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Author Topic:   Explaining the pro-Evolution position
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 37 of 393 (792291)
10-07-2016 6:22 PM
Reply to: Message 35 by PaulK
10-07-2016 5:53 PM


quote:
Ok, so those members with a beneficial mutation will increase in number. How large does that lineage have to be in order for there to be a reasonable probability of another beneficial mutation occurring on a member of that lineage?
quote:
Obviously that depends on the number of beneficial mutations available. But bear in mind that bacteria have very large populations, very short generation times and can share genetic material quite freely.

If you are going to consider the mathematics of rmns, you have to consider the size of lineages in populations, not the entire population size when computing probabilities. A beneficial mutation for one lineage may not be a beneficial mutation for a different lineage. That's what the Weinreich example is demonstrating.
quote:
My argument is not complicated but it is not trivial. I'm trying to teach you something about rmns that you have missed. Your above quote is taking you on the correct path to understand this phenomenon. If you think I have made an error, feel free to post my quote.
quote:
At this point it looks more like an attempt to get other people to do the work that you have not (and assuming the result). Anyway, your assertion that natural selection "must" increase the probability of a beneficial mutation occurring is an obvious error.

I assure you that I have already done the mathematics for rmns. Do you think in the Weinreich example that all 5 beneficial mutations occur simultaneously to give resistance to the antibiotic selection pressure? Natural selection must do something to the lineages in this population for those 5 beneficial mutations accumulate on a lineage. And that something is increase the number of members with the beneficial mutations as you previously pointed out. What happens to the probabilities of a beneficial mutation occurring if the number of members who would benefit do not increase?

This message is a reply to:
 Message 35 by PaulK, posted 10-07-2016 5:53 PM PaulK has replied

Replies to this message:
 Message 49 by PaulK, posted 10-08-2016 2:48 AM Kleinman has not replied

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


Message 38 of 393 (792294)
10-07-2016 6:29 PM
Reply to: Message 36 by Coyote
10-07-2016 6:13 PM


quote:
If natural selection is not altering the probabilities that a particular mutation will occur at a particular site in a genome, then what do you think that natural selection does?
quote:
Natural selection kills off the also-rans.

True, but the also-rans are not the ones evolving resistance to the selection pressures. To understand rmns, you need to consider what happens to those variants who are lucky enough to get the beneficial mutations.

This message is a reply to:
 Message 36 by Coyote, posted 10-07-2016 6:13 PM Coyote has not replied

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


Message 40 of 393 (792296)
10-07-2016 7:17 PM
Reply to: Message 39 by NoNukes
10-07-2016 6:49 PM


quote:
Natural selection is totally relevant. Natural selection must do something very specific in order to improve the probability that a beneficial mutation will occur.
quote:
According to the theory of evolution, natural selection affects the probability that a given mutation is actually beneficial. It is not required that natural selection affect the actual probability that mutations, beneficial or not, actually occur. After all, whether or not a given mutation is beneficial is at least in part associated with environmental factors. Examples of genetic changes that are beneficial/non-beneficial based on the environment and natural selection include melanin affecting mutations, lactase intolerance persistance, and sickle cell anemia.
If you want to argue from the premise you have presented here, you need to lay ground work to establish that your assertion is correct. So far you have not done so.

What determines whether a mutation is beneficial or not is whether it affects the fitness to reproduce.
You are correct, I should lay more groundwork to establish that my assertions are correct. Let's start with the fundamental principles of doing the mathematics of a stochastic process, in particular rmns. The first step in doing this type of mathematics is identifying the random trial(s) (experiment(s)) and possible outcomes for the random trial(s). In the case of rmns, there are two random trials. The first and key random trial is the replication of a genome. There are two possible outcomes for this random trial, a mutation does occur at a particular site in the genome or a mutation does not occur at a particular site in a genome. So we are dealing with a simple binomial probability problem. I'll talk about the second trial in a later post.

This message is a reply to:
 Message 39 by NoNukes, posted 10-07-2016 6:49 PM NoNukes has replied

Replies to this message:
 Message 48 by NoNukes, posted 10-08-2016 1:34 AM Kleinman has replied

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


Message 42 of 393 (792298)
10-07-2016 7:45 PM
Reply to: Message 41 by Genomicus
10-07-2016 7:30 PM


quote:
Good, you are on the right track for understanding how random mutation and natural selection (rmns from here on) works.
quote:
I am quite familiar with population genetics and molecular evolution, but sure, yeah -- thanks for your laudatory comments I guess?

The compliment was sincere. But being familiar with population genetics as it is taught today is not going to help you with rmns.
quote:
We'd need to know population size, fitness of wildtype viruses compared to drug-resistant mutants, mutation rate, no. of copies of mutant phenotype in the population, etc., to estimate probability of fixation of the drug-resistant mutation.
But get to the point. You don't need to walk me through pop genetics.
The point of doing the probability calculations is to determine the population size necessary based on a given mutation rate to determine the probability of a beneficial mutation occurring. Fixation of a given variant is neither necessary nor sufficient for this process to work. It is even possible for the relative frequency of a variant in a population to decrease yet the variant is still able to evolve to the selection pressure.

