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Author Topic:   Explaining the pro-Evolution position
Taq
Member
Posts: 6628
Joined: 03-06-2009
Member Rating: 4.1


Message 346 of 393 (792868)
10-14-2016 4:50 PM
Reply to: Message 343 by Kleinman
10-14-2016 4:41 PM


Re: Lenski
Kleinman writes:

rmns is suppressed long before extinction occurs. Even if the population can survive multiple different simultaneous selection pressures, you won't get the amplification necessary for rmns to work efficiently.

I already disproved that by showing how two beneficial mutations in two separate lineages can be combined into a single lineage through sexual recombination. This means that you can win two lotteries at once, or walk up two separate staircases at the same time.


This message is a reply to:
 Message 343 by Kleinman, posted 10-14-2016 4:41 PM Kleinman has not yet responded

  
Taq
Member
Posts: 6628
Joined: 03-06-2009
Member Rating: 4.1


Message 347 of 393 (792869)
10-14-2016 4:51 PM
Reply to: Message 331 by Kleinman
10-14-2016 3:23 PM


Re: Is it summation time?
Kleinman writes:

So you think that a range animal cannot be subjected to thermal stress, starvation, predation, disease, dehydration,... at the same time?

Please try to reply to what I actually said.


This message is a reply to:
 Message 331 by Kleinman, posted 10-14-2016 3:23 PM Kleinman has not yet responded

  
Taq
Member
Posts: 6628
Joined: 03-06-2009
Member Rating: 4.1


Message 348 of 393 (792870)
10-14-2016 4:54 PM
Reply to: Message 332 by Kleinman
10-14-2016 3:32 PM


Re: Mathematics cannot change reality but when done correctly can predict it
Kleinman writes:

And then there is always 3 and more different flights of stairs. What happens then?

Those adaptations are also selected for within the population and can be combined into a single lineage through sexual recombination.

Not quite yet, you still have quite a few more flights of stairs to climb. We are going to get you cardiac fit and teach you a little probability theory before this is over.

Or you could actually address my posts instead of running away from them.

You don't have to win two lotteries. The descendants of two lottery winners can marry, pooling the winnings together.

Are you going to respond to this in a meaningful manner, or not?


This message is a reply to:
 Message 332 by Kleinman, posted 10-14-2016 3:32 PM Kleinman has not yet responded

  
Kleinman
Member (Idle past 160 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 349 of 393 (792871)
10-14-2016 5:02 PM
Reply to: Message 336 by bluegenes
10-14-2016 3:40 PM


Re: Lenski: Cit+ isn't slow.
quote:
Kleinman writes:

Don't get me wrong, there's more than one way replicators can adapt to selection pressures other than rmns. Recombination is a much faster way replicators can adapt and they can do it to multiple selection pressures simultaneously. But they have to have the correct alleles already in the gene pool.
On the other hand, rmns is the creation of new alleles in order to adapt. And if the adaptation requires the creation of multiple different new alleles at different genetic loci due to multiple different selection pressures simultaneously, the chances of adaptation are extremely low and the process is extremely slow if it going to happen (see the Lenski experiment for an empirical example).

Very rapid adaptations involving new alleles occurred in all cultures in the Lenski experiment. But perhaps you are thinking of the complicated sequence of mutations that produced the Cit+ strain in just one of the twelve cultures after ~30,000 generations? Is that what you are thinking of as slow?

If so, here's something to consider. The Lenski cultures are all in the same environment and undergo the same processes. These are not actually very conducive to the emergence of Cit+ as a dominant strain. Change the circumstances, and Cit+ organisms can emerge in less than 100 generations. The potentiating, actualizing and refining mutations, a considerable sequence, can all take place in one culture in a few weeks.

Did your probability calculations tell you that?



https://en.wikipedia.org/...i_long-term_evolution_experiment
quote:
Although the bacteria in each population are thought to have generated hundreds of millions of mutations over the first 20,000 generations, Lenski has estimated that within this time frame, only 10 to 20 beneficial mutations achieved fixation in each population, with fewer than 100 total point mutations (including neutral mutations) reaching fixation in each population.[6]

That's about 1 beneficial mutation per thousand generations. If you think that's fast, would you argue about Haldane's dilemma?

