Did Darwin get anything correct and what did Darwin get wrong?

[Dale (evolutionary providentialist)]

@amkleinman

some basic probability theory.

I wonder if Dan Eastwood (@EastwoodDC) might reply here. He is a biostatistician, and you couldn’t snow him with your misperceptions (not that you have anyone else, only yourself).

[T_aquaticus]

@Dale

He is a biostatistician, and you couldn’t snow him with your misperceptions (not that you have anyone else, only yourself).

It’s a very basic mistake:

@amkleinman is painting the targets around the bullet holes.

[Dale (evolutionary providentialist)]

Ah, the Hawaiian sharpshooter. (I don’t want to be statist.)

[Dale (evolutionary providentialist)]

@Randy: His clothing is a bit of a non sequitur for Hawaii – I probably should have said Wyoming (Wyomingite?) sharpshooter. There are way more cowboys there.

[rsewell (RON SEWELL)]

@glipsnort

These aren’t relevant to the number of mutations that have occurred. The correct answer is that chimpanzees have also had every possible single-site mutation in the time since they shared a common ancestor with humans.

I realize. I was jumping ahead to what happens with these mutations. It certainly is not that chimpanzees turn into humans because humans evidenced larger populations, which is where this seemed to be going.

[amkleinman (Alan Kleinman)]

@amkleinman

Why can’t chimpanzees (another branch) get every possible mutation at every site in their genome if they do sufficient replications?

@rsewell

The usual roles of selection and drift would apply. Chimpanzees already have genes well adapted to their arboreal lifestyle.

Are chimpanzees a branch living on a branch? Why haven’t they branched out like humans?

[amkleinman (Alan Kleinman)]

@rsewell

The usual roles of selection and drift would apply. Chimpanzees already have genes well adapted to their arboreal lifestyle.

@glipsnort

These aren’t relevant to the number of mutations that have occurred. The correct answer is that chimpanzees have also had every possible single-site mutation in the time since they shared a common ancestor with humans.

Steve, you will only confuse Ron with the facts. What do you think of T_aquaticus’s claim that if a random event happens, its probability is 1?

[amkleinman (Alan Kleinman)]

@klw

Chimps and humans do not currently share a gene pool. “genes” and “gene pool” are two different things. If you don’t know these basic concepts, perhaps its time to brush up by reading a first year biology textbook.

Does your first-year biology textbook tell you that you can’t compare the reproductive fitness of different species? What if a farmer asks a biologist whether he should grow apples or oranges on his farm? Does the biologist say, sorry, I can’t tell you which would have better reproductive fitness because they are different species.

[amkleinman (Alan Kleinman)]

@amkleinman

First, learn what gene polymorphism is, then, you should learn what is meant by a selective mutation and a selective sweep.

@T_aquaticus

That’s rather rich coming from someone who claimed selective and beneficial mutations were not the same thing.

I don’t recall saying that. Post the quote where I said that. And you still haven’t told us what gene polymorphism is or what a selective sweep is.

@amkleinman

Then, try to think of any experimental or empirical examples of selective sweeps and why this is evidence that humans and chimpanzees didn’t evolve from a common ancestor.

@T_aquaticus

I already gave that to you.

To investigate how sex improves the efficiency of selection, we analysed the dynamics of adaptation. As in earlier studies21,22, asexual populations exhibit signatures of hitchhiking and clonal interference (Fig. 2a–d). Groups of functionally unrelated mutations, linked within the same genetic background, change in frequency together as clonal cohorts. The outcomes of evolution are determined by competition between these cohorts. In contrast, sexual populations are not characterized by cohorts of linked mutations (Fig. 2e–h). Instead, the dynamics of each mutation is largely independent of other variation in the population. In these populations, mutations that occur on different backgrounds fix independently, while others briefly hitchhike to moderate frequencies where they persist or are eliminated from the population.
Sex speeds adaptation by altering the dynamics of molecular evolution | Nature

Do you realize that Desai is trying to duplicate the Lenski experiment except with sexual replicators? How exactly does Desai perform his experiment to get improved fitness to reproduce from his population?

