecture. So why don't you do a search on YouTube and find some lectures geared toward high school students? You might understand those lectures (if you work really hard at it). You in the fish evolve into mammals clique really aren't very good at this math thing. Of course, that explains why you don't understand DNA evolution. But you sure know how to blow smoke. The problem is that it is really stinky smoke.

This message is a reply to:
 Message 200 by PaulK, posted 06-30-2020 1:02 PM PaulK has replied

Replies to this message:
 Message 204 by PaulK, posted 06-30-2020 3:15 PM Kleinman has replied

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


Message 205 of 239 (878475)
06-30-2020 3:38 PM
Reply to: Message 204 by PaulK
06-30-2020 3:15 PM


Re: An important note regarding models of evolution
Kleinman writes:
We keep waiting for you to show us how it works.
PaulK writes:
As I keep telling you that DNA evolution is predominantly neutral.
Until you grasp that point you will continue to blunder.
You cannot make an accurate model until you understand what you are modelling.
Does fixation ever occur with neutral evolution? Because the existing Markov models (Jukes-Cantor and the derivatives models) don't go to fixation, they go to equilibrium with a distribution of bases at that site. For example, the Jukes-Cantor and Kimura models go to frequencies of A, C, G, and T = 0.25. If there is fixation, shouldn't the frequency of one of the bases go to 1 and the others to 0? Let's see if we can get you to start thinking again.

This message is a reply to:
 Message 204 by PaulK, posted 06-30-2020 3:15 PM PaulK has replied

Replies to this message:
 Message 207 by PaulK, posted 06-30-2020 4:48 PM Kleinman has replied

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


Message 208 of 239 (878491)
06-30-2020 5:22 PM
Reply to: Message 207 by PaulK
06-30-2020 4:48 PM


Re: An important note regarding models of evolution
Kleinman writes:
Does fixation ever occur with neutral evolution?
PaulK writes:
Fixation of alleles does. But that can include a degree of polymorphism
Is that what they are modeling with these Markov chain models?
PaulK writes:
With regard to individual bases however I think it will come down to the numbers. How long does it take to reach equilibrium? The mere fact that it would eventually is insufficient. The values seen within a population are not independent. The distant descendants of an individual may be divided between two or more populations - indeed that is exactly the case that phylogenetic analysis is looking for.
Ok, so you are saying that that distant relative has some base at a site, and over time that base mutates to the 3 other bases when it reaches equilibrium? That kind of sounds like fixation in reverse. With fixation, you have all possible bases at the given site initially and with fixation, all but one of the bases disappear from the population. So which happens in the real world, equilibrium, or fixation? With regards to equilibrium, what variable in these models affects the rate of reaching equilibrium?
PaulK writes:
Further, for more distant relatives sites that freely vary are not useful because they change too quickly. So it appears that the models are accurate on that score.
Could you give us an empirical example that demonstrates this?

This message is a reply to:
 Message 207 by PaulK, posted 06-30-2020 4:48 PM PaulK has replied

Replies to this message:
 Message 209 by PaulK, posted 06-30-2020 5:32 PM Kleinman has replied

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


Message 210 of 239 (878501)
06-30-2020 6:12 PM
Reply to: Message 209 by PaulK
06-30-2020 5:32 PM


Re: An important note regarding models of evolution
Kleinman writes:
Is that what they are modeling with these Markov chain models?
PaulK writes:
Obviously not. But if you are concerned with phenotypic change the distinction is important.
I thought you said they were modeling neutral evolution. That is drift, isn't it? And doesn't fixation occur with drift? So, what exactly are they modeling with these Markov chain models?
Kleinman writes:
Ok, so you are saying that that distant relative has some base at a site, and over time that base mutates to the 3 other bases when it reaches equilibrium?
PaulK writes:
I am saying that it is possible for the site to be in equilibrium - with all four bases roughly equally represented - among the distant descendants. But at the same time the site is fixed in some or all of the populations existing at that time.
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?
Kleinman writes:
So which happens in the real world, equilibrium, or fixation?
PaulK writes:
Both. At the same time. As explained above. Fixed in some populations but not in equilibrium over all the descendants.
How do they tell when the genetic sequence they put into the model is fixed or at equilibrium? 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?

