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Author Topic:   Exposing the evolution theory. Part 2
Tanypteryx
Member
Posts: 4344
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 5.8


(3)
Message 736 of 1104 (909204)
03-29-2023 1:39 PM
Reply to: Message 735 by Kleinman
03-29-2023 1:35 PM


Conman the bullshitter writes:
Tany is a perfect example of why social promotion has failed the educational system.
Says the guy who got his MD from a Caribbean diploma mill.

Stop Tzar Vladimir the Condemned!

What if Eleanor Roosevelt had wings? -- Monty Python

One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie

If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy

The reason that we have the scientific method is because common sense isn't reliable. -- Taq


This message is a reply to:
 Message 735 by Kleinman, posted 03-29-2023 1:35 PM Kleinman has replied

Replies to this message:
 Message 737 by Kleinman, posted 03-29-2023 1:47 PM Tanypteryx has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 737 of 1104 (909205)
03-29-2023 1:47 PM
Reply to: Message 736 by Tanypteryx
03-29-2023 1:39 PM


Kleinman:
Tany is a perfect example of why social promotion has failed the educational system.
Tanypteryx:
Says the guy who got his MD from a Caribbean diploma mill.

And passed all my licensing examinations with high scores the first time through. Tell us all about your social promotions and how you can explain the evolution of drug resistance and why cancer treatments fail. We won't hold our breath for your explanation. Your school graduated some really dumb biologists, like you.

This message is a reply to:
 Message 736 by Tanypteryx, posted 03-29-2023 1:39 PM Tanypteryx has replied

Replies to this message:
 Message 738 by Tanypteryx, posted 03-29-2023 1:54 PM Kleinman has replied

  
Tanypteryx
Member
Posts: 4344
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 5.8


(1)
Message 738 of 1104 (909207)
03-29-2023 1:54 PM
Reply to: Message 737 by Kleinman
03-29-2023 1:47 PM


Oh, boohoo, the biologists are all so mean! They hurt your poor feelings when they all said you are full of shit. You're a conman and a fraud.

Stop Tzar Vladimir the Condemned!

What if Eleanor Roosevelt had wings? -- Monty Python

One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie

If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy

The reason that we have the scientific method is because common sense isn't reliable. -- Taq


This message is a reply to:
 Message 737 by Kleinman, posted 03-29-2023 1:47 PM Kleinman has replied

Replies to this message:
 Message 740 by Kleinman, posted 03-29-2023 2:05 PM Tanypteryx has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 739 of 1104 (909208)
03-29-2023 1:58 PM


Bears repeating every now and then:
Panda's Thumb Forum
Evaluating Alan Kleinman's arguments
By Joe Felsenstein
September 6, 2021 18:00 MST
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.
Let me explain.
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:
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.
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.
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.
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.
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”.
Some questions arise:
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?
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.
[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.
[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.
Evaluating Alan Kleinman's arguments

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London. Olen Suomi Soy Barcelona. I am Ukraine.

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


Replies to this message:
 Message 741 by Kleinman, posted 03-29-2023 2:17 PM Tangle has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 740 of 1104 (909209)
03-29-2023 2:05 PM
Reply to: Message 738 by Tanypteryx
03-29-2023 1:54 PM


Tanypteryx:
Oh, boohoo, the biologists are all so mean! They hurt your poor feelings when they all said you are full of shit. You're a conman and a fraud.
You must be smoking some wacky tobacky or be on the sauce. A ding-dong like you doesn't hurt my feelings. You reveal how dumb you are when you fail to explain how drug resistance evolves and why cancer treatments fail. You should stick with what you are good at, catching bugs and sticking a pin through them in a cigar box.

