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Author Topic:   Should we teach both evolution and religion in school?
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 1561 of 2073 (877942)
06-23-2020 3:20 PM
Reply to: Message 1556 by Kleinman
06-23-2020 12:29 PM


Re: If We Throw The ToE Away, What Will Replace It?
Kleinman writes:
If you want to see immediate steps, take a look at the Kishony experiment.
Your hobby horse is getting worn out.
And why am I picking out fish? Haven't you ever heard a good fish story? You heard about the one-armed fisherman? Someone asked how big the fish was that he caught. He stuck out his arm and said it was that long.
I will ask again. Out of all the non-mammalian ancestors of mammals, why did you select fish? Explain. Why not select the reptile-like mammalian transitionals?

This message is a reply to:
 Message 1556 by Kleinman, posted 06-23-2020 12:29 PM Kleinman has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 1562 of 2073 (877944)
06-23-2020 3:24 PM
Reply to: Message 1560 by Kleinman
06-23-2020 3:16 PM


Re: If We Throw The ToE Away, What Will Replace It?
quote:
The mathematical jabs are even more effective. They keep hitting home.
That’s the misdirection. And no, it doesn’t work that well.
quote:
Of course, if you think that evolution works differently than the way I've published, feel free to post your mathematical explanation. Explain to us how the Kishony and Lenski experiment works. You won't because you can't.
Or because I don’t disagree with you on those experiments. Which is in fact the case. Those papers don’t help you on the claims I take issue with. As I said, it’s just misdirection.
quote:
And you should stop indoctrinating naive school children with your mathematically irrational nonsense.
If you really thought you could show that it was mathematically irrational you would be right there laying out your arguments instead of being evasive about them and trying to change the subject to your papers.

This message is a reply to:
 Message 1560 by Kleinman, posted 06-23-2020 3:16 PM Kleinman has replied

Replies to this message:
 Message 1563 by Kleinman, posted 06-23-2020 3:56 PM PaulK has replied

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


Message 1563 of 2073 (877948)
06-23-2020 3:56 PM
Reply to: Message 1562 by PaulK
06-23-2020 3:24 PM


Re: If We Throw The ToE Away, What Will Replace It?
Kleinman writes:
And you should stop indoctrinating naive school children with your mathematically irrational nonsense.
PaulK writes:
If you really thought you could show that it was mathematically irrational you would be right there laying out your arguments instead of being evasive about them and trying to change the subject to your papers.
Read this paper which shows how the multiplication rule of probabilities applies to DNA evolution.
Just a moment...
This paper shows why it takes 3e9 replications for each evolutionary step. Microbes, weeds, and a few other replicators attain the population sizes necessary for a (small) DNA evolutionary process. Check out this link if you want to get an idea of population sizes for different organisms.
Lists of organisms by population - Wikipedia

This message is a reply to:
 Message 1562 by PaulK, posted 06-23-2020 3:24 PM PaulK has replied

Replies to this message:
 Message 1564 by PaulK, posted 06-23-2020 4:12 PM Kleinman has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 1564 of 2073 (877950)
06-23-2020 4:12 PM
Reply to: Message 1563 by Kleinman
06-23-2020 3:56 PM


Re: If We Throw The ToE Away, What Will Replace It?
quote:
Read this paper which shows how the multiplication rule of probabilities applies to DNA evolution.
And it doesn’t help your argument very much. To raise an obvious point, do the constraints on improving enzymatic function apply to the same extent to mutations that produce the anatomical changes you focus on with regard to the evolution of birds? Or was there a greater range of available trajectories?
They certainly don’t apply to the neutral changes which dominate the DNA differences between humans and chimpanzees.
quote:
This paper shows why it takes 3e9 replications for each evolutionary step.
And that is obviously incorrect. Since multiple genes can be evolving in parallel there will be more than one possible step, even aside from the possibility of more options for an individual gene.
You cannot say that a model of evolution in one gene accurately captures the evolution of the whole genome. Even if the same conditions applied to every gene - and obviously you do not show even that much.
Understanding is more than doing calculations - it is necessary to understand how they relate to the world they attempt to model. And that is where your arguments fail.