As for the Citrate metabolizer (e coli has alway been able to metabolize Citrate because it has a Krebs cycle), appeared at about generation 31500, not at 100 generations. The problem is not in the citric acid cycle for e coli, it is in the ability to transport citrate in the presence of oxygen. If I recall, those variants were spherical forms and so it may be that a mutation causing a defective cell wall allows the citrate to enter.

And yes, my equations include the possibility for this type of more rare mutation.


This message is a reply to:
 Message 336 by bluegenes, posted 10-14-2016 3:40 PM bluegenes has responded

Replies to this message:
 Message 352 by Dr Adequate, posted 10-14-2016 5:13 PM Kleinman has responded
 Message 358 by bluegenes, posted 10-14-2016 6:00 PM Kleinman has responded

  
Modulous
Member
Posts: 7407
From: Manchester, UK
Joined: 05-01-2005
Member Rating: 3.3


Message 350 of 393 (792872)
10-14-2016 5:11 PM
Reply to: Message 342 by Kleinman
10-14-2016 4:16 PM


Re: the equality of pressure?
It tends to decrease in frequency.

Yup

So we agree that random mutation does not 'consist{s} of a beneficial mutation occurring'. Good. That's all I was saying with this.

rmns is not dependent on the relative frequency of variants in a population.

Obviously.

Natural selection is the name for some of the factors that cause frequency changes in a population.

rmns is not dependent on relative frequencies of variants in the population

Obviously.

Natural selection is the name for some of the factors that cause frequency changes in a population.

Was there some reason you repeated yourself?

They are not competing for food initially because the petri dish is so large

But they don't evolve antibiotic resistance initially. So how does this demonstrate that rmns is working 'better'?

At what point do you say that the probabilities are so low that the particular outcome is impossible.

The point is that you are treating the selection pressures affecting HIV subject to combination therapy (a distinctly unnatural event) as the same as those affecting the dinosaurs and trying to conclude this means the dinosaurs could not have evolved into birds. You are trying to suggest the probabilities are the same, or worse, without providing any evidence of this. You just use the obfuscatory 'the maths is the same' line I have previously criticised as insufficient.

You might say that winning a single lottery is possible and that winning two lotteries is also still possible but not very likely and winning three lotteries, that's getting a little iffy, how about you winning 10 lotteries or a 100 lotteries?

If the odds of winning a lottery is 1 in 10,000,000 and I buy a quadrillion tickets, I expect to win a billion times in one lottery or once in a billion lotteries or any combination between.

However, you have not provided the numbers to answer the question in the case of dinosaurs, you have assumed the lottery or lotteries the dinosaurs entered was the same as the lottery or lotteries HIV enters during therapy. This is an empirically false assumption, hence your incorrect conclusion.

Despite your attempt to distract from this point, it remains the fatal flaw in your argument.

You can have amplification without any change in the relative frequency of the variants in a population by having all variants amplifying simultaneously.

It's possible, but stupendously unlikely, for this to occur in nature. It cannot happen for long.

That's what you are seeing in the video of the bacteria evolving resistance.

No, it isn't.

You see multiple different colonies forming and then you get mutant variants in several of the colonies which can then start growing on the increased concentration antibiotic bands.

But the variants that have not evolved the antibiotic resistance don't amplify. At least there is no evidence that if they do, they do so at exactly the same rate as the bacteria with the new food source. Indeed we can use the work of Lenski already presented to demonstrate adequately that having fewer food sources inhibits amplification compared with having more.


This message is a reply to:
 Message 342 by Kleinman, posted 10-14-2016 4:16 PM Kleinman has responded

Replies to this message:
 Message 359 by Kleinman, posted 10-14-2016 6:10 PM Modulous has responded

    
Kleinman
Member (Idle past 160 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 351 of 393 (792873)
10-14-2016 5:12 PM
Reply to: Message 337 by Dr Adequate
10-14-2016 3:40 PM


Re: Is it summation time?
quote:
How does evolution of drug resistance differ than evolution by rmns to any other kind of selection pressure?