This message is a reply to:
 Message 738 by Tanypteryx, posted 03-29-2023 1:54 PM Tanypteryx has not replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 741 of 1104 (909210)
03-29-2023 2:17 PM
Reply to: Message 739 by Tangle
03-29-2023 1:58 PM


Tangle's quote from Panda's Thumb:
Bears repeating every now and then:

Panda's Thumb Forum

Evaluating Alan Kleinman's arguments
By Joe Felsenstein
You wouldn't understand it but Joe Felsenstein makes a major mathematical blunder when doing his phylogenetics. He doesn't do his sample randomly.
Statistics for Dummies
quote:
How do you select a statistical sample in a way that avoids bias? The key word is random. A random sample is a sample selected by equal opportunity; that is, every possible sample of the same size as yours had an equal chance to be selected from the population. What random really means is that no subset of the population is favored in or excluded from the selection process.
Non-random (in other words bad) samples are samples that were selected in such a way that some type of favoritism and/or automatic exclusion of a part of the population was involved, whether intentional or not.
I'll make it simple for you Tangle. Felsenstein tries to determine relatedness by finding 40 or so bases to compare. He ignores all the rest of the genome that differs between the two species he is trying to compare. This is garbage.
If you don't think that is what he is doing, look at this explanation from Stanford.
How to build a phylogenetic tree
quote:
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.
His technique ignores the fundamental principles of doing statistical analysis correctly. That is why his work is garbage.

This message is a reply to:
 Message 739 by Tangle, posted 03-29-2023 1:58 PM Tangle has replied

Replies to this message:
 Message 742 by Tangle, posted 03-29-2023 3:01 PM Kleinman has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(3)
Message 742 of 1104 (909211)
03-29-2023 3:01 PM
Reply to: Message 741 by Kleinman
03-29-2023 2:17 PM


Kleinman writes:
His technique ignores the fundamental principles of doing statistical analysis correctly. That is why his work is garbage.
I've been here 12 years Keinman, I've seen dozens of fruit-loops like you claim extraordinary things. It always take the same form - 'I've found something that proves that all of science for the last 200 years is wrong'. The details of why and how vary, but it all resolves to the same thing.
The claims would instantly gain a Nobel Prize if correct, but as yet, none have materialised. Instead a few have ended in the loony bin.
The central problem is ego and an irrational blindness to legitimate criticism. You can never be a scientist because you totally lack objectivity and self-criticism. You can never accept that you might be wrong and the reason is your religious belief system. That corrupts your mind. Real scientists who also hold religious beliefs - which are the majority - are able to separate their beliefs from their science. You can't, so you are forced to fail and be embarrassing to watch.

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London. Olen Suomi Soy Barcelona. I am Ukraine.

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


This message is a reply to:
 Message 741 by Kleinman, posted 03-29-2023 2:17 PM Kleinman has replied

Replies to this message:
 Message 743 by Kleinman, posted 03-29-2023 3:19 PM Tangle has replied
 Message 745 by dwise1, posted 03-29-2023 3:52 PM Tangle has not replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 743 of 1104 (909212)
03-29-2023 3:19 PM
Reply to: Message 742 by Tangle
03-29-2023 3:01 PM


Kleinman:
His technique ignores the fundamental principles of doing statistical analysis correctly. That is why his work is garbage.
Tangle:
I've been here 12 years Keinman, I've seen dozens of fruit-loops like you claim extraordinary things. It always take the same form - 'I've found something that proves that all of science for the last 200 years is wrong'. The details of why and how vary, but it all resolves to the same thing.

The claims would instantly gain a Nobel Prize if correct, but as yet, none have materialised. Instead a few have ended in the loony bin.

Tangle, you are really slow at this. Edward Tatum (you know him, he shared 1/2 the Nobel Prize with George Beadle) in his 1958 Nobel Laureate Lecture explained the crucial principle of descent with modification and adaptation. Do I need to post his quote again for you? It is the multiplication rule of probabilities. The only thing that I have done is the mathematics of what he wrote about. If biologists don't understand the math, they need better training because this math is really simple and well-known by probability theory mathematicians. Biologists have been wrong about evolution, in particular, universal common descent and because of this, they have failed to correctly explain the evolution of drug resistance and why cancer treatments fail. Perhaps we will have to wait another century for biologists to get this physical phenomenon right.