This message is a reply to:
 Message 1563 by Kleinman, posted 06-23-2020 3:56 PM Kleinman has replied

Replies to this message:
 Message 1565 by Kleinman, posted 06-23-2020 5:38 PM PaulK has replied

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


Message 1565 of 2073 (877959)
06-23-2020 5:38 PM
Reply to: Message 1564 by PaulK
06-23-2020 4:12 PM


Re: If We Throw The ToE Away, What Will Replace It?
Kleinman writes:
This paper shows why it takes 3e9 replications for each evolutionary step.
PaulK writes:
And that is obviously incorrect. Since multiple genes can be evolving in parallel there will be more than one possible step, even aside from the possibility of more options for an individual gene.
You cannot say that a model of evolution in one gene accurately captures the evolution of the whole genome. Even if the same conditions applied to every gene - and obviously you do not show even that much.
It's correct if the mutation rate is e-9. And you need to explain why hiv can't evolve in parallel when subject to three selection pressures targeting only two genes. Or are you arguing that combination selection pressures won't work for treating hiv because evolution occurs in parallel? Read this paper if you want to understand what happens when evolution must work in parallel to multiple simultaneous selection pressures:
Just a moment...
And selection pressures can target one or more genes and the math still applies. This is why this math works for the Lenski experiment because every gene in every metabolic pathway that requires energy will be acted on by his starvation selection conditions. And beneficial mutations at any one of these genetic loci obey this math. The beneficial mutations don't have to occur in any particular gene, all they have to do is improve reproductive fitness.

This message is a reply to:
 Message 1564 by PaulK, posted 06-23-2020 4:12 PM PaulK has replied

Replies to this message:
 Message 1566 by PaulK, posted 06-23-2020 11:43 PM Kleinman has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 1566 of 2073 (877966)
06-23-2020 11:43 PM
Reply to: Message 1565 by Kleinman
06-23-2020 5:38 PM


Re: If We Throw The ToE Away, What Will Replace It?
quote:
It's correct if the mutation rate is e-9
AND there is only one beneficial mutation across the whole genome.
Which is not exactly plausible,
quote:
And you need to explain why hiv can't evolve in parallel when subject to three selection pressures targeting only two genes.
I don’t because my point was that an organism isn’t restricted to following a single trajectory - the next beneficial mutation doesn’t have to be related to the last one. Don’t forget that multiply-resistant bacteria are common although the resistances are not part of a single trajectory.
However, I can explain - and I already have explained to you in the past - that while hard selection works poorly in parallel, soft selection does. The problem for HIV is that the negative selection is so strong that the additional pressure leads to extinction. But in the case of soft selection or drift, where the population is not decreasing, that issue does not exist.

This message is a reply to:
 Message 1565 by Kleinman, posted 06-23-2020 5:38 PM Kleinman has replied

Replies to this message:
 Message 1567 by Kleinman, posted 06-24-2020 9:29 AM PaulK has replied

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


Message 1567 of 2073 (877979)
06-24-2020 9:29 AM
Reply to: Message 1566 by PaulK
06-23-2020 11:43 PM


Re: If We Throw The ToE Away, What Will Replace It?
Kleinman writes:
It's correct if the mutation rate is e-9
PaulK writes:
AND there is only one beneficial mutation across the whole genome.
Which is not exactly plausible,
You either have not followed or understood my discussion with Taq on the "Do you really understand the mathematics of evolution" topic. If you have 2 possible beneficial mutations, the number of replications required is still over a billion replications. Msg 92 in that thread shows you how to do the probability calculation if you have more than 1 possible beneficial mutation. But what happens after that first beneficial mutation occurs? Are there many beneficial mutations for the next and ensuing evolutionary steps for that selection pressure? The answer is no! Read this paper and find out why.
Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins
The reason why this happens is that whatever evolutionary trajectory has been taken by a lineage, each step on that evolutionary trajectory must give improved reproductive fitness because it takes replications for there to be a reasonable probability of the next beneficial occurring and that is on the order of a billion replications for each evolutionary step for each variant of each lineage on any evolutionary trajectory.
Kleinman writes:
And you need to explain why hiv can't evolve in parallel when subject to three selection pressures targeting only two genes.
PaulK writes:
I don’t because my point was that an organism isn’t restricted to following a single trajectory - the next beneficial mutation doesn’t have to be related to the last one. Don’t forget that multiply-resistant bacteria are common although the resistances are not part of a single trajectory.
The point is that hiv can't traverse any possible evolutionary trajectory to improved fitness in the typical lifetime of a patient taking 3 drug therapy. It takes too many replications for the virus to get the beneficial mutations necessary to occur on a single lineage even though the mutation rate for this virus is on the order of e-5.
Another point you are failing to understand is that all lineages on their own particular evolutionary trajectories must accumulate their own particular beneficial mutations. And when those mutations occur at a frequency of e-9, that's going to require about a billion replications for every variant on each evolutionary step no matter which evolutionary trajectory they are on. It is quite likely that there are multiple possible evolutionary trajectories to improved fitness for the Kishony experiment but no matter which trajectory, the variant from that particular lineage on that evolutionary step must still form its colony of about a billion members before the next beneficial mutation has a reasonable probability of occurring.
PaulK writes:
However, I can explain - and I already have explained to you in the past - that while hard selection works poorly in parallel, soft selection does. The problem for HIV is that the negative selection is so strong that the additional pressure leads to extinction. But in the case of soft selection or drift, where the population is not decreasing, that issue does not exist.
Do you think that the intensity of selection is "hard" in the Kishony and Lenski experiments? It takes only 1 beneficial mutation to give improved fitness in either of these experiments. What "hardens" or makes it more difficult for a population to follow an evolutionary trajectory is the number of mutations required to give improved fitness. That's why the Kishony experiment won't work if the step increase in drug concentration is too large requiring more than a single mutation to give improved fitness. It is the same mathematical situation if Kishony were to use 2 drugs at lower concentrations where some member of the colony in the lower drug concentration region must get two mutations before they are able to grow in the next higher drug-concentration region. The difference between your explanations and my explanations is that I publish my mathematical explanations and they predict the behavior of real evolutionary processes. Hard mathematical science is passing up your vague, unsubstantiated explanations. You just don't know it.

