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Author Topic:   Explaining the pro-Evolution position
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 5 of 393 (792238)
10-07-2016 1:20 PM
Reply to: Message 1 by PaulK
01-25-2016 2:01 PM


You will have to pardon my formatting because it has been quite a while since I've used dBCodes. But for my first response on this forum, I've chosen PaulK's post.
quote:
1) Evolution is not an all-encompassing belief system, it is a scientific theory with a limited scope. In particular, it is not a source of moral or ethical values. There are many Christians on the pro-evolution side.

There is a difference between "Evolution" and "The Theory of Evolution"
quote:
2) Science is the best way to learn about and understand the physical universe, both how it operates and its history. A well-established scientific theory should be accepted as a good approximation of the truth. (And no more than that - nobody on the mainstream pro-evolution side would claim that the current theory was absolutely correct in every little detail)

It is possible to believe that evolution occurs but that the theory of evolution is not true. In fact, I believe that is the correct view.
quote:
3) Evolution is a well-established scientific theory (this should be uncontroversial to anyone, since it is a clear fact)

Evolution may be a well-established scientific theory but the "Theory of Evolution" is not a well-established scientific theory.
This message is a reply to:
 Message 1 by PaulK, posted 01-25-2016 2:01 PM PaulK has not yet responded

Replies to this message:
 Message 6 by Tangle, posted 10-07-2016 1:23 PM Kleinman has responded
 Message 7 by ringo, posted 10-07-2016 1:29 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 8 of 393 (792243)
10-07-2016 1:43 PM
Reply to: Message 6 by Tangle
10-07-2016 1:23 PM


quote:
quote:
Kleinman writes:
....the "Theory of Evolution" is not a well-established scientific theory.

Yes it is.

Now what?



Let's see how well established the theory of evolution is. Why does combination therapy work for the treatment of HIV?
This message is a reply to:
 Message 6 by Tangle, posted 10-07-2016 1:23 PM Tangle has responded

Replies to this message:
 Message 9 by Tangle, posted 10-07-2016 1:51 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 10 of 393 (792245)
10-07-2016 1:51 PM
Reply to: Message 7 by ringo
10-07-2016 1:29 PM


quote:
quote:
Kleinman writes:
There is a difference between "Evolution" and "The Theory of Evolution"

Yes, evolution is a fact and the Theory of Evolution is the only real explanation of that fact.

You are half right ringo and to start the explanation why you are only half right, answer the same question I pose for Tangle. Why does combination therapy work for the treatment of HIV?
This message is a reply to:
 Message 7 by ringo, posted 10-07-2016 1:29 PM ringo has responded

Replies to this message:
 Message 12 by Genomicus, posted 10-07-2016 1:57 PM Kleinman has responded
 Message 51 by ringo, posted 10-08-2016 11:41 AM Kleinman has responded
 Message 53 by Dr Adequate, posted 10-08-2016 9:19 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 11 of 393 (792247)
10-07-2016 1:57 PM
Reply to: Message 9 by Tangle
10-07-2016 1:51 PM


quote:
quote:
Kleinman writes:
Let's see how well established the theory of evolution is. Why does combination therapy work for the treatment of HIV?

Nope, it doesn't work like that, it's your claim the the ToE isn't well founded. You now have to explain why.

The answer to the question I ask you contains the reason why the theory of evolution is not true. I'm trying to get you to figure this out yourself.
This message is a reply to:
 Message 9 by Tangle, posted 10-07-2016 1:51 PM Tangle has responded

Replies to this message:
 Message 17 by Tangle, posted 10-07-2016 3:11 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 13 of 393 (792249)
10-07-2016 2:04 PM
Reply to: Message 12 by Genomicus
10-07-2016 1:57 PM


quote:
You are half right ringo and to start the explanation why you are only half right, answer the same question I pose for Tangle. Why does combination therapy work for the treatment of HIV?
quote:
I'm going to take a gander and guess that you've recently read Behe's The Edge of Evolution. Right?


