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Author Topic:   Rebuttal To Creationists - "Since We Can't Directly Observe Evolution..."
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 119 of 2926 (898198)
09-20-2022 1:13 PM
Reply to: Message 117 by ringo
09-20-2022 12:42 PM


Re: Video not available
Kleinman:
Even Taq realizes that E Coli won't replicate in distilled water or even saline solution. They need energy in a form that they can metabolize.
ringo:
Duh.

But what has replication at the cellular level got to do with evolution?

That's an appropriate question. Replication (in particular replication of the genome) gives the possibility of a mutation. That is a second law of thermodynamics process that operates as a Markov chain random walk. I give a simple explanation of how that works in this paper:
The Physics of Darwinian Evolution
Anything that slows replication such as biological competition will slow that random walk. The occurrence of a reasonable probability of an adaptive mutation occurring somewhere in a population takes lots of replicatiions.

This message is a reply to:
 Message 117 by ringo, posted 09-20-2022 12:42 PM ringo has replied

Replies to this message:
 Message 120 by ringo, posted 09-20-2022 1:17 PM Kleinman has replied

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


Message 121 of 2926 (898200)
09-20-2022 1:25 PM
Reply to: Message 118 by nwr
09-20-2022 12:50 PM


Re: Apples and oranges
Kleinman:
So you are claiming that there are beneficial mutational differences between humans and chimps.
nwr:
Your mistake is to treat "beneficial" as an absolute. It isn't. What is beneficial is relative to the population.

I think you mean to say that mutations are only beneficial in the context of environmental selection conditions. Do you think that chimps and humans have the same reproductive fitness in the environment where chimps live?
Kleinman:
Why do humans have the reproductive fitness able to achieve a population of greater than 7 billion while chimpanzees have only achieved a population of 300,000?
nwr:
Likewise, you are treating "fitness" as an absolute. It isn't. Again, it is relative to the population.

There are about 1.5 billion people living in Africa. Why only 300,000 chimps? Some chimps live in Senegal but there are over 17 million humans living there. Some chimps live in Tanzania but there are about 63 million humans living there. What mutations do humans have that enable the to have this difference in reproductive fitness?

This message is a reply to:
 Message 118 by nwr, posted 09-20-2022 12:50 PM nwr has replied

Replies to this message:
 Message 127 by Taq, posted 09-20-2022 1:58 PM Kleinman has replied
 Message 128 by nwr, posted 09-20-2022 2:22 PM Kleinman has replied

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


Message 122 of 2926 (898201)
09-20-2022 1:30 PM
Reply to: Message 120 by ringo
09-20-2022 1:17 PM


Re: Video not available
Kleinman:
The occurrence of a reasonable probability of an adaptive mutation occurring somewhere in a population takes lots of replicatiions.
ringo:
*shrug*

But evolution does happen. So the rate of mutation doesn't seem to be significant.

You are right, evolution does happen and the mutation rate is not the significant variable in the process. This is clearly demonstrated by the fact that HIV has a very high mutation rate but still cannot evolve efficiently to 3-drug combination therapy. The mathematical limitation of this evolutionary process is the multiplication rule of probabilities.

This message is a reply to:
 Message 120 by ringo, posted 09-20-2022 1:17 PM ringo has replied

Replies to this message:
 Message 123 by ringo, posted 09-20-2022 1:36 PM Kleinman has not replied
 Message 126 by Taq, posted 09-20-2022 1:56 PM Kleinman has not replied

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


Message 129 of 2926 (898208)
09-20-2022 2:44 PM
Reply to: Message 127 by Taq
09-20-2022 1:58 PM


Re: Apples and oranges
Kleinman:
Perhaps it is silly to ask you a question you can't answer
Taq:
When the question is so vague it can’t be answered the silliness is definitely with the asker. I don’t notice you answering it either. Nor do I notice you giving any reason why microevolutionary events can’t add up to macroevolution.

Didn't you say you could add up microevolution changes to get a macroevolutionary change? I'm asking you what microevolutionary changes occurred to give the reproductive advantage that humans have over chimps. What's so vague about that? You won't even tell us how many microevolutionary changes have occurred to give the variants that can grow in the high concentration drug region of the Kishony experiment.
Kleinman:
Biological evolutionary competition (Darwinian competition) is a conservation of energy (first law of thermodynamics) process.
Taq:
What physical process isn't?

Is your grand contribution to biology the rather obvious observation that resources are limited? If so, you are a bit late to the game.