This message is a reply to:
 Message 1566 by PaulK, posted 06-23-2020 11:43 PM PaulK has replied

Replies to this message:
 Message 1568 by AZPaul3, posted 06-24-2020 9:49 AM Kleinman has replied
 Message 1572 by PaulK, posted 06-24-2020 12:38 PM Kleinman has replied
 Message 1605 by Taq, posted 06-25-2020 12:15 PM Kleinman has not replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 1568 of 2073 (877980)
06-24-2020 9:49 AM
Reply to: Message 1567 by Kleinman
06-24-2020 9:29 AM


Re: If We Throw The ToE Away, What Will Replace It?
The difference between your explanations and my explanations is that I publish my mathematical explanations and they predict the behavior of real evolutionary processes.
The rest of the discipline doesn't believe you. Another crack in the pot there Kleinman.

Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 1567 by Kleinman, posted 06-24-2020 9:29 AM Kleinman has replied

Replies to this message:
 Message 1569 by Kleinman, posted 06-24-2020 10:02 AM AZPaul3 has replied

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


Message 1569 of 2073 (877981)
06-24-2020 10:02 AM
Reply to: Message 1568 by AZPaul3
06-24-2020 9:49 AM


Re: If We Throw The ToE Away, What Will Replace It?
Kleinman writes:
The difference between your explanations and my explanations is that I publish my mathematical explanations and they predict the behavior of real evolutionary processes.
AZPaul3 writes:
The rest of the discipline doesn't believe you. Another crack in the pot there Kleinman.
Your clique has no mathematical discipline.

This message is a reply to:
 Message 1568 by AZPaul3, posted 06-24-2020 9:49 AM AZPaul3 has replied

Replies to this message:
 Message 1570 by AZPaul3, posted 06-24-2020 10:03 AM Kleinman has replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 1570 of 2073 (877982)
06-24-2020 10:03 AM
Reply to: Message 1569 by Kleinman
06-24-2020 10:02 AM


Re: If We Throw The ToE Away, What Will Replace It?
Apparently neither do you.

Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 1569 by Kleinman, posted 06-24-2020 10:02 AM Kleinman has replied

Replies to this message:
 Message 1571 by Kleinman, posted 06-24-2020 10:18 AM AZPaul3 has replied

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


Message 1571 of 2073 (877984)
06-24-2020 10:18 AM
Reply to: Message 1570 by AZPaul3
06-24-2020 10:03 AM


Re: If We Throw The ToE Away, What Will Replace It?
Kleinman writes:
The difference between your explanations and my explanations is that I publish my mathematical explanations and they predict the behavior of real evolutionary processes.
AZPaul3 writes:
The rest of the discipline doesn't believe you. Another crack in the pot there Kleinman.
Kleinman writes:
Your clique has no mathematical discipline.
AZPaul3 writes:
Apparently neither do you.
It is not apparent to you and other members of your clique but it is apparent to the peer-reviewers and publishers of my papers and to the librarians at the National Library of Medicine.

