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Author Topic:   Explaining the pro-Evolution position
Kleinman
Member (Idle past 954 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 301 of 393 (792817)
10-14-2016 12:58 PM
Reply to: Message 280 by Dr Adequate
10-14-2016 12:07 PM


Re: Lenski
quote:
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).

But the Lenski experiment seems to be an example of the exact opposite. The environment was constant, so we know that no selection pressures were added. And looking at the data from the experiment, we see that improvements in fitness started off fast and slowed down. This is consistent with my math and my reasoning --- to begin with, there were lots of potential beneficial mutations, and the chance of any one of them was relatively high. But as they occurred and became fixed, there were fewer potential beneficial mutations left, and the rate of the process slowed down. But if you were right, then every time a beneficial mutation spread though the population it would remove a (non-conservative) selection pressure, and the process would speed up.

That's the point, Lenski is using only a single directional selection pressure, starvation. He is selecting for the most efficient energy users. And if Lenski were to add a second simultaneous selection pressure, for example, thermal stress, the amplification of the mutations which increase energy efficiency will be slowed by the thermal stress applied to these populations. Now if you want to get variants which are thermal stress tolerant and energy efficient replicators, use the selection pressures sequentially. Contact Lenski and ask him to do the experiment and prove me wrong.
This message is a reply to:
 Message 280 by Dr Adequate, posted 10-14-2016 12:07 PM Dr Adequate has responded

Replies to this message:
 Message 303 by Taq, posted 10-14-2016 1:10 PM Kleinman has responded
 Message 308 by Dr Adequate, posted 10-14-2016 1:27 PM Kleinman has responded

  
Kleinman
Member (Idle past 954 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 302 of 393 (792818)
10-14-2016 1:07 PM
Reply to: Message 285 by Dr Adequate
10-14-2016 12:17 PM


Re: Is it summation time?
quote:
And I think you haven't read my responses to Dr Adequate.

Or maybe he's read my responses to your responses.

Once again, let me point out that it is manifestly the case that the genes that make birds birds and not dinosaurs are in fact fixed in birds. It's not like some (< 100%) proportion of birds are birds and the rest of the birds are dinosaurs. The probability of this fixation happening and the time it would take for this to happen if we started with dinosaurs is therefore what you need to be calculating. If your take on evolution can't even cope with the concept of fixation, then what this shows is not that the concept of fixation is bad, but that your ideas are inadequate to address this question.



Don't get me wrong Doc, allele frequencies are important when you are considering random recombination. But when it comes to rmns, it's the actual population size for a given lineage that is important and used to determine the probabilities (that and the number of generations the lineage replicates), not the relative frequency of the particular variant wrt the rest of the population.

For a lineage on a particular rmns evolutionary trajectory, it doesn't matter what other lineages are doing (unless those other lineages are competitors for the resources of the environment).


This message is a reply to:
 Message 285 by Dr Adequate, posted 10-14-2016 12:17 PM Dr Adequate has not yet responded

  
Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 303 of 393 (792819)
10-14-2016 1:10 PM
Reply to: Message 301 by Kleinman
10-14-2016 12:58 PM


Re: Lenski
That's the point, Lenski is using only a single directional selection pressure, starvation. He is selecting for the most efficient energy users. And if Lenski were to add a second simultaneous selection pressure, for example, thermal stress, the amplification of the mutations which increase energy efficiency will be slowed by the thermal stress applied to these populations.

As long as the thermal stress was not lethal, the adaptation for energy efficiency would not be slowed. Bacteria with adaptations to just one of the selection pressures would outcompete bacteria with none of the adaptations.


This message is a reply to:
 Message 301 by Kleinman, posted 10-14-2016 12:58 PM Kleinman has responded

Replies to this message:
 Message 320 by Kleinman, posted 10-14-2016 2:29 PM Taq has responded

  
Kleinman
Member (Idle past 954 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 304 of 393 (792820)
10-14-2016 1:13 PM
Reply to: Message 287 by PaulK
10-14-2016 12:21 PM


Re: Is it summation time?
quote:
I have a question for you Kleinman. Since you militantly refuse to understand rmns how can you possibly know that a proper understanding would falsify evolution ?

There's some very smart people who peer reviewed and published my work on rmns. They see the importance of understanding the physics and mathematics of rmns because of its impact on the evolution of drug resistance.
This message is a reply to:
 Message 287 by PaulK, posted 10-14-2016 12:21 PM PaulK has responded

Replies to this message:
 Message 306 by PaulK, posted 10-14-2016 1:24 PM Kleinman has responded
 Message 309 by Taq, posted 10-14-2016 1:29 PM Kleinman has not yet responded

  
Kleinman
Member (Idle past 954 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 305 of 393 (792822)
10-14-2016 1:21 PM
Reply to: Message 288 by Taq
10-14-2016 12:27 PM


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


I think you will find some disagreement with other posters on this thread. As long as mutation are random events, beneficial mutations are just a subset of all mutations.


