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Author Topic:   Explaining the pro-Evolution position
Kleinman
Member (Idle past 188 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 331 of 393 (792852)
10-14-2016 3:23 PM
Reply to: Message 323 by Taq
10-14-2016 2:36 PM


Re: Is it summation time?
quote:
Kleinman writes:

How does evolution of drug resistance differ than evolution by rmns to any other kind of selection pressure?


Selection pressures are rarely binary between survival and death. It wasn't as if a species with scales would go extinct in a single generation if it didn't evolve feathers.

So you think that a range animal cannot be subjected to thermal stress, starvation, predation, disease, dehydration,... at the same time?
This message is a reply to:
 Message 323 by Taq, posted 10-14-2016 2:36 PM Taq has responded

Replies to this message:
 Message 347 by Taq, posted 10-14-2016 4:51 PM Kleinman has not yet responded

  
Kleinman
Member (Idle past 188 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 332 of 393 (792853)
10-14-2016 3:32 PM
Reply to: Message 324 by Taq
10-14-2016 2:37 PM


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

Try climbing two different flights of stairs at the same time.


That's exactly what sexual species do.

And then there is always 3 and more different flights of stairs. What happens then?
quote:
You win a lottery, everyone wants to marry you.

Your tacit admission of defeat is accepted.



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.
This message is a reply to:
 Message 324 by Taq, posted 10-14-2016 2:37 PM Taq has responded

Replies to this message:
 Message 348 by Taq, posted 10-14-2016 4:54 PM Kleinman has not yet responded

  
Modulous
Member
Posts: 7410
From: Manchester, UK
Joined: 05-01-2005


(1)
Message 333 of 393 (792854)
10-14-2016 3:36 PM
Reply to: Message 327 by Kleinman
10-14-2016 3:00 PM


Re: the equality of pressure?
What do you think happens if the mutation is detrimental?

It tends to decrease in frequency.

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.

Random mutation can impact frequencies.

Drift can impact frequencies.

Here's an example where rmns is occurring in an environment where variants are not competing for resources in the environment:
http://www.slate.com/...cteria_evolving_drug_resistance.html

No it isn't. The bacteria are competing for food. The reach a certain population size. In that environment certain mutations help them (make them more efficiently utilize the limited food, or opening up new food sources), others hinder them.

. So saying that the selection pressures in one case demonstrates evolution is impossible in other cases is kind of silly isn't it?
Feel free to quote me if you think I said that.

No problem.

rmns will not transform reptiles into birds.

There is a specific mathematical reason why combination therapy works for the treatment of HIV.

the reason rmns can't do it is the multiplication rule of probabilities.

You seem throughout to be arguing that because HIV combination therapy inhibits evolution, then evolution in contexts such as dinosaur->bird is likewise inhibited to the same kind of degree. This assumes the selection pressures moving dinosaurs towards birds are on a par with the selection pressures applied to HIV during combination therapy. This is silly.

What I have said and will continue to say because it is a mathematical and empirical fact of life is that rmns only works efficiently when a single gene is targeted by a single selection pressure at a time.

Natural history has proven natural selection to be inefficient. Efficiency doesn't provide us any cause to suspect the evolution to birds is impossible. Natural selection does not target. SELECTION may be more efficient this way, but natural selection does not target. Natural selection is MASSIVELY INEFFICIENT. This has long been observed. What does efficiency matter and how does it prevent dinosaur to bird evolution? You have not said.

And this process does not work by changing the relative frequencies of variants in a population but works by amplification of the particular variants.

How do those variants get amplified in nature if not by increasing their frequency in the population?

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 327 by Kleinman, posted 10-14-2016 3:00 PM Kleinman has responded

Replies to this message:
 Message 342 by Kleinman, posted 10-14-2016 4:16 PM Modulous has responded

    
Kleinman
Member (Idle past 188 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 334 of 393 (792855)
10-14-2016 3:38 PM
Reply to: Message 325 by PaulK
10-14-2016 2:40 PM


Re: Is it summation time?
quote:
quote:

How does evolution of drug resistance differ than evolution by rmns to any other kind of selection pressure?


If you had been paying attention you would know. For drug resistance selection pressure comes in the form of an environmental factor which greatly reduces the fitness of all non-resistant members of the population.

