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Author Topic:   Explaining the pro-Evolution position
Tangle
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Posts: 9489
From: UK
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Member Rating: 4.9


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Message 31 of 393 (792284)
10-07-2016 5:06 PM
Reply to: Message 30 by Kleinman
10-07-2016 4:54 PM


Kleinman writes:
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?
Oops, that's embarassing.

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"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
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This message is a reply to:
 Message 30 by Kleinman, posted 10-07-2016 4:54 PM Kleinman has not replied

  
PaulK
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Posts: 17822
Joined: 01-10-2003
Member Rating: 2.3


Message 32 of 393 (792285)
10-07-2016 5:08 PM
Reply to: Message 30 by Kleinman
10-07-2016 4:54 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?
Natural selection increases the probability that a beneficial mutation will be retained (and spread) in a population and the probability that deleterious mutations will be lost.
quote:
I have nothing to apologise for here. You have something to apologise for by not correctly describing how rmns works.
You have been extremely evasive about your argument and now it turns out that you have made a basic error. And I am certainly not going to apologise for disagreeing with your erroneous opinion.

This message is a reply to:
 Message 30 by Kleinman, posted 10-07-2016 4:54 PM Kleinman has replied

Replies to this message:
 Message 34 by Kleinman, posted 10-07-2016 5:42 PM PaulK has replied

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


Message 33 of 393 (792287)
10-07-2016 5:32 PM
Reply to: Message 29 by New Cat's Eye
10-07-2016 4:52 PM


quote:
quote:
Mutations are random events and rare events as well.
quote:
I don't believe you.
Do you think that mutations are not random events?
quote:
I think that they are not rare events.
I think that they are random with respect to fitness.
I think they may or may not be truly random like Brownian Motion, depending on the mutation.

They are rare events when a particular mutation must occur at a particular site in the genome to improve fitness. And natural selection must do something specifically to improve the probability that a particular mutation will occur at a particular site in a genome to improve fitness.
If you think that mutations are not random, you need to give us an empirical example of this claim.
quote:
Can you predict when a mutation will occur?
quote:
Me personally? No.
Scientists? Maybe.

In any stochastic process, it is not possible to predict the outcome of any random experiment. What probability theory does is enable one to predict the relative frequencies of outcomes when the random experiment is done many times. A simple example is tossing a coin. You can not predict whether a head or a tail comes up with any toss. What you can predict is that if you toss the coin many times, about half the outcomes will be heads, the other half of the outcomes will be tails.
quote:
So what is the frequency of a mutation occurring at a particular site in a genome?
quote:
Which mutation and which site?

Any particular mutation at any particular site. What I'm trying to get at is the definition of mutation rate. The mutation rate is the probability that mutation will occur at a given site in the genome in a single replication.
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:
No, that's complete nonsense. Natural selection doesn't do stuff.

It certainly does, natural selection changes the probabilities of particular mutations occurring by changing population sizes.
quote:
There are factors which can alter mutation rates but these factors do not alter whether mutations are random or not.
quote:
I bet if I subjected my balls to some particular radiation that we could cause particular mutations that I could pass on to my offspring, but that's the kind of stuff that I'm calling irrelevant.

You are changing the mutation rate but you are not changing the fact that mutations are random events. Mutation rates are a factor when computing the probabilities of a particular beneficial mutation occurring but there is a much more important factor for rmns to work.
quote:
Mutations are always random.
quote:
No, not necessarily. And it depends what you mean by "random".
Like, there is a series of events that causes a particular mutation to happen. It may be that once that process is kicked off, that it is inevitable that the particular mutation will occur. That would not be random. That would be repeatable and testable.
And like the paper that you linked to said, for some mutations there are particular pathways that are more probable to occur than others.

You need to give us an empirical example where a mutation is not a random event. Random means something that occurs by chance, not predictable.
What Weinreich is talking about, for an evolutionary trajectory to have a reasonable probability of occurring, the sequence of mutations must always give improved fitness to reproduce.
quote:
Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins.
"This implies that the protein tape of life may be largely reproducible and even predictable."
quote:
Does that sound random to you?

Natural selection in the Weinreich experiment is not random but the mutations which give improved fitness are random. Natural selection can also be random but in that case, we are not talking about rmns. So how does non-random natural selection and random mutation work?

This message is a reply to:
 Message 29 by New Cat's Eye, posted 10-07-2016 4:52 PM New Cat's Eye has replied

Replies to this message:
 Message 93 by New Cat's Eye, posted 10-10-2016 10:12 AM Kleinman has not replied

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


Message 34 of 393 (792288)
10-07-2016 5:42 PM
Reply to: Message 32 by PaulK
10-07-2016 5:08 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 increases the probability that a beneficial mutation will be retained (and spread) in a population and the probability that deleterious mutations will be lost.