This message is a reply to:
 Message 41 by Genomicus, posted 10-07-2016 7:30 PM Genomicus has not replied

Replies to this message:
 Message 140 by Taq, posted 10-11-2016 10:21 AM Kleinman has replied

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


Message 44 of 393 (792300)
10-07-2016 9:03 PM
Reply to: Message 43 by jar
10-07-2016 8:40 PM


quote:
Kleinman writes:
Natural selection must do something very specific in order to improve the probability that a beneficial mutation will occur.
quote:
Utter and complete bull...

I wonder if you will ever understand how rmns works. It requires some skill in physics and mathematics. Perhaps you want to give it a shot and explain why combination therapy works for the treatment of HIV.

This message is a reply to:
 Message 43 by jar, posted 10-07-2016 8:40 PM jar has replied

Replies to this message:
 Message 50 by jar, posted 10-08-2016 8:28 AM Kleinman has not replied
 Message 54 by AZPaul3, posted 10-09-2016 4:18 AM Kleinman has replied

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


Message 46 of 393 (792302)
10-07-2016 9:57 PM
Reply to: Message 45 by kjsimons
10-07-2016 9:40 PM


quote:
Coyote writes:
Natural selection kills off the also-rans.
quote:
And/or decreases the amount of genetic material passed on. Not all selection is about killing off an individual.

Correct, kjsimons, selection reduces the diversity of populations, mutations increase the diversity of populations.

This message is a reply to:
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Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 55 of 393 (792421)
10-09-2016 7:42 PM
Reply to: Message 47 by Coyote
10-07-2016 10:35 PM


Re: This seems like a good place...
quote:
The bottom line: evolution works.
But rmns will not transform reptiles into birds.

This message is a reply to:
 Message 47 by Coyote, posted 10-07-2016 10:35 PM Coyote has replied

Replies to this message:
 Message 63 by Theodoric, posted 10-09-2016 8:36 PM Kleinman has replied
 Message 67 by Theodoric, posted 10-09-2016 8:57 PM Kleinman has not replied
 Message 75 by Coyote, posted 10-09-2016 9:59 PM Kleinman has not replied

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


Message 56 of 393 (792422)
10-09-2016 7:47 PM
Reply to: Message 48 by NoNukes
10-08-2016 1:34 AM


quote:
If you are going to consider the mathematics of rmns, you have to consider the size of lineages in populations, not the entire population size when computing probabilities.
quote:
That is obviously incorrect. It is not true when you are considering the probability of a mutation appearing in a population, nor is it true when there is exchange of genetic material between lineages.

Do you think that every mutation is beneficial? If lineages are exchanging genetic material, why can HIV evolve resistance efficiently to combination therapy?

This message is a reply to:
 Message 48 by NoNukes, posted 10-08-2016 1:34 AM NoNukes has not replied

Replies to this message:
 Message 89 by PaulK, posted 10-10-2016 5:12 AM Kleinman has not replied

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


Message 57 of 393 (792423)
10-09-2016 7:50 PM
Reply to: Message 48 by NoNukes
10-08-2016 1:34 AM


quote:
However, your private probability argument is completely irrelevant to your assertion that the theory of evolution is nor a well established theory. so that claim remains completely unsupported.
My argument is totally public and shows both mathematically and empirically why the theory of evolution is not true.

This message is a reply to:
 Message 48 by NoNukes, posted 10-08-2016 1:34 AM NoNukes has not replied

Replies to this message:
 Message 90 by PaulK, posted 10-10-2016 5:17 AM Kleinman has not replied

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


Message 58 of 393 (792424)
10-09-2016 7:56 PM
Reply to: Message 48 by NoNukes
10-08-2016 1:34 AM


quote:
There are two possible outcomes for this random trial, a mutation does occur at a particular site in the genome or a mutation does not occur at a particular site in a genome. So we are dealing with a simple binomial probability problem.
quote:
Not necessarily a simple binomial problem. It is possible that the probability that a mutation occurs at a given site is affected by environmental concerns. But the evidence suggests that this probability is not, generally speaking, correlated with the mutation being beneficial in any given environment, let alone the environment that produced the increased rate. For example, radiation may produce mutations, but those mutations generally don't make it more likely that the offspring are radiation proof.

There are factors which can alter the mutation rate but when DNA is replicated, there are only two possible outcomes for that replication process. Either the correct base is duplicated at the particular site or there is an error in replication at the particular site, that is a mutation has occurred.
quote:
You are correct, I should lay more groundwork to establish that my assertions are correct...
I'll talk about the second trial in a later post.
quote:
It is an improvement that you are electing to add to the discussion. But let me note that in your current posts you do not present mathematics. You merely talk about the need to do so.

We are doing the first steps of the mathematics right here. The first step in analyzing a stochastic process is identifying the random trial(s) (experiment(s)) and the possible outcomes for the random trial.