Evolution to drug resistance occurs in the face of the hardest hard selection that our brightest and best scientists can devise. As I have proved, the hardness of the selection is a crucial variable in the math, you can't ignore it.

You think starvation is a soft selection pressure?

All adaption by rmns requires lineages to address nested binomial probability problems. It doesn't matter whether they are antimicrobial agents, starvation, dehydration, thermal stress, predation, diseases, you name it. And why do you keep ignoring my question whether the intensity of selection alters the evolutionary trajectory to adaptation? If the same selection pressure is applied at low intensity, does it require different mutations for adaptation than if the selection pressure occurs at high intensity?


This message is a reply to:
 Message 337 by Dr Adequate, posted 10-14-2016 3:40 PM Dr Adequate has responded

Replies to this message:
 Message 353 by Dr Adequate, posted 10-14-2016 5:18 PM Kleinman has responded
 Message 356 by Taq, posted 10-14-2016 5:37 PM Kleinman has not yet responded

  
Dr Adequate
Member
Posts: 15934
Joined: 07-20-2006
Member Rating: 3.4


Message 352 of 393 (792874)
10-14-2016 5:13 PM
Reply to: Message 349 by Kleinman
10-14-2016 5:02 PM


Re: Lenski: Cit+ isn't slow.
That's about 1 beneficial mutation per thousand generations. If you think that's fast, would you argue about Haldane's dilemma?

Well, it's fast enough: see post #275.


This message is a reply to:
 Message 349 by Kleinman, posted 10-14-2016 5:02 PM Kleinman has responded

Replies to this message:
 Message 360 by Kleinman, posted 10-14-2016 6:17 PM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 15934
Joined: 07-20-2006
Member Rating: 3.4


Message 353 of 393 (792876)
10-14-2016 5:18 PM
Reply to: Message 351 by Kleinman
10-14-2016 5:12 PM


Re: Is it summation time?
You think starvation is a soft selection pressure?

That depends crucially on whether it's hard or soft.

All adaption by rmns requires lineages to address nested binomial probability problems.

Well, perhaps you could show us some math.

And why do you keep ignoring my question whether the intensity of selection alters the evolutionary trajectory to adaptation?

Where did you ask me that?

The answer is obviously yes.

If the same selection pressure is applied at low intensity, does it require different mutations for adaptation than if the selection pressure occurs at high intensity?

It may.


This message is a reply to:
 Message 351 by Kleinman, posted 10-14-2016 5:12 PM Kleinman has responded

Replies to this message:
 Message 362 by Kleinman, posted 10-14-2016 6:28 PM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 15934
Joined: 07-20-2006
Member Rating: 3.4


Message 354 of 393 (792877)
10-14-2016 5:19 PM


Simulation
So, here are the results of some simulations differing only in the number of selection pressures operating.

Click to enlarge.

As you can see, the rate of adaptation is faster the more selection pressures are operating, in line with (a) my math (b) common sense.

Edited by Dr Adequate, : No reason given.


Replies to this message:
 Message 364 by Kleinman, posted 10-14-2016 6:31 PM Dr Adequate has responded

  
Kleinman
Member (Idle past 160 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 355 of 393 (792878)
10-14-2016 5:33 PM
Reply to: Message 339 by Modulous
10-14-2016 3:51 PM


Re: Lenski
quote:
Lenski's starvation stress slows the doubling time for his population to about every 7 hours.

I was referring to the number of generations, not hours. Thus everything else you said is irrelevant. Unless you think that dinosaur generation time was changed from 2 years to 20 years because they weren't birds?

So do you think the amplification time (starvation alone=>about 1000 generations per beneficial mutation) would speed up if a small thermal stress was added to his populations or would the number of generations per beneficial mutation increase?
quote:
In fact, if there is too many selection pressures on the population yet the population is not driven to extinction, what you will see is the population will just drift. This is what happens to HIV when subjected to the three drug therapies.