This message is a reply to:
 Message 209 by PaulK, posted 06-30-2020 5:32 PM PaulK has replied

Replies to this message:
 Message 211 by PaulK, posted 07-01-2020 7:47 AM Kleinman has replied

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


Message 212 of 239 (878534)
07-01-2020 9:41 AM
Reply to: Message 211 by PaulK
07-01-2020 7:47 AM


Re: An important note regarding models of evolution
Kleinman writes:
I thought you said they were modeling neutral evolution. That is drift, isn't it? And doesn't fixation occur with drift
PaulK writes:
Fixation occurs within a population and populations are outside the scope of the model. It’s a model of DNA evolution, not population genetics.
Population Genetics (Stanford Encyclopedia of Philosophy)
Population Genetics writes:
Population genetics is a field of biology that studies the genetic composition of biological populations, and the changes in genetic composition that result from the operation of various factors, including natural selection. 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.
Competition, drift, DNA evolution, recombination,... are all part of population genetics. You are very confused about this subject.
Kleinman writes:
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?
PaulK writes:
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.
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?
Kleinman writes:
That's part of the problem with these DNA evolution models.
PaulK writes:
No, it really isn’t a problem. These are models of neutral evolution. They are used to estimate divergence times between species. Since neutral evolution dominates and since it is not practical to identify which loci were selected in the distant past - except by divergence from these models - that’s obviously a sensible thing.
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?
Kleinman writes:
How do they tell when the genetic sequence they put into the model is fixed or at equilibrium?
PaulK writes:
Why would they need to? That isn’t what these models are about.
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?
Kleinman writes:
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?
PaulK writes:
For the purposes of this discussion that doesn’t matter at all. The models don’t deal with populations and don’t need to.
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.

This message is a reply to:
 Message 211 by PaulK, posted 07-01-2020 7:47 AM PaulK has replied

Replies to this message:
 Message 213 by PaulK, posted 07-01-2020 1:21 PM Kleinman has replied

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


Message 214 of 239 (878560)
07-01-2020 2:01 PM
Reply to: Message 213 by PaulK
07-01-2020 1:21 PM


Re: An important note regarding models of evolution
Kleinman writes:
Competition, drift, DNA evolution, recombination,... are all part of population genetics. You are very confused about this subject.
PaulK writes:
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,
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.
Kleinman writes:
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
PaulK writes:
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)
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?
Kleinman writes:
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?
PaulK writes:
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).
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?

This message is a reply to:
 Message 213 by PaulK, posted 07-01-2020 1:21 PM PaulK has replied

Replies to this message:
 Message 215 by PaulK, posted 07-01-2020 4:05 PM Kleinman has replied

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


Message 216 of 239 (878569)
07-01-2020 4:58 PM
Reply to: Message 215 by PaulK
07-01-2020 4:05 PM


Re: An important note regarding models of evolution
Kleinman writes:
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.
PaulK writes:
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.
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?
Kleinman writes:
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?
PaulK writes:
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.
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?