@T_aquaticus

I also showed you the math.

“The mutation rate is about 50 to 100 per individual per generation. This means about 50 to 100 neutral mutations reach fixation in the human population per generation. Over 5 million years, that’s about 200,000 generations since sharing common ancestry with chimps which gives us 10 to 20 million mutations that reach fixation in both lineages. This is in line with the approximately 35 million mutations that separate humans and chimps. This is just for neutral mutations. Beneficial mutations would reach fixation even faster. The number of mutations that separate chimps and humans is entirely in line with what we would expect to see.”

Do you think that humans got improved fitness to reproduce over chimpanzees by neutral evolution? If so, explain how.

@amkleinman

Are you claiming that every human has every mutation that every other human has had overall time?

@T_aquaticus

I am claiming that there are mutations that have fixed across the entire human population, and that is due to common ancestry.

So, how did the 17 mutations from your chimp/human example fix?

@amkleinman

What is the probability of selecting two aces out of the deck?

@T_aquaticus

It’s the same as selecting any two specific cards out of the deck. Just the act of drawing two cards guarantees that you will have a highly improbable outcome.

Why would drawing any two cards be highly improbable? It is only when you draw specific cards that the probabilities become a factor.

@amkleinman

Just because you selected the first ace does not make its probability equal one. You don’t understand basic probability theory.

@T_aquaticus

You aren’t predicting which mutations will occur before they happen. Your argument boils down to this:

I deal a 5 card hand from a poker deck. The cards are 3 of hearts, 2 of spades, king of diamonds, jack of diamonds, and 8 of clubs. What is the probability of getting that hand? It is given by the combinations function in math which is :

C ( n , r ) = ( n r ) = n ! ( r ! ( n − r ) ! )
The odds of getting that hand are about 1 in 2.6 million. You can plug the numbers in here if you want:

You are half right that I’m not predicting which mutations will occur before the happen. When a replicator does 1/(mutation rate) replications (actually slightly more because multiple different mutations can occur at a given site), it is doing an exhaustive search of the sample space, that is, a mutation occurs at every site in the genome. That’s how the Kishony experiment works. In that colony of a billion, there is at least one member in that colony with a mutation at every site in the genome. That lucky member with an adaptive mutation at the correct site can grow in the next higher drug concentration region.

Descent with modification does not depend on combinatorial math. Recombination does.

[amkleinman (Alan Kleinman)]

@amkleinman

some basic probability theory.

@evolutionary providentialist

I wonder if Dan Eastwood (@EastwoodDC) might reply here. He is a biostatistician, and you couldn’t snow him with your misperceptions (not that you have anyone else, only yourself).

Maybe he can correct T_aquaticus’s strange idea that when an event happens, its probability goes to 1. He can check out the math I had published which was peer-reviewed by experts in Probability theory and Statistics. He can try and find an error in the nath, which I doubt he will.

Good luck with your Texas sharpshooter argument because that’s exactly how descent with modification and adaptation works. Only when the population does 1/(mutation rate) replications do you get a reasonable probability that at least 1 adaptive mutation occurs. That’s how the Kishony experiment works, that’s how the Lenski experiment works and that is why humans and chimps did not descend from a common ancestor. You don’t have nearly enough replications.

I’m still waiting on your experts in biology and mathematics to explain how drug resistance evolves and why cancer treatments fail.

[Dale (evolutionary providentialist)]

@amkleinman

Maybe he can correct T_aquaticus’s strange idea that when an event happens, its probability goes to 1.

That’s exactly what it does. You are mistakenly thinking about the probability of the next event.

[T_aquaticus]

@amkleinman

I don’t recall saying that. Post the quote where I said that.

“Read carefully, I wrote selective, not beneficial mutations.” --@amkleinman

@amkleinman

And you still haven’t told us what gene polymorphism is or what a selective sweep is.

I’m not your dictionary.

@amkleinman

Do you realize that Desai is trying to duplicate the Lenski experiment except with sexual replicators? How exactly does Desai perform his experiment to get improved fitness to reproduce from his population?