You can see this same thing with drug selection pressures, watch this video:
http://www.slate.com/...cteria_evolving_drug_resistance.html
quote:
What happens in the case of soft selection where the fitness of the "original" strain remains high ? Where the only factor reducing it below 1 is competition with other members of the species who possess a recent mutation (or a mutation recently become advantageous due to environmental change)

You are describing the Lenski experiment which takes more than a thousand generations per beneficial mutation. Do you think his experiment would run faster if Lenski applied a little thermal stress to his population as well?
This message is a reply to:
 Message 325 by PaulK, posted 10-14-2016 2:40 PM PaulK has responded

Replies to this message:
 Message 341 by PaulK, posted 10-14-2016 3:59 PM Kleinman has not yet responded

  
Dr Adequate
Member
Posts: 15946
Joined: 07-20-2006
Member Rating: 3.5


Message 335 of 393 (792856)
10-14-2016 3:38 PM
Reply to: Message 326 by Kleinman
10-14-2016 2:48 PM


Re: Lenski
Lenski's experiment works because he doesn't starve his populations to death.

Yes. Extinction does stop evolution, it's probably the only thing that can.

So if you put starvation pressure and thermal stress on the population at the same time, well you figure it out.

I figured it out, it turns out that the results of the experiment depend on how hard the selection is.

Why doesn't anything evolve resistance to Iodine? The reason is that Iodine is a very reactive molecule binding to all kinds of biological molecules, denaturing the molecules, far too many targets for rmns to have any chance for a replicator to evolve resistance to this chemical.

Yes, it's the ultimate in hard selection --- it kills everything.

That's not an answer to my point. Let me ask again --- how would make a difference in the math whether you have one selection pressure acting on many loci, or a different selection pressure for each of the loci?


This message is a reply to:
 Message 326 by Kleinman, posted 10-14-2016 2:48 PM Kleinman has responded

Replies to this message:
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bluegenes
Member
Posts: 3119
From: U.K.
Joined: 01-24-2007
Member Rating: 3.3


(1)
Message 336 of 393 (792857)
10-14-2016 3:40 PM
Reply to: Message 276 by Kleinman
10-14-2016 12:01 PM


Lenski: Cit+ isn't slow.
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?


This message is a reply to:
 Message 276 by Kleinman, posted 10-14-2016 12:01 PM Kleinman has responded

Replies to this message:
 Message 349 by Kleinman, posted 10-14-2016 5:02 PM bluegenes has responded

  
Dr Adequate
Member
Posts: 15946
Joined: 07-20-2006
Member Rating: 3.5


Message 337 of 393 (792858)
10-14-2016 3:40 PM
Reply to: Message 321 by Kleinman
10-14-2016 2:34 PM


Re: Is it summation time?
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.


This message is a reply to:
 Message 321 by Kleinman, posted 10-14-2016 2:34 PM Kleinman has responded

Replies to this message:
 Message 351 by Kleinman, posted 10-14-2016 5:12 PM Dr Adequate has responded

  
Kleinman
Member (Idle past 188 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 338 of 393 (792859)
10-14-2016 3:48 PM
Reply to: Message 328 by Modulous
10-14-2016 3:12 PM


Re: Lenski
quote:
So if you put starvation pressure and thermal stress on the population at the same time, well you figure it out.

All things being equal it would take the same generational time as the starvation experiment plus the generational time of the thermal stress experiment. That is, if the second experiment was as lethal as the first (ie., the number of bacteria that died without reproducing in the starvation experiment is the same the number of bacteria dying w/o reproduction in the starvation + thermal stress test), then it would just be a case of evolving one (which we know how long that takes) then evolving the other (and we know that too).

If the experiments were MORE lethal, then they couldn't be easily compared, we'd need to know population size per generation before being able to estimate. That's a bit like the difference between being a dinosaur in a normal environment and a virus being bombarded with disparate poisons that have been tailored to kill it. One is a little more lethal and the results consequently may differ.



Lenski's starvation stress slows the doubling time for his population to about every 7 hours. Under ideal conditions, bacteria can double every 20 minutes. Stress these bacteria more and it will only slow their generation time which will in turn, slow the amplification time which will in turn slow the evolutionary process even more so. 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.
This message is a reply to:
 Message 328 by Modulous, posted 10-14-2016 3:12 PM Modulous has responded

Replies to this message:
 Message 339 by Modulous, posted 10-14-2016 3:51 PM Kleinman has responded

  
Modulous
Member
Posts: 7410
From: Manchester, UK
Joined: 05-01-2005


Message 339 of 393 (792860)
10-14-2016 3:51 PM
Reply to: Message 338 by Kleinman
10-14-2016 3:48 PM


Re: Lenski
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?

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.