Biological evolutionary modification isn't a first law of thermodynamics process, it is a second law of thermodynamics process. That process is not conservative.
Somebody had to explain to Lenski why biological evolutionary competition slows biological evolutionary adaptation. He's limiting his resources. Kishony doesn't limit the resources as much so his populations evolve far more rapidly but it still takes a billion replications for each adaptive mutation. Why don't you show us how the addition rule explains the reason it takes a billion replications for each adaptive mutation?
Kleinman:
Do you think that chimps and humans have the same reproductive fitness in the environment where chimps live?
Taq:
Do you think a polar bear is well adapted to the Arctic? Do you think a polar bear is well adapted to the Sahara desert?

There are humans living both in the Arctic (about 4 million) and the Sahara (2.5 million) but no chimps in either environment. What adaptive mutations do humans have in order to survive and reproduce in these environments that chimps don't have?

Edited by Kleinman, .


This message is a reply to:
 Message 127 by Taq, posted 09-20-2022 1:58 PM Taq has replied

Replies to this message:
 Message 131 by PaulK, posted 09-20-2022 2:55 PM Kleinman has not replied
 Message 132 by Taq, posted 09-20-2022 3:08 PM Kleinman has replied

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


Message 130 of 2926 (898209)
09-20-2022 2:50 PM
Reply to: Message 128 by nwr
09-20-2022 2:22 PM


Re: Apples and oranges
Kleinman:
There are about 1.5 billion people living in Africa. Why only 300,000 chimps?
nwr:
And the number of ants greatly exceeds the number of humans. You are making inappropriate comparisons.

Now nwr thinks ants are our closest biological relatives. Very strange way of thinking!

This message is a reply to:
 Message 128 by nwr, posted 09-20-2022 2:22 PM nwr has seen this message but not replied

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


Message 133 of 2926 (898212)
09-20-2022 3:23 PM
Reply to: Message 132 by Taq
09-20-2022 3:08 PM


Re: Apples and oranges
Kleinman:
Didn't you say you could add up microevolution changes to get a macroevolutionary change? I'm asking you what microevolutionary changes occurred to give the reproductive advantage that humans have over chimps.
Taq:
Compare the human and chimp genomes. Find the differences.

I'm not the one claiming that humans and chimps arose from a common ancestor. You still haven't shown how every human alive today has 200,000 beneficial mutations that give the reproductive advantage over chimps. You have about 100 billion replications, 99% of which have occurred in the last 10,000 years for that kind of genetic transformation. You need a much larger envelope.

This message is a reply to:
 Message 132 by Taq, posted 09-20-2022 3:08 PM Taq has replied

Replies to this message:
 Message 134 by Taq, posted 09-20-2022 3:40 PM Kleinman has replied

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


Message 135 of 2926 (898214)
09-20-2022 4:11 PM
Reply to: Message 134 by Taq
09-20-2022 3:40 PM


Re: Apples and oranges
Kleinman:
You still haven't shown how every human alive today has 200,000 beneficial mutations that give the reproductive advantage over chimps.
Taq:
Are you aware that mutations happen? It's really a thing.

Sure mutations happen. You just have to learn the accounting rules for a lineage to accumulate a set of beneficial mutations. You understand that competition is a first law of thermodynamics process. Do you understand that mutations are random events? And that accumulation of beneficial mutations on a lineage is a Markov process where the joint probability of beneficial mutations occurring is governed by the multiplication rule of probabilities. That is a second law of thermodynamics process. That's why your back-of-the-envelope calculation of humans having 200,000 beneficial mutations is wrong. You are using a simple neutral evolution calculation and assuming that 10% of the mutations are beneficial based on rank speculation. Why don't you learn how the Kishony and Lenski experiments work?

This message is a reply to:
 Message 134 by Taq, posted 09-20-2022 3:40 PM Taq has replied

Replies to this message:
 Message 136 by Taq, posted 09-20-2022 4:35 PM Kleinman has replied

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


Message 137 of 2926 (898216)
09-20-2022 4:44 PM
Reply to: Message 136 by Taq
09-20-2022 4:35 PM


Re: Apples and oranges
Kleinman:
Why don't you learn how the Kishony and Lenski experiments work?
Taq:
I already know how they work.

Why does it take a billion replications in each of their lineages to accumulate each of their beneficial mutations?