This message is a reply to:
 Message 742 by Tangle, posted 03-29-2023 3:01 PM Tangle has replied

Replies to this message:
 Message 744 by Tangle, posted 03-29-2023 3:32 PM Kleinman has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(2)
Message 744 of 1104 (909213)
03-29-2023 3:32 PM
Reply to: Message 743 by Kleinman
03-29-2023 3:19 PM


I'm not interested Kleinman; it's not me you have to convince, it's the guys that work in the disciplines you are trying to say are wrong.
Nobody recognises your amazing insights. The reason is that you're both wrong and delusional.

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London. Olen Suomi Soy Barcelona. I am Ukraine.

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


This message is a reply to:
 Message 743 by Kleinman, posted 03-29-2023 3:19 PM Kleinman has replied

Replies to this message:
 Message 746 by Kleinman, posted 03-29-2023 3:58 PM Tangle has not replied

  
dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 745 of 1104 (909215)
03-29-2023 3:52 PM
Reply to: Message 742 by Tangle
03-29-2023 3:01 PM


That corrupts your mind. Real scientists who also hold religious beliefs - which are the majority - are able to separate their beliefs from their science.
For example, there is at least one YEC associated with the Institute for Creation Research (ICR, the organization which created "creation science") who has actual training in science and had published actual scientific papers. The difference is that his scientific work did not depend on nor include his YEC beliefs, whereas his creationist work plays as fast and loose with science as any other creationist's work does. Come to think of it, all his actual scientific work was before he joined the ICR, after which there's nothing but YEC stuff.
To draw from the teachings of Mr. Miyagi: Either do science-yes or science-no, but not science-maybe. Do science-maybe and you get squished like a grape.
FWIW, the character of Mr. Miyagi was based on my own sensei, Fumio Demura.

This message is a reply to:
 Message 742 by Tangle, posted 03-29-2023 3:01 PM Tangle has not replied

Replies to this message:
 Message 747 by Kleinman, posted 03-29-2023 4:05 PM dwise1 has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 746 of 1104 (909216)
03-29-2023 3:58 PM
Reply to: Message 744 by Tangle
03-29-2023 3:32 PM


Tangle:
I'm not interested Kleinman; it's not me you have to convince, it's the guys that work in the disciplines you are trying to say are wrong.

Nobody recognises your amazing insights. The reason is that you're both wrong and delusional.
Tangle, you are just one of the pawns that blindly follow whatever you are told. Go join Phat in the land of the uninterested. Drug resistance and cancer treatment failure are just too difficult a topic for you and biologists.

This message is a reply to:
 Message 744 by Tangle, posted 03-29-2023 3:32 PM Tangle has not replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 747 of 1104 (909217)
03-29-2023 4:05 PM
Reply to: Message 745 by dwise1
03-29-2023 3:52 PM


Tangle:
That corrupts your mind. Real scientists who also hold religious beliefs - which are the majority - are able to separate their beliefs from their science.
dwise1:
For example, there is at least one YEC associated with the Institute for Creation Research (ICR, the organization which created "creation science") who has actual training in science and had published actual scientific papers. The difference is that his scientific work did not depend on nor include his YEC beliefs, whereas his creationist work plays as fast and loose with science as any other creationist's work does. Come to think of it, all his actual scientific work was before he joined the ICR, after which there's nothing but YEC stuff.

To draw from the teachings of Mr. Miyagi: Either do science-yes or science-no, but not science-maybe. Do science-maybe and you get squished like a grape.

FWIW, the character of Mr. Miyagi was based on my own sensei, Fumio Demura.

Since it seems that you understand a little bit of probability theory, why don't you teach biologists about the "at least one" rule and the multiplication rule of probabilities? Taq still has difficulty understanding that one uses the multiplication rule when computing the joint probability of two random events. That includes the joint probability of the recombination of two adaptive alleles.

This message is a reply to:
 Message 745 by dwise1, posted 03-29-2023 3:52 PM dwise1 has replied

Replies to this message:
 Message 748 by dwise1, posted 03-29-2023 5:34 PM Kleinman has replied

  
dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 748 of 1104 (909218)
03-29-2023 5:34 PM
Reply to: Message 747 by Kleinman
03-29-2023 4:05 PM


Since it seems that you understand a little bit of probability theory, why don't you teach biologists about the "at least one" rule and the multiplication rule of probabilities?
I have. You are the one who refuses to learn.
And just what the fuck does your "reply" have to do with anything that I had written there?
Are replies yet another thing that you refuse to understand?
Stupid troll!