Nope, do you want to try to answer this question? Why does combination therapy work for the treatment of HIV?
This message is a reply to:
 Message 12 by Genomicus, posted 10-07-2016 1:57 PM Genomicus has responded

Replies to this message:
 Message 14 by Genomicus, posted 10-07-2016 2:08 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 15 of 393 (792251)
10-07-2016 2:17 PM
Reply to: Message 14 by Genomicus
10-07-2016 2:08 PM


quote:
Why does combination therapy work for the treatment of HIV?
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.

Next.




Good, you are on the right track for understanding how random mutation and natural selection (rmns from here on) works. rmns is governed by the theorems of probability theory. So consider the simpler case when HIV evolves very rapidly to single drug therapy. How do compute this probability?
This message is a reply to:
 Message 14 by Genomicus, posted 10-07-2016 2:08 PM Genomicus has responded

Replies to this message:
 Message 16 by Taq, posted 10-07-2016 3:00 PM Kleinman has responded
 Message 41 by Genomicus, posted 10-07-2016 7:30 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 18 of 393 (792256)
10-07-2016 3:18 PM
Reply to: Message 16 by Taq
10-07-2016 3:00 PM


quote:
Kleinman writes:
So consider the simpler case when HIV evolves very rapidly to single drug therapy. How do compute this probability?
quote:
The probability would be 1 in 1, because HIV evolved rapidly to single drug therapy. When something happens the odds of it happening are 1 in 1.


Let's try to be a little more precise on the problem. Let's assume that it takes 3 mutations to give resistance to a single drug. How does a lineage of the virus achieve that 1 in 1 probability for all 3 mutations?
This message is a reply to:
 Message 16 by Taq, posted 10-07-2016 3:00 PM Taq has responded

Replies to this message:
 Message 20 by Taq, posted 10-07-2016 3:24 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 19 of 393 (792257)
10-07-2016 3:23 PM
Reply to: Message 17 by Tangle
10-07-2016 3:11 PM


quote:
Kleinman writes:
The answer to the question I ask you contains the reason why the theory of evolution is not true. I'm trying to get you to figure this out yourself.
quote:
Sorry, if you want to challenge 150 years of scientific effort and concensus YOU have to do the heavy lifting. Persuade us.

And, by the way, put away the patronising bollox, it's not helping you.




I've already done the heavy lifting, I'm trying to teach you how to do some heavy mathematical scientific lifting. Taq is trying to do it. If you have trouble doing it, that's ok, I'll do it for you.
This message is a reply to:
 Message 17 by Tangle, posted 10-07-2016 3:11 PM Tangle has responded

Replies to this message:
 Message 22 by Tangle, posted 10-07-2016 3:41 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 21 of 393 (792259)
10-07-2016 3:34 PM
Reply to: Message 20 by Taq
10-07-2016 3:24 PM


quote:
Kleinman writes:
Let's try to be a little more precise on the problem. Let's assume that it takes 3 mutations to give resistance to a single drug.
quote:
Let's not assume that, since it is rarely true. Even in Behe's famous example of drug resistance in falciparum it turned out to be false. Behe tried to claim that there were only two mutations that could confer resistance, and that they had to happen at the same time. He was wrong on both counts.

Your first job is to show that there are only 3 mutations that can produce HIV resistance to a given drug.




I'm going to disagree with you that single mutations commonly give resistance to antimicrobial agents. So if you don't want to do this with HIV, let's do this with a real, measured and repeatable example of rmns.
http://isites.harvard.edu/...Papers/Weinreich-et-al-2006.pdf
In this example, it takes 5 mutations for the e coli to achieve resistance to this antibiotic. How do you compute the probability for those 5 mutations to occur, that is the probability is 1?
This message is a reply to:
 Message 20 by Taq, posted 10-07-2016 3:24 PM Taq has not yet responded

Replies to this message:
 Message 24 by New Cat's Eye, posted 10-07-2016 3:58 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 23 of 393 (792262)
10-07-2016 3:47 PM
Reply to: Message 22 by Tangle
10-07-2016 3:41 PM


quote:
Kleinman writes:
I've already done the heavy lifting
quote:
Fantastic so why not just explain it all to us, then collect your Nobel prize?