This message is a reply to:
 Message 136 by Taq, posted 09-20-2022 4:35 PM Taq has replied

Replies to this message:
 Message 138 by Taq, posted 09-20-2022 4:55 PM Kleinman has replied

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


Message 139 of 2926 (898218)
09-20-2022 5:08 PM
Reply to: Message 138 by Taq
09-20-2022 4:55 PM


Re: Apples and oranges
Kleinman:
Why does it take a billion replications in each of their lineages to accumulate each of their beneficial mutations?
Taq:
Because of the stringency of the fitness landscape. There are only 1 or a few mutations that will allow adaptation to the new conditions. In the Lenski experiment it required a very rare recombination event to evolve aerobic citrate metabolism. In the case of antibiotic resistance there can be as few as 1 mutation that confers resistance. Some adaptations are just harder to come by than others.

Why don't you tell Lenski and Kishony how to make their experiments perform more rapidly? And there are multiple different mutations that give antibiotic resistance. Each must take their own evolutionary trajectory. Read this:
JSTOR: Access Check
Taq:
On top of that, bacteria are asexual. A lack of recombination in each generation limits the mixing of different mutations and different alleles.
Why doesn't recombination defeat combination therapy for the treatment of HIV? Why don't you tell us the mathematics which describes random recombination if you can? I'll even give you a hint. You do that math using the trinomial distribution.

This message is a reply to:
 Message 138 by Taq, posted 09-20-2022 4:55 PM Taq has replied

Replies to this message:
 Message 140 by Taq, posted 09-20-2022 5:17 PM Kleinman has replied

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


Message 141 of 2926 (898221)
09-20-2022 5:38 PM
Reply to: Message 140 by Taq
09-20-2022 5:17 PM


Re: Apples and oranges
Kleinman:
Why don't you tell Lenski and Kishony how to make their experiments perform more rapidly?
Taq:
I don't see why the speed of the experiment matters.

You are claiming that the stringent standards of the experiment are what is causing it to take a billion replications for each beneficial mutation. How can they make their experiment less stringent?
Kleinman:
Why doesn't recombination defeat combination therapy for the treatment of HIV?
Taq:
It does.
quote:
Human immunodeficiency virus (HIV) is a diploid virus: each virion carries two complete RNA genomic strands. Homologous recombination can occur when a cell is coinfected with two different but related strains. Naturally occurring recombinant HIV strains have been found in infected patients in regions of the world where multiple genotypic variants cocirculate. One recombinant HIV strain has spread rapidly to millions of persons in Southeast Asia. Recombination is a mechanism whereby high level and multidrug-resistant strains may be generated in individual treated patients. Recombination also poses theoretical problems for the development of a safe HIV vaccine. Certain features of HIV replication, such as syncytium formation and transactivation, may be best understood as components of a sexual reproductive cycle. Recombination may be an important HIV evolutionary strategy.
Recombination in HIV: an important viral evolutionary strategy. - PMC


You and the people who wrote your 1997 reference need to come up to date on the empirical evidence. 3 drug combination therapy for the treatment of HIV works successfully despite the fact that the virus does recombination. If you understood the mathematics of random recombination, you would know why.
Kleinman:
Why don't you tell us the mathematics which describes random recombination if you can? I'll even give you a hint. You do that math using the trinomial distribution.
Taq:
Mathematics is meaningless unless you understand the process you are applying it to. From what I can see, you simply don't understand how evolution or biology works.

The paper in the following link shows you how to do the mathematics of random recombination:
Random recombination and evolution of drug resistance

This message is a reply to:
 Message 140 by Taq, posted 09-20-2022 5:17 PM Taq has replied

Replies to this message:
 Message 142 by Taq, posted 09-20-2022 5:48 PM Kleinman has replied

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


Message 143 of 2926 (898223)
09-20-2022 6:58 PM
Reply to: Message 142 by Taq
09-20-2022 5:48 PM


Re: Apples and oranges
Kleinman:
You are claiming that the stringent standards of the experiment are what is causing it to take a billion replications for each beneficial mutation.
Taq:
I am claiming that the beneficial mutations for the adaptation they are studying are rare. That is the stringency I am talking about.

