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Author Topic:   Explaining the pro-Evolution position
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 270 of 393 (792784)
10-14-2016 11:35 AM
Reply to: Message 258 by RAZD
10-14-2016 8:52 AM


Re: Mathematics cannot change reality but when done correctly can predict it
quote:
... What I do remember is that they listed at least 8 genes necessary to be transformed. ...

Excuse me for coming in late in the discussion. I have received your pdfs but not had time to look them over yet. Can you answer a simple question for me, even if it has already been asked?

What is the probability that a mutation will be beneficial?



Your question hasn't been asked and my answer is I don't know. But this is not a number which you have to know to understand how rmns works.
quote:
I think we can all agree that mutations are random -- leaving aside for the moment that the probability of mutations varies with the section of DNA involved -- and that some are immediately deleterious or immediately beneficial, while others are immediately neutral and their relative deleterious\beneficial value can be important later.

We also have cases where a mutation is somewhat deleterious but leads later to beneficial results because of changing environmental conditions.

So how can we predict the probability of a mutation being beneficial?



Most people say that most mutations are neutral. Mutations are fairly rare to begin with. Most DNA replication is done with high fidelity. As you read my papers on rmns, you will see that I address the possibility that even though a mutation occurs at the correct site in a genome, it has to be the correct mutation to improve fitness. Just getting an accurate mutation rate is a challenging problem and then determining the fraction of the mutations which are beneficial, neutral and detrimental is even more challenging. But the mutation rate is not the dominant factor in the rmns problem, it is the multiplication rule of probabilities that drives this phenomenon. It is the joint probability that two or more beneficial mutation occur on a lineage which drives this problem.
This message is a reply to:
 Message 258 by RAZD, posted 10-14-2016 8:52 AM RAZD has responded

Replies to this message:
 Message 277 by Dr Adequate, posted 10-14-2016 12:02 PM Kleinman has responded
 Message 374 by RAZD, posted 10-14-2016 10:39 PM Kleinman has not yet responded

  
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 272 of 393 (792787)
10-14-2016 11:44 AM
Reply to: Message 271 by 1.61803
10-14-2016 11:36 AM


Re: Bumblebees can't fly...
The problem for the theory of evolution is that you don't have a big enough engine to make it fly.
This message is a reply to:
 Message 271 by 1.61803, posted 10-14-2016 11:36 AM 1.61803 has responded

Replies to this message:
 Message 273 by 1.61803, posted 10-14-2016 11:46 AM Kleinman has not yet responded

  
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 274 of 393 (792789)
10-14-2016 11:51 AM


Re: Mathematics cannot change reality but when done correctly can predict it
There seems to be some misunderstanding to my argument. rmns is a mechanism of evolution which does occur and I have explained exactly how it works. It is the theory of evolution, the notion that some primordial replicator through rmns evolved into all the life forms we see today is a mathematically irrational belief system.

rmns is too important a phenomenon not to be correctly understood. Antimicrobial drug resistance is becoming a more common problem in the medical field, cancer treatments can and often do fail due to rmns. Herbicide resistance and pesticide resistance is a problem due to rmns. Addressing these problems requires a correct understanding of the physics and mathematics of how rmns operates.


Replies to this message:
 Message 278 by ringo, posted 10-14-2016 12:03 PM Kleinman has responded
 Message 279 by Taq, posted 10-14-2016 12:03 PM Kleinman has not yet responded

  
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 276 of 393 (792791)
10-14-2016 12:01 PM
Reply to: Message 261 by bluegenes
10-14-2016 9:08 AM


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

I don't think this case will rescue the theory of evolution because the empirical evidence already shows that combination selection pressures stifles rmns (eg combination herbicides) for this class of replicators.


Really? So, if a group of grizzly-like bears moves north and starts living off a diet of seals, they couldn't make multiple adaptations to multiple pressures? They couldn't evolve meat ripping teeth, ice-gripping claws, larger feet for ice walking and swimming, longer necks for swimming, and a suitable camouflage because these are multiple adaptations to multiple pressures and, according to the Kleinman theory of evolution, changes involving many mutations can't happen?

You seem to have a problem with the idea that eight or more genes might be involved in the difference between scales and feathers. Why? Siblings can have different alleles on more than eight genes, so why shouldn't diverging populations of dinosaurs and proto-birds?

You also seem to think that population groups have to be threatened with extinction before significant change takes place. Things like dinosaurs to birds, tree squirrels to "flying" squirrels, and non-polar to polar bears have much more to do with highly successful models diversifying into new niches. There's no hurry. There's also no target.

Mrs. Bird winning a lottery with one million participants is a one in a million chance, but someone winning is 1/1. Evolution doesn't care what wins.



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).


This message is a reply to:
 Message 261 by bluegenes, posted 10-14-2016 9:08 AM bluegenes has responded

Replies to this message:
 Message 280 by Dr Adequate, posted 10-14-2016 12:07 PM Kleinman has responded
 Message 290 by Taq, posted 10-14-2016 12:30 PM Kleinman has responded
 Message 291 by Modulous, posted 10-14-2016 12:33 PM Kleinman has responded
 Message 336 by bluegenes, posted 10-14-2016 3:40 PM Kleinman has responded

  
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 281 of 393 (792796)
10-14-2016 12:08 PM
Reply to: Message 262 by bluegenes
10-14-2016 9:20 AM


Re: Is it summation time?
quote:
Would there be any objections if I dropped this thread into summation mode?