This message is a reply to:
 Message 215 by PaulK, posted 07-01-2020 4:05 PM PaulK has replied

Replies to this message:
 Message 217 by PaulK, posted 07-02-2020 1:52 AM Kleinman has replied

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


Message 218 of 239 (878592)
07-02-2020 5:41 AM
Reply to: Message 217 by PaulK
07-02-2020 1:52 AM


Re: An important note regarding models of evolution
Kleinman writes:
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.
PaulK writes:
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.
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.
Kleinman writes:
Sure, but you aren't going to do it by cherrypicking the genome for tiny homologous portions.
PaulK writes:
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.
Kleinman writes:
In fact, you have to use the entire genome and account for all the differences
PaulK writes:
Statisticians would disagree. Proper sampling should be quite adequate.
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.
Kleinman writes:
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.
PaulK writes:
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,
Why don't you do the math?
Regulatory DNA sequences, human genome
Wikipedia on the Human Genome writes:
The human genome has many different regulatory sequences which are crucial to controlling gene expression. Conservative estimates indicate that these sequences make up 8% of the genome,[56] however extrapolations from the ENCODE project give that 20[57]-40%[58] of the genome is gene regulatory sequence. Some types of non-coding DNA are genetic "switches" that do not encode proteins, but do regulate when and where genes are expressed (called enhancers).[59]
And
Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA genes, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined.[17]
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?
Kleinman writes:
It only takes a mere 50 million generations to reach equilibrium. Do you want to explain that to us, Professor Corey?
PaulK writes:
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
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.

This message is a reply to:
 Message 217 by PaulK, posted 07-02-2020 1:52 AM PaulK has replied

Replies to this message:
 Message 219 by PaulK, posted 07-02-2020 11:54 AM Kleinman has replied

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


Message 220 of 239 (878626)
07-02-2020 12:47 PM
Reply to: Message 219 by PaulK
07-02-2020 11:54 AM


Re: An important note regarding models of evolution
PaulK writes:
I think that replying to this part is all that needs to be said:
Kleinman writes:
Sure, but you aren't going to do it by cherrypicking the genome for tiny homologous portions.
PaulK writes:
Sure, the strawman you invented isn’t going to work.
Kleinman writes:
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.
PaulK writes:
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
A high school student from Egypt writes:
How do scientists construct phylogenetic trees and know the degree of relatedness between living organisms by DNA?
Do they just look for similarities between the whole genomes? Or just specific genes? Or RNA? Or what exactly?
And the answer is...
Allison Zhang, Stanford University writes:
The first thing to do is align the two DNA sequences together that you’re going to compare. Make sure you’re comparing the same gene! (Or other sequence.) Otherwise you are comparing apples to oranges.
This sequence alignment is often done with the help of computer programs. The strategy is to find the alignment that has the most matches and the least mismatches.
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.

This message is a reply to:
 Message 219 by PaulK, posted 07-02-2020 11:54 AM PaulK has replied

Replies to this message:
 Message 221 by PaulK, posted 07-02-2020 1:22 PM Kleinman has replied

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


Message 222 of 239 (878635)
07-02-2020 1:39 PM
Reply to: Message 221 by PaulK
07-02-2020 1:22 PM


Re: An important note regarding models of evolution
Kleinman writes:
If there was a league of lazy dumb asses, you would be on the all-star team
PaulK writes:
I’d refuse to play in any team that had you as the captain.
Well, you are the king, take that.
Kleinman writes:
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.
PaulK writes:
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.
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.

This message is a reply to:
 Message 221 by PaulK, posted 07-02-2020 1:22 PM PaulK has replied

Replies to this message:
 Message 223 by PaulK, posted 07-02-2020 2:05 PM Kleinman has replied

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


Message 224 of 239 (878639)
07-02-2020 2:24 PM
Reply to: Message 223 by PaulK
07-02-2020 2:05 PM


Re: An important note regarding models of evolution
Kleinman writes:
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
PaulK writes:
That’s the contact information for the publishers, not the author. Unlike you, I’m not too lazy to find out that much.
Maybe the king can find the contact information by reading some fossil tea-leaves.
Kleinman writes:
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
PaulK writes:
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.
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.

This message is a reply to:
 Message 223 by PaulK, posted 07-02-2020 2:05 PM PaulK has replied

Replies to this message:
 Message 225 by PaulK, posted 07-02-2020 4:39 PM Kleinman has replied

  
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