The probability of any mutation occurring, not just beneficial mutations are rare. They occur at a frequency of about 1/(mutation rate) replications. There is nothing you can do to change that mathematical fact of life.
Taq:
For the Lenski experiment, they had no idea how long it would take which was part of the experiment. It could have taken just a few days, but it didn't. In the case of the Kishony experiment they would have known the rate of adaptation for the conditions they put the bacteria under so that they could get the results they wanted within the experimental design. The same can be said for classical experiments like the Luria-Delbruck fluctuation experiment and the Lederbergs' plate replica experiment.
What Lenski found is that it took billions of replications for each beneficial mutation to occur on his most fit lineage and Kishony found that it requires a colony size of a billion for a beneficial mutation to occur. This should not have been a surprise since beneficial (and all) mutations occur at a frequency of about 1/(mutation rate) replications.
Kleinman:
3 drug combination therapy for the treatment of HIV works successfully despite the fact that the virus does recombination. If you understood the mathematics of random recombination, you would know why.
Taq:
What does that have to do with human evolution?

The mathematics of random recombination works the same for all replicators. The probability of a particular random recombination event occurring will be low unless the frequency of the two alleles is high in the population. You should try to do the math yourself.
Taq:
To use an analogy, you are pretending that the odds of winning the lottery can be applied to flipping a coin.
If you are talking about whether an adaptive mutation will occur or not, it is similar to a coin tossing problem. The difference is that coin tossing is symmetric with a probability of 0.5 for each outcome. The outcomes for whether an adaptive mutation occurs or not is highly asymmetric with a probability of the beneficial mutation rate and 1-(the beneficial mutation rate). When it comes to getting two or more adaptive mutations, it's like winning two or more lotteries. That math is governed by the multiplication rule.

This message is a reply to:
 Message 142 by Taq, posted 09-20-2022 5:48 PM Taq has replied

Replies to this message:
 Message 144 by vimesey, posted 09-20-2022 10:53 PM Kleinman has replied
 Message 150 by Taq, posted 09-21-2022 10:55 AM Kleinman has replied

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


Message 146 of 2926 (898230)
09-21-2022 8:05 AM
Reply to: Message 144 by vimesey
09-20-2022 10:53 PM


Re: Apples and oranges
Kleinman:
The probability of a particular random recombination event occurring will be low unless the frequency of the two alleles is high in the population.
vimesey:
There we have it - the Texas sharpshooter fallacy.

Vimsey thinks that an Australian Aborigine with a beneficial allele and an Arctic Eskimo with a different beneficial allele will meet, have children and recombine those two beneficial alleles. They must have done it on recombination.com. Quite a sharp argument you have there.

This message is a reply to:
 Message 144 by vimesey, posted 09-20-2022 10:53 PM vimesey has not replied

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


Message 147 of 2926 (898231)
09-21-2022 8:07 AM
Reply to: Message 145 by Tanypteryx
09-20-2022 11:32 PM


Re: Video not available
ringo:
So it's hard to figure out what you're trying to accomplish here.
Tanypteryx:
It looks like he's trying to generate traffic on his papers. He doesn't have many reads or citations.

Why not, it's working. However, that's not what motiviated me to start posting here again. One of your administrators sent me an email with a list of topics and this was one of them. Perhaps this administrator was trying to generate traffic on what is a pretty boring discussion. Anyway, I like teaching biologists the physics and mathematics of biological evolution. But I have to keep the discussion at a beginner's level because of their minimal training and very biased understanding of the subject. It's hard to teach the physical and mathematical facts of life about biological evolution when all the student knows is what is taught in his fossil tea-leaf reading courses. Why so few transitional fossils (are there really any?) when it takes a billion replications for each transitional adaptational step in the Kishony and Lenski experiments?

This message is a reply to:
 Message 145 by Tanypteryx, posted 09-20-2022 11:32 PM Tanypteryx has replied

Replies to this message:
 Message 148 by nwr, posted 09-21-2022 10:52 AM Kleinman has replied
 Message 151 by Tanypteryx, posted 09-21-2022 12:24 PM Kleinman has not replied
 Message 157 by ringo, posted 09-21-2022 3:08 PM Kleinman has replied

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


Message 152 of 2926 (898242)
09-21-2022 12:41 PM
Reply to: Message 148 by nwr
09-21-2022 10:52 AM


A response to Percy
This message is a response to Percy, now nwr. Sorry Percy, I clicked the wrong reply button.
Kleinman:
You seem to be good at formatting, I'll leave that to you.
Percy:
Oh, Professor Kleinman, you are too funny, talking of math while presenting no equations. I get it. You want us to create the equations ourselves.