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:
I have nothing to apologise for here. You have something to apologise for by not correctly describing how rmns works.
quote:
You have been extremely evasive about your argument and now it turns out that you have made a basic error. And I am certainly not going to apologise for disagreeing with your erroneous opinion.

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.

This message is a reply to:
 Message 32 by PaulK, posted 10-07-2016 5:08 PM PaulK has replied

Replies to this message:
 Message 35 by PaulK, posted 10-07-2016 5:53 PM Kleinman has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.3


Message 35 of 393 (792289)
10-07-2016 5:53 PM
Reply to: Message 34 by Kleinman
10-07-2016 5:42 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?
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.
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.
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.

This message is a reply to:
 Message 34 by Kleinman, posted 10-07-2016 5:42 PM Kleinman has replied

Replies to this message:
 Message 37 by Kleinman, posted 10-07-2016 6:22 PM PaulK has replied

  
Coyote
Member (Idle past 2105 days)
Posts: 6117
Joined: 01-12-2008


Message 36 of 393 (792290)
10-07-2016 6:13 PM
Reply to: Message 30 by Kleinman
10-07-2016 4:54 PM


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?
Natural selection kills off the also-rans.

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This message is a reply to:
 Message 30 by Kleinman, posted 10-07-2016 4:54 PM Kleinman has replied

Replies to this message:
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Kleinman
Member (Idle past 334 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 334 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:
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NoNukes
Inactive Member


Message 39 of 393 (792295)
10-07-2016 6:49 PM
Reply to: Message 27 by Kleinman
10-07-2016 4:38 PM


Natural selection is totally relevant. Natural selection must do something very specific in order to improve the probability that a beneficial mutation will occur.
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.

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This message is a reply to:
 Message 27 by Kleinman, posted 10-07-2016 4:38 PM Kleinman has replied

Replies to this message:
 Message 40 by Kleinman, posted 10-07-2016 7:17 PM NoNukes has replied

  
Kleinman
Member (Idle past 334 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

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 41 of 393 (792297)
10-07-2016 7:30 PM
Reply to: Message 15 by Kleinman
10-07-2016 2:17 PM


Good, you are on the right track for understanding how random mutation and natural selection (rmns from here on) works.
I am quite familiar with population genetics and molecular evolution, but sure, yeah -- thanks for your laudatory comments I guess?
So consider the simpler case when HIV evolves very rapidly to single drug therapy. How do compute this probability?
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.

This message is a reply to:
 Message 15 by Kleinman, posted 10-07-2016 2:17 PM Kleinman has replied

Replies to this message:
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Kleinman
Member (Idle past 334 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:
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Replies to this message:
 Message 140 by Taq, posted 10-11-2016 10:21 AM Kleinman has replied

  
jar
Member (Idle past 393 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 43 of 393 (792299)
10-07-2016 8:40 PM
Reply to: Message 27 by Kleinman
10-07-2016 4:38 PM


more utter bullshit.
Kleinman writes:
Natural selection must do something very specific in order to improve the probability that a beneficial mutation will occur.
Utter and complete bullshit. Total crappola.
Sorry but that is simply so wrong that at best it might be considered a poor attempt at a sophomoric joke.
Natural select simply selects those things that are not so destructive that the critter cannot live long enough to reproduce. The mutations that happen are totally unrelated to Natural Selection as anyone over the age of about ten should be able to understand.
The mutations happen.
Good mutations happen.
Neutral mutations happen.
Destructive mutations happen.
Natural Selection don't really give a damn. Natural Selection has NOTHING to do with what mutations happen.
Stop making such utterly stupid assertions, please.

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This message is a reply to:
 Message 27 by Kleinman, posted 10-07-2016 4:38 PM Kleinman has replied

Replies to this message:
 Message 44 by Kleinman, posted 10-07-2016 9:03 PM jar has replied

  
Kleinman
Member (Idle past 334 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:
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 Message 54 by AZPaul3, posted 10-09-2016 4:18 AM Kleinman has replied

  
kjsimons
Member
Posts: 821
From: Orlando,FL
Joined: 06-17-2003
Member Rating: 6.7


Message 45 of 393 (792301)
10-07-2016 9:40 PM
Reply to: Message 36 by Coyote
10-07-2016 6:13 PM


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

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

Replies to this message:
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