This message is a reply to:
 Message 747 by Kleinman, posted 03-29-2023 4:05 PM Kleinman has replied

Replies to this message:
 Message 752 by Kleinman, posted 03-29-2023 5:58 PM dwise1 has not replied

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


Message 749 of 1104 (909219)
03-29-2023 5:39 PM
Reply to: Message 733 by Kleinman
03-29-2023 12:56 PM


Kleinman writes:
Take Punnett's square or anything else you know about genetics and you still can't explain the evolution of drug resistance or why cancer treatments fail.
I already did that in this thread:
https://www.evcforum.net/dm.php?control=msg&t=20319
Biologists failed at understanding the fundamental principle of descent with modification and adaptation.
No, they didn't. You fail at even the basics of sexual reproduction. That is why you keep bringing up the multiplication rule which does not apply to sexual reproduction.

This message is a reply to:
 Message 733 by Kleinman, posted 03-29-2023 12:56 PM Kleinman has not replied

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


Message 750 of 1104 (909220)
03-29-2023 5:52 PM
Reply to: Message 731 by Kleinman
03-29-2023 12:51 PM


Re: problems with detecting design
Kleinman writes:
Let's consider another one of your irrational ideas in more detail, that of ERVs. You claim that humans and chimps share 203,000 ERVs because a common ancestorial lineage had these ERVs before the human and chimp lineages branched.
Humans have 203,000 ERVs. Period. How much we share with chimps is a separate question. You can't even accept the fact that there are 203,000 ERVs in our genome as detailed in the 2001 human genome paper.
Were ERVs being accumulated in the genomes of the earliest life forms? If so, what is the percentage of the genome of these ERVs accumulated? And when were these ERVs accumulated in human/chimpanzee lineage.
I already answered those questions. Here it is again. Please read it this time:
I'm not sure when the earliest retroviruses started inserting themselves into the genomes of host organisms. However, as they accumulate mutations, recombine, and are deleted by indel events they are no longer recognizable as retroviral insertions by the algorithms used to detect such sequences. So you have really old insertions that are either completely removed by indel events or mutated to the point that they are no longer recognizable as ERV's. There are other older insertions that are just on the edge of being detected. Then there are progressively newer insertions that are increasingly easier to recognize as ERV's.

The 8% figure for the human genome also includes MaLR's which is a combination of transposon and retroviral repeats. It is a transposon that has picked up a retroviral LTR and is populating the human genome through transposon activity. I usually don't count these as ERV's. The figure I use is 4.7% from ERV classes I-III as detailed in the 2001 human genome paper. The vast majority of those insertions are just solo LTR's due to homologous recombination between the homologous LTR's.
Viruses attack every life form.
Retroviruses don't. You were asking about retroviruses. The origin of retroviruses put them in the Paleozoic:
quote:
Recent research employing a wide variety of bioinformatic approaches has demonstrated that retroviruses evolved during the early Palaeozoic Era, between 460 and 550 million years ago, providing the oldest inferred date estimate for any virus group.
Origin of the retroviruses: when, where, and how? - PubMed
As far as I know, retroviruses only infect vertebrates.
The probability of an adaptive recombination event occurring depends on the frequencies of each of the adaptive alleles. You compute that joint probability by multiplying each of the frequencies of those alleles.
You have claimed that the multiplication rule is the probability of two mutations occurring in the same lineage without any recombination.
If this is your new multiplication rule, then how is it a problem for evolution? As two beneficial mutations both increase in frequency due to natural selection they will inevitably end up in the same genome.

This message is a reply to:
 Message 731 by Kleinman, posted 03-29-2023 12:51 PM Kleinman has replied

Replies to this message:
 Message 757 by Kleinman, posted 03-29-2023 6:12 PM Taq has replied

  
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