This message is a reply to:
 Message 1570 by AZPaul3, posted 06-24-2020 10:03 AM AZPaul3 has replied

Replies to this message:
 Message 1574 by AZPaul3, posted 06-24-2020 1:46 PM Kleinman has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 1572 of 2073 (877990)
06-24-2020 12:38 PM
Reply to: Message 1567 by Kleinman
06-24-2020 9:29 AM


Re: If We Throw The ToE Away, What Will Replace It?
quote:
You either have not followed or understood my discussion with Taq on the "Do you really understand the mathematics of evolution" topic. If you have 2 possible beneficial mutations, the number of replications required is still over a billion replications.
Actually if you do the calculation 2 possible mutations nearly doubles the probability, and so nearly halves the number of replications required. And everyone with basic probability theory knows that’s what you expect when the probabilities are low.
But what if there are 10 or 100 or 1000 ? Given that mammals have tens of thousands of genes the idea that there are only one or two possible beneficial mutations under every set of possible conditions doesn’t seem very plausible and certainly demands more support than a study looking at a single gene adapting to a single function.
quote:
Are there many beneficial mutations for the next and ensuing evolutionary steps for that selection pressure? The answer is no!
You are assuming a single selection pressure and a single solution. That may well be the case in antibiotic resistance but generally? Of course not. And citing a paper on the evolution of antibiotic resistance is not at all helpful In that respect. I’m so sorry you failed to learn from our previous interactions.
quote:
Another point you are failing to understand is that all lineages on their own particular evolutionary trajectories must accumulate their own particular beneficial mutations. And when those mutations occur at a frequency of e-9, that's going to require about a billion replications for every variant on each evolutionary step no matter which evolutionary trajectory they are on.
That is an assumption that I consider highly questionable. As you yourself pointed out the evolution of birds from pre-dinosaurian reptiles included quite a number of anatomical changes. The idea that they had to appear in a neat sequence - each one completing before the next could start is certainly questionable. Stephen Jay Gould described archaeopteryx as a good example of a transitional because that was clearly not what was happening.
quote:
Do you think that the intensity of selection is "hard" in the Kishony and Lenski experiments?
Hard versus soft selection is qualitative not quantitive. In hard selection the population is declining under selection pressure and mutation is required to raise the fitness or the population will go extinct. In soft selection the population is not declining but the mutants have an advantage which causes them to do better. Soft selection carries no risk of extinction at all.

This message is a reply to:
 Message 1567 by Kleinman, posted 06-24-2020 9:29 AM Kleinman has replied

Replies to this message:
 Message 1573 by Kleinman, posted 06-24-2020 1:30 PM PaulK has replied

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


Message 1573 of 2073 (877993)
06-24-2020 1:30 PM
Reply to: Message 1572 by PaulK
06-24-2020 12:38 PM