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 338 by Kleinman, posted 10-14-2016 3:48 PM Kleinman has responded

Replies to this message:
 Message 355 by Kleinman, posted 10-14-2016 5:33 PM Modulous has responded

    
Kleinman
Member (Idle past 188 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 340 of 393 (792861)
10-14-2016 3:53 PM
Reply to: Message 329 by Taq
10-14-2016 3:13 PM


Re: Lenski
quote:
Kleinman writes:

So if you put starvation pressure and thermal stress on the population at the same time, well you figure it out.


Perhaps you should figure it out.

I have figured it out, I published the mathematics of random mutation and natural selection for multiple simultaneous selection pressures. But in order to understand this paper, you need to understand the difference between complementary events and additive events.
quote:
Why doesn't anything evolve resistance to Iodine? The reason is that Iodine is a very reactive molecule binding to all kinds of biological molecules, denaturing the molecules, far too many targets for rmns to have any chance for a replicator to evolve resistance to this chemical.

You claim that RMNS can't produce the features we do see. Why don't you focus on the features we do see instead of the features we don't see.



I have done this, all my mathematics is done based on real, measurable and repeatable examples of rmns.
This message is a reply to:
 Message 329 by Taq, posted 10-14-2016 3:13 PM Taq has responded

Replies to this message:
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 Message 375 by Admin, posted 10-15-2016 8:48 AM Kleinman has responded

  
PaulK
Member
Posts: 12863
Joined: 01-10-2003
Member Rating: 3.4


Message 341 of 393 (792862)
10-14-2016 3:59 PM
Reply to: Message 334 by Kleinman
10-14-2016 3:38 PM


Re: Is it summation time?
quote:

You can see this same thing with drug selection pressures

That drug selection pressures have the same effect as drug selection pressures is hardly a great insight.

quote:

You are describing the Lenski experiment which takes more than a thousand generations per beneficial mutation.

I'm describing a general situation which is not expected to reduce the frequency of beneficial mutations. If you think it did in the Lenski experiments you need to show evidence and reasoning - to support both the claim of frequency, and that it is caused by soft selection.


This message is a reply to:
 Message 334 by Kleinman, posted 10-14-2016 3:38 PM Kleinman has not yet responded

    
Kleinman
Member (Idle past 188 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 342 of 393 (792863)
10-14-2016 4:16 PM
Reply to: Message 333 by Modulous
10-14-2016 3:36 PM


Re: the equality of pressure?
quote:
What do you think happens if the mutation is detrimental?

It tends to decrease in frequency.

Yup, and it will also decrease in number and that's why it's very unlikely that you will get a beneficial mutation on a member of this lineage
quote:
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.

Random mutation can impact frequencies.

Drift can impact frequencies.



But the mathematical fact of life is that rmns is not dependent on relative frequencies of variants in the population, it is dependent on the ability of a particular lineage to amplify.
quote:
Here's an example where rmns is occurring in an environment where variants are not competing for resources in the environment:
http://www.slate.com/...cteria_evolving_drug_resistance.html

No it isn't. The bacteria are competing for food. The reach a certain population size. In that environment certain mutations help them (make them more efficiently utilize the limited food, or opening up new food sources), others hinder them.



They are not competing for food initially because the petri dish is so large, if you tried to run this experiment in a standard sized petri dish then competition for resources would start almost immediately and it would be much less likely that you would see the evolution of drug resistance.
quote:
. So saying that the selection pressures in one case demonstrates evolution is impossible in other cases is kind of silly isn't it?
Feel free to quote me if you think I said that.

No problem.

rmns will not transform reptiles into birds.

There is a specific mathematical reason why combination therapy works for the treatment of HIV.

the reason rmns can't do it is the multiplication rule of probabilities.

You seem throughout to be arguing that because HIV combination therapy inhibits evolution, then evolution in contexts such as dinosaur->bird is likewise inhibited to the same kind of degree. This assumes the selection pressures moving dinosaurs towards birds are on a par with the selection pressures applied to HIV during combination therapy. This is silly.



At what point do you say that the probabilities are so low that the particular outcome is impossible. 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 you have enough significant figures on your calculator, you might claim this is still possible but you better have a lot of significant figures on your calculator, otherwise, it will say 0.
quote:
What I have said and will continue to say because it is a mathematical and empirical fact of life is that rmns only works efficiently when a single gene is targeted by a single selection pressure at a time.