The number of pressures is considerably less important than their magnitude. This is the central problem with your whole thesis. You need to address this.



Large numbers of low intensity selection pressures do not cause rmns to work, you get drift under these conditions.
This message is a reply to:
 Message 339 by Modulous, posted 10-14-2016 3:51 PM Modulous has responded

Replies to this message:
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Taq
Member
Posts: 6628
Joined: 03-06-2009
Member Rating: 4.1


Message 356 of 393 (792879)
10-14-2016 5:37 PM
Reply to: Message 351 by Kleinman
10-14-2016 5:12 PM


Re: Is it summation time?
Kleinman writes:

All adaption by rmns requires lineages to address nested binomial probability problems. It doesn't matter whether they are antimicrobial agents, starvation, dehydration, thermal stress, predation, diseases, you name it.

Asexual species overcome these problems by conquering one at a time, not all at once.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 351 by Kleinman, posted 10-14-2016 5:12 PM Kleinman has not yet responded

  
Kleinman
Member (Idle past 160 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 357 of 393 (792880)
10-14-2016 5:47 PM
Reply to: Message 344 by Taq
10-14-2016 4:45 PM


Re: Lenski
quote:
What you are not seeing is that the thermal stress will be impairing the replication of the energy fit variants when compared to running the experiment at the ideal temperature. The ability to amplify any beneficial mutation for a given selection pressure can and is impaired by other selection pressures.

Thermal stress is imparing the energy fit and the less energy fit by the same amount in the hotter environment. What differentiates the energy fit and the less energy fit in the same environment is their energy efficiency. This causes an amplification of the energy fit in that environment.

Of course, that's what selection pressures do. Selection pressures drive down populations unless the populations can adapt to those pressures.
quote:
So if the probability of a beneficial mutation occurring for a population size N is let's say 0.6 and you double the population size to 2N, the probability becomes 1.2?

The probability of drawing the Ace of Spades is 1 in 52 attempts. The odds of drawing the Ace of spaces in 104 draws is 2. Not that hard to figure out.



Taq, there is no such thing as a probability value over 1. Why don't you watch some youtube videos on probability theory, eg Khan Academy
https://www.youtube.com/watch?v=uzkc-qNVoOk&list=PL06A16C...
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bluegenes
Member
Posts: 3119
From: U.K.
Joined: 01-24-2007
Member Rating: 3.5


(1)
Message 358 of 393 (792883)
10-14-2016 6:00 PM
Reply to: Message 349 by Kleinman
10-14-2016 5:02 PM


Re: Lenski: Cit+ isn't slow.
Kleinman writes:

As for the Citrate metabolizer (e coli has alway been able to metabolize Citrate because it has a Krebs cycle), appeared at about generation 31500, not at 100 generations.

I said "change the circumstances". I know the Lenski experiment took over 30,000 generations for Cit+. The multi-mutation adaptation can happen in less than 100 generations in other circumstances.

http://jb.asm.org/content/198/7/1022.full

That, ironically, is a paper by creationists who didn't like the idea that the occurrence of Cit+ in Lenski is special, and set out to show that it could happen easily. It can.

So, where are your calculations? Surely they're not based on the view that an adaptation involving 5 or more mutations in sequence would take ~31,000 generations in a culture of bacteria in any or all environments? How are environments factored in?

You still seem to be assuming that organisms have to be threatened with extinction in order to evolve, as suggested before. They don't. Flying squirrels evolve alongside the non-flying versions they descend from, and both thrive. It's just better to be able to glide in certain environments. Same with dinosaurs. The fliers existed alongside the non-fliers for tens of millions of years. They just fill different niches.


This message is a reply to:
 Message 349 by Kleinman, posted 10-14-2016 5:02 PM Kleinman has responded

Replies to this message:
 Message 368 by Kleinman, posted 10-14-2016 6:46 PM bluegenes has responded

  
Kleinman
Member (Idle past 160 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 359 of 393 (792884)
10-14-2016 6:10 PM
Reply to: Message 350 by Modulous
10-14-2016 5:11 PM


Re: the equality of pressure?
quote:
They are not competing for food initially because the petri dish is so large

But they don't evolve antibiotic resistance initially. So how does this demonstrate that rmns is working 'better'?