Re: If We Throw The ToE Away, What Will Replace It?
Kleinman writes:
You either have not followed or understood my discussion with Taq on the "Do you really understand the mathematics of evolution" topic. If you have 2 possible beneficial mutations, the number of replications required is still over a billion replications.
PaulK writes:
Actually if you do the calculation 2 possible mutations nearly doubles the probability, and so nearly halves the number of replications required. And everyone with basic probability theory knows that’s what you expect when the probabilities are low.
So if the number of possible beneficial mutations is X and the probability of one of those beneficial mutations occurring is 0.6, then if there are 2*X possible beneficial mutations then that probability goes to 1.2? It is easy to see why you think that fish evolve into mammals and reptiles evolve into birds. Learn what the difference is between additive and complementary events. You might not make so many mathematical blunders.
PaulK writes:
But what if there are 10 or 100 or 1000 ? Given that mammals have tens of thousands of genes the idea that there are only one or two possible beneficial mutations under every set of possible conditions doesn’t seem very plausible and certainly demands more support than a study looking at a single gene adapting to a single function.
Of course, thousands of possible beneficial mutations exist to a given selection pressure. But they only exist in your mind. You obviously didn't understand the link to the Weinreich paper about "Darwinian Evolution Can Follow. Only Very Few Mutational Paths to Fitter Proteins" which means you don't know where Weinreich makes a mathematical error in his paper.
Kleinman writes:
Are there many beneficial mutations for the next and ensuing evolutionary steps for that selection pressure? The answer is no!
PaulK writes:
You are assuming a single selection pressure and a single solution. That may well be the case in antibiotic resistance but generally? Of course not. And citing a paper on the evolution of antibiotic resistance is not at all helpful In that respect. I’m so sorry you failed to learn from our previous interactions.
The only thing that I've learned from our previous interactions is that you don't understand introductory probability theory. How do you think the Lenski experiment will work if he runs the experiment at a non-optimal temperature? In other words, both starvation and thermal stress simultaneously? Do you think you will get the same mutations for adaptation to the thermal stress as you would get for the starvation stress?
Kleinman writes:
Another point you are failing to understand is that all lineages on their own particular evolutionary trajectories must accumulate their own particular beneficial mutations. And when those mutations occur at a frequency of e-9, that's going to require about a billion replications for every variant on each evolutionary step no matter which evolutionary trajectory they are on.
PaulK writes:
That is an assumption that I consider highly questionable. As you yourself pointed out the evolution of birds from pre-dinosaurian reptiles included quite a number of anatomical changes. The idea that they had to appear in a neat sequence - each one completing before the next could start is certainly questionable. Stephen Jay Gould described archaeopteryx as a good example of a transitional because that was clearly not what was happening.
I get the "transitional" argument made by believers in the fossil record story. The problem with that story is that you can say nothing about the genetics based on gross anatomy. DNA evolution must be measured on the molecular level because that's where these events happen. And the most common erroneous argument made on this subject is that a series of microevolutionary changes add up to a macroevolutionary change. Microevolutionary changes are not linked by the addition rule. Mutations are random events so the joint probability of these events are linked by the multiplication rule. You won't understand this because you don't understand the theorems and axioms of probability theory. You demonstrated that above when you applied the addition rule to complementary events.
Kleinman writes:
Do you think that the intensity of selection is "hard" in the Kishony and Lenski experiments?
PaulK writes:
Hard versus soft selection is qualitative not quantitive. In hard selection the population is declining under selection pressure and mutation is required to raise the fitness or the population will go extinct. In soft selection the population is not declining but the mutants have an advantage which causes them to do better. Soft selection carries no risk of extinction at all.
Really???? So the Lenski experiment has hard selection since variants in his populations go extinct and selection in the Kishony experiment is soft because none of his populations go extinct? Is the use of combination therapy for the treatment of hiv soft selection because you don't drive the population to extinction? The reason you can't quantify selection is that you don't understand how it works. Combine that with the fact that you don't understand introductory probability theory means you have a lot of homework to do if you want to understand the physics and mathematics of evolution.

This message is a reply to:
 Message 1572 by PaulK, posted 06-24-2020 12:38 PM PaulK has replied

Replies to this message:
 Message 1576 by PaulK, posted 06-24-2020 2:42 PM Kleinman has not replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 1574 of 2073 (877994)
06-24-2020 1:46 PM
Reply to: Message 1571 by Kleinman
06-24-2020 10:18 AM


Re: If We Throw The ToE Away, What Will Replace It?
it is apparent to the peer-reviewers and publishers of my papers
Yes, I know. You're one of those that slipped through.
Problems with peer review | The BMJ

Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 1571 by Kleinman, posted 06-24-2020 10:18 AM Kleinman has replied

Replies to this message:
 Message 1575 by Kleinman, posted 06-24-2020 2:09 PM AZPaul3 has replied

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


Message 1575 of 2073 (877995)
06-24-2020 2:09 PM
Reply to: Message 1574 by AZPaul3
06-24-2020 1:46 PM


Re: If We Throw The ToE Away, What Will Replace It?
Kleinman writes:
it is apparent to the peer-reviewers and publishers of my papers
AZPaul3 writes:
Yes, I know. You're one of those that slipped through.
None of those peer-reviewers were mathematical wizards like you. They didn't know that the number of replications needed for a beneficial mutation to occur was between 1 and an indeterminant amount. Such brilliance on your part. You should publish your findings.
You can publish a series of papers. The number of replications required for 2 beneficial mutations to occur is between 2 and 2*an indeterminant amount. Your contribution to society is innumerable (that is the number of drug-resistant infections and failed cancer treatments).

This message is a reply to:
 Message 1574 by AZPaul3, posted 06-24-2020 1:46 PM AZPaul3 has replied

Replies to this message:
 Message 1585 by AZPaul3, posted 06-24-2020 6:18 PM Kleinman has replied

  
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