Desai introduces rounds of sexual reproduction in some populations and only asexual reproduction in others. He got different results in the different populations. Why do you think he got different results?

@amkleinman

Do you think that humans got improved fitness to reproduce over chimpanzees by neutral evolution?

No, I don’t. I am showing you the math for how many mutations we would expect to see if humans and chimps evolved from a common ancestor. You continue to ignore it.

@amkleinman

So, how did the 17 mutations from your chimp/human example fix?

I don’t even know if all 17 are fixed since it is only a comparison of two genomes.

@amkleinman

Why would drawing any two cards be highly improbable?

I just showed you.

@amkleinman

It is only when you draw specific cards that the probabilities become a factor.

It is only when you SPECIFY AHEAD OF TIME that probabilities become a factor. You aren’t doing that with mutations. You are specifying AFTER THEY HAVE APPEARED. It is absolutely guaranteed that there are going to be DNA differences between two primate species if they have evolved for 5 million years from a common ancestor. The differences that do result after evolution are always going to be extremely improbable. The very act of evolution guarantees that we will get a mixture of mutations that are extremely improbable in the very same way that drawing 5 cards guarantees that I will have a hand with a probability of 1 in 2.6 million.

Also, you keep using the mutation rate in bacteria to model humans. This is wrong. The mutation rates are different by a factor of about 10. You also assume that there is only one mutation at any one time that can be beneficial. This is wrong for the vast, vast majority of cases in nature. The paper I gave you for human skin color is a perfect example of this, as is the multiple different beneficial mutations for lactase persistence.

[klw]

Yes my first year biology textbook told me that. And I have taught the same to my own university students for the last 25 years. And it appears even in Wikipedia so apparently is pretty universally known.

The question you pose about the farmer contemplating his choice of crops, is a question of which species is better adapted for the prevailing environmental conditions (best able to exist in a certain ecological niche) and is also a question of economics and the markets. Adaptations to different niches is different than “quantitatively comparing the fitness of two species” which is impossible.

[T_aquaticus]

@amkleinman

Only when the population does 1/(mutation rate) replications do you get a reasonable probability that at least 1 adaptive mutation occurs.

it is absolutely ridiculous to think that there is only 1 possible beneficial mutation in the human genome across all of the environments that humans live in.

@amkleinman

That’s how the Kishony experiment works, that’s how the Lenski experiment works and that is why humans and chimps did not descend from a common ancestor. You don’t have nearly enough replications.

There are plenty, as shown by the math for the fixation of neutral mutations.

@amkleinman

I’m still waiting on your experts in biology and mathematics to explain how drug resistance evolves and why cancer treatments fail.

That’s completely irrelevant to human evolution.

[T_aquaticus]

Another paper showing the math:

Finally, the results for selection acting on 100 loci are shown in Figs. 2E and 2F. In this case, there is a striking difference between the asexual and sexual populations. The initial population contains only low-fitness genotypes where we expect an average of only five favorable alleles per chromosome—given that there are 100 loci and a frequency of 0.05 for the favorable allele at each locus (see Hickey and Golding 2018). The asexual population is again limited to selecting among such low-fitness genotypes. In contrast to this, the sexual population can use recombination to gradually assemble chromosomes with increasing numbers of favorable alleles per chromosome as the frequencies of the favorable alleles rise in response to selection. At the end of the selection period, the sexual population consists of individuals that are homozygous for the favored allele at all 100 loci.
https://cdnsciencepub.com/doi/full/10.1139/gen-2019-0051?rfr_dat=cr_pub++0pubmed&url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org

Simulations of asexual and sexual populations show that in asexual populations just a few of the beneficial alleles can reach fixation because of clonal interference. However, sexual reproduction allows for the shuffling of mutations across the genome which can fix all 100 beneficial loci.

