Rebuttal To Creationists - "Since We Can't Directly Observe Evolution..."

I tried to find your paper and ended up reading a rebuttal direceted at you over at Panda's Thumb. Why did they ban you?

Joe Felsenstein:

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Evaluating Alan Kleinman's arguments
By Joe Felsenstein
September 6, 2021 18:00 MST

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Alan Kleinman has been commenting on various threads here at PT, in ways that repeatedly argue that he has done the first correct probabilistic analysis of “DNA evolutionary adaptation” and “competition”, and that call for evolutionary biologists to provide an analysis of the Lenski and Kishony experiments in bacterial evolution. He also argues that we have not provided a correct analysis of bacterial antibiotic resistence or of the evolution of drug resistance in cancer. This thread is intended to allow discussion of these assertions, without disrupting discussions of other topics at PT.

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Let me explain.

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Kleinman has published 7 papers on modeling evolutionary processes. I have provided links to PDFs of these, when I encountered ones that might be free:

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Kleinman, A. 2014. The basic science and mathematics of random mutation and natural selection Statistics in Medicine 33 (29): 5074–5080 (PDF)
Kleinman, A. 2015. Random recombination and evolution of drug resistance. Statistics in Medicine 34 (11): 1977–1980.
Kleinman, A. 2016. The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance. Statistics in Medicine 35 (29): 5391-5400
Kleinman, A. 2018a. Random mutation and natural selection in competitive and noncompetitive environments. Biomedical Journal of Scientific & Technical Research 9 (1): 6903–6906. (PDF)
Kleinman, A. 2018b. Malaria and other infectious diseases, Suppression of the evolution of drug resistance. Biomedical Journal of Scientific & Technical Research 12 (2): 9083-9085. (PDF)
Kleinman, A. 2019. Fixation and adaptation in the Lenski E. coli Long Term Evolution Experiment. Biomedical Journal of Scientific & Technical Research 20 (1): 14754–14760. (PDF)
Kleinman, A. M. 2020. Drug resistance, An enemy of targeted cancer therapies. Annals of Clinical and Medical Case Reports 4 (9): 1–4.

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He has also brought his argument up repeatedly at Peaceful Science and at Panda"s Thumb, usually in the middle of threads devoted to other issues.

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The basic calculation he does is to consider a haploid clonally-reproducing organism such a bacterial culture, one which has no recombination. He develops a formula for the probability that the clone has beneficial mutations occuring at n sites, where the first such mutation has nGA generations to occur, the second has nGB generations to occur, and so on. Note that an important feature of his model is that he considers, not the time in generations but the number of cells that have ever arisen in the clone. So with a probability mu PA for each new cell that it has a beneficial mutation, it takes about 1/(mu PA) cells before there is a reasonable probability of seeing the beneficial mutation once.

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A mystery (to me, anyway) is where selection is in all this. We are computing probabilities that, when a given number of cells has arisen, we have had beneficial mutation at all of the n sites. Once one has occurred, there seems to be no futher mutation at that site. Why? This calculation is supposed to show us the fundamental mathematical theory of mutation and selection, but aside from waiting until a mutation labelled “beneficial” occurs, there is no further effect of selection.

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The same theory is also used in most of his other papers (an exception being the paper on recombination which I will get back to later). He has an idiosyncratic terminology. As far as I can tell it involves calling the occurrence of beneficial mutations by mutation “DNA adaptive evolution” while he calls their subsequent changes of gene frequency in the population “competition”.

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Some questions arise:

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Kleinman sees two processes at work: “competition” which is survival of the fittest, and “DNA evolutionary adaptation” which is changes of genotypes by mutation, either deleterious or beneficial. Is this terminology helpful?
His equations are all about how many organisms (or cells) need to have arisen to get a given probability that a beneficial allele will arise by mutation. The theory uses the stochastic process of mutation. How does natural selection affect this?
His treatment of recombination between genotypes with two or more loci assumes that offspring of a cross between a haploid Ab genotype and a haploid aB genotype will all be AB. Is that true?
He seems to think that he is the first to give a correct mathematical theory of mutation and natural selection. Was he? For example, his first paper has the rather astonishingly grand title “The basic science and mathematics of random mutation and natural selection”. Would RA Fisher (1922) or JBS Haldane (1924) have agreed? I think he is off by 97-99 years.
Is he really the first to apply the mathematics of population genetics theory to evolution or drug resistance in cancer, or to success of multidrug therapies for diseases?

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Anyway, I must be misunderstanding how his theory works, and I hope that this thread will explain his theory to me. After all, if it is the fundamental mathematical theory of my own field, then it is surely important to know. By doing the discussion here, we can avoid being so rudely interrupted by the folks in the previous threads who were trying to discuss arguments other than Kleinman"s.

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[Note added 9 October 2021] After 2,111 comments in this thread, many by AK, I am placing him on pre-moderation and limiting him to 1 comment per day. I will accumulate his future comments and release them at a rate of 1 per day. People who consider this unreasonable suppression of discussion are invited to read his past comments and consider his responses to counterarguments.

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[Note added 10 October 2021] Owing in part to remarks addressed to me today in comments at the thread Return of the God of the Gaps, Alan Kleinman has been banned from PT.

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Theodoric:

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You are an idiot. He agrees.