Natural history has proven natural selection to be inefficient. Efficiency doesn't provide us any cause to suspect the evolution to birds is impossible. Natural selection does not target. SELECTION may be more efficient this way, but natural selection does not target. Natural selection is MASSIVELY INEFFICIENT. This has long been observed. What does efficiency matter and how does it prevent dinosaur to bird evolution? You have not said.

And this process does not work by changing the relative frequencies of variants in a population but works by amplification of the particular variants.

How do those variants get amplified in nature if not by increasing their frequency in the population?



You can have amplification without any change in the relative frequency of the variants in a population by having all variants amplifying simultaneously. That's what you are seeing in the video of the bacteria evolving resistance. 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. On the other hand, you can have fixation without any amplification. Simply kill off all the variants except the one which is now fixed.
This message is a reply to:
 Message 333 by Modulous, posted 10-14-2016 3:36 PM Modulous has responded

Replies to this message:
 Message 350 by Modulous, posted 10-14-2016 5:11 PM Kleinman has responded

  
Kleinman
Member (Idle past 188 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 343 of 393 (792865)
10-14-2016 4:41 PM
Reply to: Message 335 by Dr Adequate
10-14-2016 3:38 PM


Re: Lenski
quote:
Lenski's experiment works because he doesn't starve his populations to death.

Yes. Extinction does stop evolution, it's probably the only thing that can.

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. That's what all the real, measurable and repeatable examples of rmns show.
quote:
So if you put starvation pressure and thermal stress on the population at the same time, well you figure it out.

I figured it out, it turns out that the results of the experiment depend on how hard the selection is.



So let's say you put an itsy bitsy little bit of thermal stress on the Lenski bacteria, do you think the evolutionary process will speed up (more beneficial mutations per generation) of slow down? Do you think the evolutionary trajectories and the mutations for adaptation depend on the intensity of selection?
quote:
Why doesn't anything evolve resistance to Iodine? The reason is that Iodine is a very reactive molecule binding to all kinds of biological molecules, denaturing the molecules, far too many targets for rmns to have any chance for a replicator to evolve resistance to this chemical.

Yes, it's the ultimate in hard selection --- it kills everything.



Actually, you might find a target gene, you might get a spore that can survive.
quote:
That's not an answer to my point. Let me ask again --- how would make a difference in the math whether you have one selection pressure acting on many loci, or a different selection pressure for each of the loci?

There's no real difference in the math. You are still dealing with nested binomial probability problems. We can get a sense what goes with a selection pressure that target many genes with the Lenski experiment. The improvement in fitness is so small with each beneficial mutation that amplification is very difficult for that slightly more fit variant due to competition with other variants. Lenski is running his experiment in 10ml tubes. If he ran the experiment in 1 liter containers, you might see amplification occur more quickly because you are allowing for larger populations than his e7-e8.

On the other hand, you can see from the video of bacteria evolving resistance on the large petri dish, you don't have the environmental resource limitation, only the targeted antibiotic selection pressure so that rmns process works very quickly.


This message is a reply to:
 Message 335 by Dr Adequate, posted 10-14-2016 3:38 PM Dr Adequate has not yet responded

Replies to this message:
 Message 346 by Taq, posted 10-14-2016 4:50 PM Kleinman has not yet responded

  
Taq
Member
Posts: 6787
Joined: 03-06-2009
Member Rating: 3.9


Message 344 of 393 (792866)
10-14-2016 4:45 PM
Reply to: Message 330 by Kleinman
10-14-2016 3:18 PM


Re: Lenski
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.

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.


This message is a reply to:
 Message 330 by Kleinman, posted 10-14-2016 3:18 PM Kleinman has responded

Replies to this message:
 Message 357 by Kleinman, posted 10-14-2016 5:47 PM Taq has not yet responded

  
Taq
Member
Posts: 6787
Joined: 03-06-2009
Member Rating: 3.9


Message 345 of 393 (792867)
10-14-2016 4:47 PM
Reply to: Message 340 by Kleinman
10-14-2016 3:53 PM


Re: Lenski
Kleinman writes:

I have figured it out, I published the mathematics of random mutation and natural selection for multiple simultaneous selection pressures. But in order to understand this paper, you need to understand the difference between complementary events and additive events.

I already demonstrated that it is you who doesn't understand the difference.

I have done this, all my mathematics is done based on real, measurable and repeatable examples of rmns.

All your mathematics have shown that what we observe has evolved through RMNS. You have never shown a real difference between two species that could not be produced by RMNS.


This message is a reply to:
 Message 340 by Kleinman, posted 10-14-2016 3:53 PM Kleinman has not yet responded

  
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