[Mervin_Bitikofer]

@amkleinman

I’m still waiting on …

Are you really? By now we’ve seen you pour forth a multitude of ‘questions’ - every one of which seems to have been answered (many repeatedly) by mainly @T_aquaticus, @klw, and others too. And I thank you for those questions - even if poorly motivated -, because they do make an excellent springboard for knowledgeable people here to continue to educate many of us (like me) who would not be able to answer your questions, and might otherwise be cowed into thinking that perhaps there are problems, where in fact there are none.

It does seem that a want of humility on your part may be preventing you from really benefitting from the answers supplied you here, though. It is the same scourge that reveals so much ideological fruit today for what it really is, and this does not go unnoticed by the observant young. You could be advancing your own knowledge instead of sacrificing it to the service of an ideology that has not served you or others well.

[amkleinman (Alan Kleinman)]

@amkleinman

I’m still waiting on …

@Mervin_Bitikofer

Are you really? By now we’ve seen you pour forth a multitude of ‘questions’ - every one of which seems to have been answered (many repeatedly) by mainly @T_aquaticus, @klw, and others too. And I thank you for those questions - even if poorly motivated -, because they do make an excellent springboard for knowledgeable people here to continue to educate many of us (like me) who would not be able to answer your questions, and might otherwise be cowed into thinking that perhaps there are problems, where in fact there are none.

It does seem that a want of humility on your part may be preventing you from really benefitting from the answers supplied you here, though. It is the same scourge that reveals so much ideological fruit today for what it really is, and this does not go unnoticed by the observant young. You could be advancing your own knowledge instead of sacrificing it to the service of an ideology that has not served you or others well.

Do you think that claiming the probability of an event happening makes that probability go to 1 is a rational answer? Perhaps that is why T_aquaticus can’t explain the evolution of drug resistance and why cancer treatments fail. Doesn’t anyone post on this forum that understands basic probability theory? After all, descent with modification and adaptation is a stochastic process. I’m waiting for a scientific answer, not some weird misunderstanding of well know mathematical principles.

[T_aquaticus]

@amkleinman

Doesn’t anyone post on this forum that understands basic probability theory?

Lots of people do, but apparently you don’t. You actually think you can apply mutation rates in bacteria to human populations. You also think you can apply the probability of antibiotic resistance occurring in bacteria to primate populations. This is all wrong. You act as if one beneficial mutation per billion replications is some sort of physical law. It isn’t. You also can’t understand that drawing a 3 of clubs and a 5 of hearts has the same probability as drawing an ace of spades and an ace of clubs.

You can’t even understand the difference between sexual and asexual reproduction. You can’t understand how there is more than one gene in a genome and how those genes are shuffled in sexual reproduction. Nope. For you, beneficial mutations can only happen in one gene, and one gene only. And no matter what, the rate at which those beneficial alleles appear has to be once in 1 billion replications, no matter what. Never mind you that even the rate of evolution for different single selective pressures in E. coli can differ 1,000 fold.

The culture is fully sensitive to the phage T-1, as well as to streptomycin, and like most E. coli strains gives rise to resistant mutants at rates of approximately 10-7 and 10-10 per division, respectively.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169282/pdf/jbacter00003-0114.pdf

That’s a 1,000 fold difference in the rate of resistance to phage and antibiotic in just one species of bacteria.

[Dale (evolutionary providentialist)]

@amkleinman

Do you think that claiming the probability of an event happening makes that probability go to 1 is a rational answer?

That question is not even constructed properly. You just said a probability of an event makes the probability go to 1. Talk about irrational. The probability of an event happening is 100%… when it has already happened. That’s what you’re not getting (among manifold other things). The probability of the next event is not 1. But like all the rest, the question has already been asked and answered, and more than once. I think the probability of this happening again is high.

[Dale (evolutionary providentialist)]

@T_aquaticus

You also can’t understand that drawing a 3 of clubs and a 5 of hearts has the same probability as drawing an ace of spades and an ace of clubs.

@amkleinman: Let’s try this. If you have a 3 of clubs and a 5 of hearts in your hand, what’s the probability of your having a 3 of clubs and a 5 of hearts in your hand? Or what’s the probability of your having already drawn a 3 of clubs and a 5 of hearts?