Do you mean like
P(Ac)=((1-P(BeneficialA)mu)^n)^nGA=(1-P(BeneficialA)mu)^n*nGA ?
It looks so much prettier the say you format it. I notice you didn't put the greek letter "mu", you used "u". You should correct that.
Kleinman:
You do seem to be having some difficulty with physics and math.
Percy:
Oh, yes, Professor Kleinman, I have many problems with physics and math. In the mathemacian/physicist/engineer jokes, I was the engineer who proceeded half the distance to the beautiful woman on each strike of the clock, and I was the mathematician who let the fire burn once he knew there was a solution, and I was the physicist who thought that 9 not being a prime number could be experimental error.

I'm not familiar with your last two jokes. But I do think you finally get that biological evolutionary competition is a conservation of energy problem, not a conservation of space problem.
Kleinman:
For example, you seem to think that populations are competing for space.
Percy:
I am so embarrassed about my wrong guess that you meant lebensraum. Are they maybe competing for poker chips?

There's a lot of guessing and speculation that goes on in this topic and not very much systematic study and logic. I wasn't the first to describe biological competition as a conservation of energy process. The first time I encounter this idea was when I read this paper:
https://www.ncbi.nlm.nih.gov/...33847/pdf/pnas00072-0402.pdf
What I did was make this concept a bit simpler so that biologists and laymen could understand it.
Kleinman:
Percy has posted equation (5) from my paper:
The basic science and mathematics of random mutation and natural selection
Percy:
That would be this equation:
(Percy nicely formatted equation (5) here)
Kleinman:
And wants to know the difference between that equation and equation [3] from the Lenski team paper.
Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations
Percy:
That would be this equation:

(Percy nicely formatted equation [3] from Lenski paper here)

You implied this equation was wrong when you said, "Their problem is that they are assuming that biological evolution obeys an exponential (or exponential-like) distribution function," in Message 59. But your equation has exponentials, too. You didn't provide any equations yourself, so first tell me if I've chosen the right equations, because it is very difficult to tell which equations you mean you when just post a link to a paper and do not specify which equation. If I selected the wrong equations then please post the correct ones.

And if I selected the correct equations then why don't they appear comparable, since one is probability for a single mutation and the other is just a distribution of probabilities across multiple mutations. Except for the distribution aspect, shouldn't these equations be very similar?



Lenski's equation [3] is not erroneous, it is just not the correct probability distribution equation for DNA evolutionary modification. Go back to the fundamentals of probability theory. Identify the random trial(s). In the random mutation process, the replication is the primary random trial with two possible outcomes, a mutation occurs or a mutation doesn't occur. There is a second random trial that also occurs in this process and that is the mutation itself which has possible outcomes of base substitutions, insertions, deletions, double insertions... Different probability distributions have a lot of similarities. For example, the Poisson distribution is a limiting case for the binomial distribution. Lenski might be able to get his exponential distribution to approximately fit his data but I think it is much more instructive to derive the correct distribution function(s) if you are able to. BTW, if Lenski and his team were to derive an "at least one" probability equation, it would be very similar to the one I derived. One last point, the DNA evolutionary process is actually a Markov random walk process. I derived a slightly different Markov model than biologists use. My model is a non-stationary non-equilibrium model which gives a good prediction of the distribution of variants for the Kishony experiment. This model also gives results consistent with my binomial probability model. If you want to read that paper, you can find it here:
The Kishony Mega-Plate Experiment, a Markov Process

Edited by Kleinman, : Msg should be directed to Percy


This message is a reply to:
 Message 148 by nwr, posted 09-21-2022 10:52 AM nwr has seen this message but not replied

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


Message 156 of 2926 (898251)
09-21-2022 1:21 PM
Reply to: Message 150 by Taq
09-21-2022 10:55 AM


Re: Apples and oranges
Kleinman:
What Lenski found is that it took billions of replications for each beneficial mutation to occur on his most fit lineage and Kishony found that it requires a colony size of a billion for a beneficial mutation to occur. This should not have been a surprise since beneficial (and all) mutations occur at a frequency of about 1/(mutation rate) replications.
Taq:
You are again assuming all adaptations are the same. They aren't. Let's take a look at a classic paper, the Lederbergs' plate replica paper:

Not at all, but use whatever reference you want and give us the correct mathematical explanation for the Kishony and Lenski experiments.

This message is a reply to:
 Message 150 by Taq, posted 09-21-2022 10:55 AM Taq has replied

Replies to this message:
 Message 163 by Taq, posted 09-21-2022 6:11 PM Kleinman has replied

  
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