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Then you are both wrong. The difference between an open and closed system is that in the closed system, neither energy, matter, nor entropy can be transported across that boundary. In an open system, energy, matter, and entropy can be transported that boundary and you must include those components in your calculation. The laws of thermodynamics apply to both open and closed systems and you had better choose a better expert. Here are a couple of links that show you how to calculate entropy in an open system.
Second law of thermodynamics - Wikipedia
Starts at 6.10 Applications of the second law of thermodynamics in open systems – Introduction to Engineering Thermodynamics Real engineering (and biological) problems involve open systems. And both open and closed systems are governed by the laws of thermodynamics. You and your so-called expert can't solve real problems including descent with modification.You have a made-up expert that doesn't understand the difference between an open and closed system.

Phat:

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I tried to find your paper and ended up reading a rebuttal direceted at you over at Panda's Thumb. Why did they ban you?

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Which paper are you looking for? Felsenstein banned me because I told him he would be held accountable for his blunders. His two blunders are that he uses the wrong equation(s) to do his phylogenetics in his statistical model. And much worse than that, he doesn't do random sampling of his data when doing his statistical analysis. In addition, he refuses to apply any of his models to real examples of evolution, the Kishony and Lenski experiment. All his work is strictly theoretical, he refuses to apply any of his models to actual examples of biological evolution that are real, measurable, and repeatable. I believe he won't do this because he knows his models are wrong. Here's what he said on the "Sandwalk" blog:
Contingency, selection, and the long-term evolution experiment

Joe Felsenstein:

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I am not going to do some long study of the LTEE, but I thought I should document my assertion that Alan Kleinman's work ignores natural selection. Let me concentrate on his 2014 paper in the journal Statistics in Medicine, which is his first on mutation and natural selection, and is grandly entitled "The basic science and mathematics of random mutation and natural selection". It turns out to be a lot narrower than that, analysing a model where 5 favorable mutations can occur at a locus, but only if they occur in a particular order, first A, then B, then C, then D, then E.

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Kleinman starts out correctly, computing in his equations (4) through (9) the probability that mutation A will not occur in the first nGA generations in a population of size n. Then he goes on in equation (10) to mutation B, trying to compute the probability of it not occurring in a subsequent GB generations. There is where things go wrong. He assumes that the 'subpopulation size" of A-containing members of the population is nA. Although he later acknowledges that the numbers of those in the population will change, he does not allow that in his math, keeping nA constant in each of the subsequent nGB generations. There is the point where I first find an error. Perhaps Alan Kleinman can explain that one specific point, rather than demanding that we all discuss the LTEE in detail.

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It should be pointed out that Felsenstein does his phylogenetics with equations that don't include natural selection. Descent with modification does not include a term for natural selection (relative fitness) because it is a different process than biological competition (which Felsenstein also does not include in his math). That's why his math won't work for the Lenski experiment, Felsenstein doesn't include biological competition.And my math is correct, once an adaptive mutation occurs, it doesn't matter how many replications that variant does because the number of those beneficial mutations will always be much larger than any that occur by further mutation. That's exactly what the Kishony experiment demonstrated.In addition, Felsenstein doesn't understand how thermodynamics applies to biological evolution. He tries to figure it out in this Cambridge Lecture:
https://www.youtube.com/watch?v=ZF3nIMvBBDw&ab_channel=Fi...
His discussion on thermodynamics starts at about 21:58 but he still doesn't understand the distinction between biological competition and descent with modification.

But you do not seem to grasp that in an open system there is no limit on usable energy.

Explain the equation and the energy component.

Theodoric:

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But you do not seem to grasp that in an open system there is no limit on usable energy.

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An infinite carrying capacity environment only exists in your imagination. But, go for it, tell us where there is an environment with no limit on usable energy.

I am always stunned by the hubris of cranks and trolls. The amount of narcissism it must take in order to believe you know more than every expert in the field. To think that you are the world's leading expert in a subject you have no advanced education in is not just stunning but shows a severe mental health defect.
You are truly a god among me. Not because of your knowledge or scientific arguments, but because of your conceit, hubris, and narcissism.

Theodoric:

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Explain the equation and the energy component.

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Which equation and what energy? If you are talking about biological competition and descent with modification, I've already explained how energy relates to biological competition and the Markov equation explains how entropy increases. The Markov process can't occur if there isn't sufficient energy for replication.

We are talking about life and life processes. So on Earth, the usable energy is (for all intents and purposes) unlimited.

The equation in the wiki article you linked to.

Theodoric:

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I am always stunned by the hubris of cranks and trolls. The amount of narcissism it must take in order to believe you know more than every expert in the field. To think that you are the world's leading expert in a subject you have no advanced education in is not just stunning but shows a severe mental health defect.
You are truly a god among me. Not because of your knowledge or scientific arguments, but because of your conceit, hubris, and narcissism.

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I guess that means you won't tell us of an environment with infinite carrying capacity. Perhaps your expert can help you. You know, the one that thinks that the laws of thermodynamics don't apply to open systems.

Another strawman. I never said anything about infinite carrying capacity. Liar, dishonest, narcissistic crank.I hope Admin takes the lead of Panda's Thumb and deals with you.

Theodoric:

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We are talking about life and life processes. So on Earth, the usable energy is (for all intents and purposes) unlimited.

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Is that so, so no overpopulation and no competition? And unlimited energy?

Another strawman.

Theodoric:

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The equation in the wiki article you linked to.

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In which case? That's a general equation and several of the terms go to zero for the Kishony and Lenski experiments. But, at least you know that very stupid idea that the laws of thermodynamics don't apply to open systems is wrong. Your so-called expert should know that the laws of thermodynamics apply to open systems even if someone so poorly trained as you don't.