But the populations are amplifying improving the probability that the first beneficial mutation will land on some member of a population
quote:
At what point do you say that the probabilities are so low that the particular outcome is impossible.

The point is that you are treating the selection pressures affecting HIV subject to combination therapy (a distinctly unnatural event) as the same as those affecting the dinosaurs and trying to conclude this means the dinosaurs could not have evolved into birds. You are trying to suggest the probabilities are the same, or worse, without providing any evidence of this. You just use the obfuscatory 'the maths is the same' line I have previously criticised as insufficient.



I disagree with you. I think combination selection pressures are the rule in nature. Drought, starvation, thermal stress, disease, predation,...
quote:
You might say that winning a single lottery is possible and that winning two lotteries is also still possible but not very likely and winning three lotteries, that's getting a little iffy, how about you winning 10 lotteries or a 100 lotteries?

If the odds of winning a lottery is 1 in 10,000,000 and I buy a quadrillion tickets, I expect to win a billion times in one lottery or once in a billion lotteries or any combination between.

However, you have not provided the numbers to answer the question in the case of dinosaurs, you have assumed the lottery or lotteries the dinosaurs entered was the same as the lottery or lotteries HIV enters during therapy. This is an empirically false assumption, hence your incorrect conclusion.

Despite your attempt to distract from this point, it remains the fatal flaw in your argument.



How large is that population size for dinosaurs? And remember, or learn, that rmns occurs on lineages, you know, common descent. And that quadrillion population is now reduced to a new lineage of 1 with that first beneficial mutation. And until that variant amplifies, the probabilities are very low that the 2nd beneficial mutation will occur on one of its descendants.
quote:
You can have amplification without any change in the relative frequency of the variants in a population by having all variants amplifying simultaneously.

It's possible, but stupendously unlikely, for this to occur in nature. It cannot happen for long.



Well then how did Weinreich measure so many different variants from his one targeted antibiotic selection pressure?
quote:
That's what you are seeing in the video of the bacteria evolving resistance.

No, it isn't.



What do you think you are seeing in the video. Do you think that all the colonies are giving the same variants?
quote:
You see multiple different colonies forming and then you get mutant variants in several of the colonies which can then start growing on the increased concentration antibiotic bands.

But the variants that have not evolved the antibiotic resistance don't amplify. At least there is no evidence that if they do, they do so at exactly the same rate as the bacteria with the new food source. Indeed we can use the work of Lenski already presented to demonstrate adequately that having fewer food sources inhibits amplification compared with having more.



The non-antibiotic resistant variants amplify until the resources of the plate are exhausted. They were not able to do enough replication trials to get that beneficial mutation.
This message is a reply to:
 Message 350 by Modulous, posted 10-14-2016 5:11 PM Modulous has responded

Replies to this message:
 Message 365 by Dr Adequate, posted 10-14-2016 6:32 PM Kleinman has responded
 Message 370 by Modulous, posted 10-14-2016 7:27 PM Kleinman has not yet responded

  
Kleinman
Member (Idle past 160 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 360 of 393 (792885)
10-14-2016 6:17 PM
Reply to: Message 352 by Dr Adequate
10-14-2016 5:13 PM


Re: Lenski: Cit+ isn't slow.
quote:
That's about 1 beneficial mutation per thousand generations. If you think that's fast, would you argue about Haldane's dilemma?

Well, it's fast enough: see post #275.

Fast enough for what? This is an experiment with only a single selection pressure. Somehow you have gotten in your mind that adding selection pressures will speed up this process. rmns is nothing more than nested binomial probability problems, that's the mathematical fact of life. And adding more selection pressures simply adds more binomial probability problems for the lineage to solve.
This message is a reply to:
 Message 352 by Dr Adequate, posted 10-14-2016 5:13 PM Dr Adequate has responded

Replies to this message:
 Message 361 by Dr Adequate, posted 10-14-2016 6:28 PM Kleinman has not yet responded

  
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