I don't see how that addresses anything in my post.

Let's use military tanks as an example. Let's say that two possible upgrades for a tank are thicker armor and a more powerful main gun. A tank with either thicker armor or a more powerful gun would be better. A tank with BOTH thicker armor and a more powerful gun would be better than a tank with just one upgrade. The upgrades are additive in that both upgrades add up to a better tank than a single upgrade by itself.



Are you suggesting that putting a bigger gun and more armor on a tank are random processes?
quote:
This is often how beneficial mutations work. A beneficial mutation is beneficial all by itself. When it is combined with another beneficial mutation, the individual with two beneficial mutations is more fit than an individual with just one of those beneficial mutations.

That may be true but the probability for that member getting both those beneficial mutations is computed using the multiplication rule, not the addition rule.

Here's a simple question for you Taq. If you double the population size, do you double the probability that a beneficial mutation will occur?


This message is a reply to:
 Message 288 by Taq, posted 10-14-2016 12:27 PM Taq has responded

Replies to this message:
 Message 307 by Taq, posted 10-14-2016 1:26 PM Kleinman has not yet responded

  
PaulK
Member
Posts: 15334
Joined: 01-10-2003
Member Rating: 2.7


Message 306 of 393 (792823)
10-14-2016 1:24 PM
Reply to: Message 304 by Kleinman
10-14-2016 1:13 PM


Re: Is it summation time?
Your problem is not understanding rmns in terms of drug resistance. Your problem is that you refuse to understand that drug resistance is a special case. And you will never understand rmns until you take off those blinkers and consider it in other contexts.
This message is a reply to:
 Message 304 by Kleinman, posted 10-14-2016 1:13 PM Kleinman has responded

Replies to this message:
 Message 321 by Kleinman, posted 10-14-2016 2:34 PM PaulK has responded

    
Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 307 of 393 (792824)
10-14-2016 1:26 PM
Reply to: Message 305 by Kleinman
10-14-2016 1:21 PM


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

Are you suggesting that putting a bigger gun and more armor on a tank are random processes?

It's an analogy, chief.

That may be true but the probability for that member getting both those beneficial mutations is computed using the multiplication rule, not the addition rule.

You are wrong. Both beneficial alleles will become common in the population, making offspring with both beneficial alleles a nearly unavoidable outcome. The appearance of individuals with both beneficial alleles will only be limited by the least beneficial allele spreading through the population. The time needed to start seeing individuals with both beneficial alleles is much, much less than your claimed multiplicative probability.


This message is a reply to:
 Message 305 by Kleinman, posted 10-14-2016 1:21 PM Kleinman has not yet responded

  
Dr Adequate
Member
Posts: 16097
Joined: 07-20-2006


Message 308 of 393 (792825)
10-14-2016 1:27 PM
Reply to: Message 301 by Kleinman
10-14-2016 12:58 PM


Re: Lenski
That's the point, Lenski is using only a single directional selection pressure, starvation.

But this exerts pressure on a whole lot of loci. Why would it make a difference if each locus had the same amount of pressure on it, but from a different underlying environmental cause? How in the world would that show up in the math? By the time you've put it into numbers and put the numbers into the equations, you can't tell if both loci are under pressure from starvation, or if one is under pressure from starvation and the other from fire-breathing dragons. That disappears from the math just like the color of objects disappears from problems in kinetics.

Unless you can show me some math which does take into account the causes of the pressures, and explain to me how and why it does so ...


This message is a reply to:
 Message 301 by Kleinman, posted 10-14-2016 12:58 PM Kleinman has responded

Replies to this message:
 Message 326 by Kleinman, posted 10-14-2016 2:48 PM Dr Adequate has responded

  
Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 309 of 393 (792826)
10-14-2016 1:29 PM
Reply to: Message 304 by Kleinman
10-14-2016 1:13 PM


Re: Is it summation time?
Kleinman writes:

There's some very smart people who peer reviewed and published my work on rmns. They see the importance of understanding the physics and mathematics of rmns because of its impact on the evolution of drug resistance.

Evolution of drug resistance is a really poor model for things like the evolution of feathers. Quite obviously, tetrapods with scales instead of feathers are still doing quite well. They aren't facing complete extinction in one generation if they don't develop feathers all at once.

What feathers allowed a lineage to do is move to a niche with less competition. This is VERY different from the evolution of drug resistance.


This message is a reply to:
 Message 304 by Kleinman, posted 10-14-2016 1:13 PM Kleinman has not yet responded

  
Dr Adequate
Member
Posts: 16097
Joined: 07-20-2006


Message 310 of 393 (792828)
10-14-2016 1:33 PM
Reply to: Message 298 by Taq
10-14-2016 12:53 PM


Re: Mathematics cannot change reality but when done correctly can predict it
I would think that it would be self evident.

Not quite; maybe I don't know enough about medicine. But I would have thought that since no drug is 100% effective, each drug is just getting a shot, with a certain probability of success, of killing each viral particle. One which is immune to one of the drugs (I would have thought) would therefore have a greater probability of survival. Stop me if I'm wrong.