Don't be impatient, perhaps Taq will figure it out.
This message is a reply to:
 Message 22 by Tangle, posted 10-07-2016 3:41 PM Tangle has not yet responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 25 of 393 (792266)
10-07-2016 4:16 PM
Reply to: Message 24 by New Cat's Eye
10-07-2016 3:58 PM


quote:
In this example, it takes 5 mutations for the e coli to achieve resistance to this antibiotic. How do you compute the probability for those 5 mutations to occur, that is the probability is 1?
quote:
Ah, I get it. You don't understand what it means for a mutation to be random.

In Message 15 you wrote:

quote:
rmns is governed by the theorems of probability theory.
quote:
So really, it isn't. Mutations aren't necessarily purely random like Brownian Motion.

And the link you provided confirms that:

"Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins"

The randomness of mutations is with respect to fitness, not randomness like Brownian Motion.

There can be predictable causes of mutations, its just that you can't predict them from the perspective of the phenotype. But down at the genotypic level, you very well may be able to.

So this game you're trying to play is to get to: "See, the probability is so low that those mutations couldn't have been random, so therefore the Theory of Evolution is wrong because it requires mutations to be random."

The fact that we'd all see through that baloney is why you have to take this convoluted route of asking questions that you already know the answers to and trying to "help" us figure out what you're getting at.






Mutations are random events and rare events as well. So how can natural selection change the probabilities so that the probability that 5 rare mutations can occur on a lineage, that is the probability is 1 to give drug resistance to an antibiotic?
This message is a reply to:
 Message 24 by New Cat's Eye, posted 10-07-2016 3:58 PM New Cat's Eye has responded

Replies to this message:
 Message 26 by New Cat's Eye, posted 10-07-2016 4:20 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 27 of 393 (792273)
10-07-2016 4:38 PM
Reply to: Message 26 by New Cat's Eye
10-07-2016 4:20 PM


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? Can you predict when a mutation will occur? So what is the frequency of a mutation occurring at a particular site in a genome?
quote:
So how can natural selection change the probabilities so that the probability that 5 rare mutations can occur on a lineage, that is the probability is 1 to give drug resistance to an antibiotic?
quote:
Natural selection (NS) does not change the probabilities. (well, I mean it can, but that's irrelevant to this)

With respect to fitness (i.e. where NS operates), the mutations are random.

With respect to the genome, the mutations may not be truly random like Brownian Motion is.




Natural selection is totally relevant. Natural selection must do something very specific in order to improve the probability that a beneficial mutation will occur. There are factors which can alter mutation rates but these factors do not alter whether mutations are random or not. Mutations are always random.
This message is a reply to:
 Message 26 by New Cat's Eye, posted 10-07-2016 4:20 PM New Cat's Eye has responded

Replies to this message:
 Message 28 by PaulK, posted 10-07-2016 4:41 PM Kleinman has responded
 Message 29 by New Cat's Eye, posted 10-07-2016 4:52 PM Kleinman has responded
 Message 39 by NoNukes, posted 10-07-2016 6:49 PM Kleinman has responded
 Message 43 by jar, posted 10-07-2016 8:40 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 30 of 393 (792279)
10-07-2016 4:54 PM
Reply to: Message 28 by PaulK
10-07-2016 4:41 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:
Natural selection does not improve the probability of beneficial mutations occurring. If you think that evolutionary theory claims otherwise you really need to take a step back and apologise for running through this silly routine of yours.


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? I have nothing to apologise for here. You have something to apologise for by not correctly describing how rmns works.
This message is a reply to:
 Message 28 by PaulK, posted 10-07-2016 4:41 PM PaulK has responded

Replies to this message:
 Message 31 by Tangle, posted 10-07-2016 5:06 PM Kleinman has not yet responded
 Message 32 by PaulK, posted 10-07-2016 5:08 PM Kleinman has responded
 Message 36 by Coyote, posted 10-07-2016 6:13 PM Kleinman has responded

  
Kleinman
Member (Idle past 946 days)
Posts: 136
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 responded

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

  
Kleinman
Member (Idle past 946 days)
Posts: 136
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 responded

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

  
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