This message is a reply to:
 Message 48 by NoNukes, posted 10-08-2016 1:34 AM NoNukes has not replied

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


Message 59 of 393 (792425)
10-09-2016 8:02 PM
Reply to: Message 51 by ringo
10-08-2016 11:41 AM


quote:
Why does combination therapy work for the treatment of HIV?
quote:
You might as well ask why lead works for bullets. There is an explanation but it has nothing to do with the topic. All that matters is that it does work.
The same applies to the Theory of Evolution. All that matters is that it works as an explanation of the fact of evolution. Nobody is claiming that the Theory of Evolution is "absolute truth". They're only saying that it works. And it's the only explanation that works.

There is a specific mathematical reason why combination therapy works for the treatment of HIV. And that mathematical reason is tied to how rmns works. And don't get me wrong, evolution does occur, but the mechanisms of evolution, in particular, rmns, can not make the genetic transformations necessary for the theory of evolution to be true.

This message is a reply to:
 Message 51 by ringo, posted 10-08-2016 11:41 AM ringo has replied

Replies to this message:
 Message 149 by ringo, posted 10-11-2016 12:00 PM Kleinman has replied

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


Message 60 of 393 (792426)
10-09-2016 8:06 PM
Reply to: Message 52 by Tangle
10-08-2016 2:38 PM


quote:
You've got two jobs to do Kleinman
1. Explain this great secret you're teasing us with
2. Explain why it shatters the ToE
At the moment you're behaving like a troll.
Be patient, I'm not trying to tease you, I'm trying to introduce you to the concepts required to understand how rmns works. If you follow all the posts, you will see the reason.

This message is a reply to:
 Message 52 by Tangle, posted 10-08-2016 2:38 PM Tangle has replied

Replies to this message:
 Message 87 by Tangle, posted 10-10-2016 2:28 AM Kleinman has not replied

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


Message 61 of 393 (792427)
10-09-2016 8:19 PM
Reply to: Message 53 by Dr Adequate
10-08-2016 9:19 PM


quote:
Why does combination therapy work for the treatment of HIV?
quote:
See here.
Anything else I can help you with, Alan?

It's been a while Doc. What happened to the Randi Forum? Now you as a mathematician should know that I am looking for a mathematical reason. And actually, Genomicus gave the correct reason in post 10 when he said:
quote:
Multi-valent drug approaches to HIV are more effective because there is a lower probability of the HIV population hitting on the right mutations to counter both drugs simultaneously.
rmns is not a linear algebra problem, it is a stochastic phenomenon which requires the application of probability theory to correctly analyze. The reason why combination therapy works for the treatment of HIV is the multiplication rule of probabilities. So do you want to try to compute the probability that a single beneficial mutation will occur on some member of a lineage?

This message is a reply to:
 Message 53 by Dr Adequate, posted 10-08-2016 9:19 PM Dr Adequate has not replied

Replies to this message:
 Message 141 by Taq, posted 10-11-2016 10:30 AM Kleinman has not replied

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


Message 62 of 393 (792428)
10-09-2016 8:25 PM
Reply to: Message 54 by AZPaul3
10-09-2016 4:18 AM


Re: Failing Peer Review
quote:
Kleinman, people are getting testy with you. Your approach here is not welcome.
You have the wrong idea about what is happening on this forum when it comes to presenting alternative ideas.
If you have a proposal to make then make it, in toto. Explain to us what your hypothesis actually is. Explain the problem, state your assumptions, show us your data, show us your process (complete with the math you hint is necessary) and show us your conclusions. Do it all in one post, or, if that complex, in as few as possible for complete understanding.
Stop trying to teach us through this demeaning question/hint crap. This is not your classroom.
This is your peer review and so far you are failing.
If you want to peer review my work, you had better have a good understanding of probability theory. Here's the short answer why the theory of evolution is not true, it's the multiplication rule of probabilities which makes the theory of evolution not true. For those who don't understand probability theory, it takes a much, much longer answer. It requires teaching you probability theory and how to analyze a stochastic process.

This message is a reply to:
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Replies to this message:
 Message 65 by Theodoric, posted 10-09-2016 8:41 PM Kleinman has not replied
 Message 86 by PaulK, posted 10-10-2016 12:21 AM Kleinman has not replied
 Message 91 by Rrhain, posted 10-10-2016 6:57 AM Kleinman has replied

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


Message 64 of 393 (792430)
10-09-2016 8:37 PM
Reply to: Message 54 by AZPaul3
10-09-2016 4:18 AM


Re: Why the Theory of Evolution is not true
Since AZPaul3 doesn't have the mathematical skill to peer review a probability problem, let's call this thread Why the Theory of Evolution is not true

This message is a reply to:
 Message 54 by AZPaul3, posted 10-09-2016 4:18 AM AZPaul3 has replied

Replies to this message:
 Message 66 by Theodoric, posted 10-09-2016 8:43 PM Kleinman has not replied
 Message 68 by AZPaul3, posted 10-09-2016 9:01 PM Kleinman has replied

  
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