This message is a reply to:
 Message 298 by Taq, posted 10-14-2016 12:53 PM Taq has not yet responded

Replies to this message:
 Message 312 by PaulK, posted 10-14-2016 1:53 PM Dr Adequate has not yet responded

  
Kleinman
Member (Idle past 954 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 311 of 393 (792829)
10-14-2016 1:40 PM
Reply to: Message 290 by Taq
10-14-2016 12:30 PM


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


Recombination events are random mutations, and recombination events can produce new alleles.

Recombination can occasionally create chimeric alleles but they are simply handled in the "..." term of the possible outcomes for a mutation. But by far, most recombination events do not create new alleles.
This message is a reply to:
 Message 290 by Taq, posted 10-14-2016 12:30 PM Taq has not yet responded

  
PaulK
Member
Posts: 15334
Joined: 01-10-2003
Member Rating: 2.7


Message 312 of 393 (792830)
10-14-2016 1:53 PM
Reply to: Message 310 by Dr Adequate
10-14-2016 1:33 PM


Re: Mathematics cannot change reality but when done correctly can predict it
I would expect resistance to one drug to have a small benefit. The important thing is that the fitness remains noticably less than 1, even with resistance to one drug.
This message is a reply to:
 Message 310 by Dr Adequate, posted 10-14-2016 1:33 PM Dr Adequate has not yet responded

    
Kleinman
Member (Idle past 954 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 313 of 393 (792831)
10-14-2016 1:54 PM
Reply to: Message 291 by Modulous
10-14-2016 12:33 PM


Re: the equality of pressure?
quote:
On the other hand, rmns is the creation of new alleles in order to adapt.

Yet more evidence I am correct in my assessment of your argument. Random mutations create new alleles. Natural selection does not create new alleles. And NONE OF IT happens 'in order to adapt'.

rmns consists of a cycle. The first half of the cycle consists of a beneficial mutation occurring, the other half of the cycle (natural selection) consists of amplification of that beneficial mutation in order to improve the probability of the next beneficial mutation occurring on some member of that population who has the previous beneficial mutation.
quote:
The new alleles are in competition with the other alleles. If it replicates at a faster rate than they, they will increase in frequency - else they won't. That's natural selection. It doesn't create alleles it's just the phenomena that alleles which are able to replicate more, will be more replicated.

There can be competition between different variants if there are limited resources in the environment. rmns works best in environments that are not limited in the resources.
quote:
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

If apply pressure to carbon, will I get a diamond? Surely it depends on the magnitude of the pressure. Why do you assume all pressures are equal in biology?



Selection pressures kill or impair the ability of some or all members in a population to reproduce. These pressures can vary in intensity.
This message is a reply to:
 Message 291 by Modulous, posted 10-14-2016 12:33 PM Modulous has responded

Replies to this message:
 Message 317 by Modulous, posted 10-14-2016 2:20 PM Kleinman has responded

  
Kleinman
Member (Idle past 954 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 314 of 393 (792832)
10-14-2016 2:06 PM
Reply to: Message 295 by Dr Adequate
10-14-2016 12:43 PM


Re: Mathematics
quote:
Time is not measured in seconds, minutes, hours for rmns, the measure of time for rmns is replications (generations).

Quite: so generation time is also something you'd need to know.

Ok, go for it, how much time for a generation for your dinosaur.
quote:
The reason I answer I don't know to a question is I don't know.

But why did you say you didn't need to know?



Because the mutation rate is going to be higher than the beneficial mutation rate.
quote:
What you can do with calculations like mine are obtain estimates of the upper limits of the probabilities for rmns. Assume that when the mutation occurs at the particular site, it is always the beneficial mutation, that will raise your probabilities slightly but it will not make the multiplication rule go away when more than a single beneficial mutation must occur on a lineage.

Again, the probability of that is 1 --- given enough time.



--- given enough time and your population doesn't go extinct.
This message is a reply to:
 Message 295 by Dr Adequate, posted 10-14-2016 12:43 PM Dr Adequate has not yet responded

  
Kleinman
Member (Idle past 954 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 315 of 393 (792833)
10-14-2016 2:09 PM
Reply to: Message 297 by Taq
10-14-2016 12:51 PM


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

You don't think that the multiplication rule of probabilities is a roadblock?


No more so than having more than one step in a flight of stairs is a problem. All you do is rinse and repeat the same process.

Try climbing two different flights of stairs at the same time.
quote:
I hope your expectations aren't too high when you buy tickets to two different lotteries and think you are going to win both.

You don't have to win both. The descendants of two winners can meet up and combine their winnings. That is how sexual recombination works.



You win a lottery, everyone wants to marry you.
This message is a reply to:
 Message 297 by Taq, posted 10-14-2016 12:51 PM Taq has responded

Replies to this message:
 Message 324 by Taq, posted 10-14-2016 2:37 PM Kleinman has responded

  
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