Why do that? I want to hear the Kleinman theory. I want to know what the limit is to the number of new alleles that can go to fixation by positive selection in a population group of 100,000 in 1,000,000 generations, and why it wouldn't be enough to transform a land animal into a flier.

I'm fascinated! Please let it roll! (Or you could suggest that Kleinman opens a thread outlining his "falsification" of evolutionary theory, and we could discuss it there).



I appreciate your interest bluegenes. I'm not falsifying evolutionary theory, I'm explaining correctly how rmns works. Once you understand how rmns works, what it does is falsify is the theory of evolution, the notion that some primordial replicator through rmns became all the life forms we see today.

And I think you haven't read my responses to Dr Adequate. The notion of "fixation" is neither necessary nor sufficient for rmns to operate. In fact, the notion of fixation is not even a factor in rmns.


This message is a reply to:
 Message 262 by bluegenes, posted 10-14-2016 9:20 AM bluegenes has not yet responded

Replies to this message:
 Message 285 by Dr Adequate, posted 10-14-2016 12:17 PM Kleinman has responded
 Message 287 by PaulK, posted 10-14-2016 12:21 PM Kleinman has responded

  
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 282 of 393 (792797)
10-14-2016 12:12 PM
Reply to: Message 263 by Dr Adequate
10-14-2016 10:25 AM


Re: Waiting For Goddidit, we know rmnsdidn'tdoit
quote:
It is a bit glacial, isn't it? Still, we may as well see if anything else is going to happen.

Thanks Doc. BTW, if you think that fixation and amplification are the same thing, do you think that mass and density are the same thing?
This message is a reply to:
 Message 263 by Dr Adequate, posted 10-14-2016 10:25 AM Dr Adequate has responded

Replies to this message:
 Message 286 by Dr Adequate, posted 10-14-2016 12:18 PM Kleinman has not yet responded

  
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 283 of 393 (792798)
10-14-2016 12:16 PM
Reply to: Message 265 by Taq
10-14-2016 10:59 AM


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

Once you get above the transformation of a single gene by a single selection pressure, rmns is stifled. How much is it stifled? Consider the evolution of HIV where only 2 genes are targeted by 3 selection pressures and you have people surviving for decades instead of weeks.


The main problem with your HIV example is that the beneficial mutations are not additive. In most situations, beneficial mutations are additive.

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.
This message is a reply to:
 Message 265 by Taq, posted 10-14-2016 10:59 AM Taq has responded

Replies to this message:
 Message 288 by Taq, posted 10-14-2016 12:27 PM Kleinman has responded

  
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 294 of 393 (792809)
10-14-2016 12:40 PM
Reply to: Message 277 by Dr Adequate
10-14-2016 12:02 PM


Re: Mathematics
quote:
It is the joint probability that two or more beneficial mutation occur on a lineage which drives this problem.

Well, that probability's going to be 1, given enough time. So the only problem with, for example, dinosaur-to-bird evolution can be time. So we need to do a calculation about time. This is going to involve knowing things like the probability that a mutation will be beneficial. So why, when asked for this probability, do you say:

My answer is I don't know. But this is not a number which you have to know to understand how rmns works.


Time is not measured in seconds, minutes, hours for rmns, the measure of time for rmns is replications (generations). And under the right circumstances, the probability of two beneficial mutations occurring on a lineage can go to 1 if there is sufficient amplification (and fixation is not necessary).

The reason I answer I don't know to a question is I don't know. And the notion of a beneficial mutation is a slippery thing as well. Sickle cell trait might be beneficial in one environment with Malaria but in an environment without Malaria, at best that mutation is neutral and under some circumstances detrimental.

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.


This message is a reply to:
 Message 277 by Dr Adequate, posted 10-14-2016 12:02 PM Dr Adequate has responded

Replies to this message:
 Message 295 by Dr Adequate, posted 10-14-2016 12:43 PM Kleinman has responded

  
Kleinman
Member (Idle past 949 days)
Posts: 136
From: United States
Joined: 10-06-2016


Message 296 of 393 (792811)
10-14-2016 12:47 PM
Reply to: Message 278 by ringo
10-14-2016 12:03 PM


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

There seems to be some misunderstanding to my argument. rmns is a mechanism of evolution which does occur and I have explained exactly how it works. It is the theory of evolution, the notion that some primordial replicator through rmns evolved into all the life forms we see today is a mathematically irrational belief system.


The challenge for you is to show what could prevent random mutation and natural selection from evolving a primordial replicator into all the life forms we see today. You need to show a physical/chemical/biological roadblock, not just a mathematical fantasy.

You don't think that the multiplication rule of probabilities is a roadblock? 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 had better buy a lot of tickets. And then if you think about the length of the human genome, 3e9, how many tickets do you need to buy to win all those lotteries?
This message is a reply to:
 Message 278 by ringo, posted 10-14-2016 12:03 PM ringo has responded

Replies to this message:
 Message 297 by Taq, posted 10-14-2016 12:51 PM Kleinman has responded
 Message 299 by PaulK, posted 10-14-2016 12:56 PM Kleinman has responded
 Message 300 by ringo, posted 10-14-2016 12:56 PM Kleinman has responded

  
Kleinman
Member (Idle past 949 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 949 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

  
Kleinman
Member (Idle past 949 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 949 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

  
Kleinman
Member (Idle past 949 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

  
Kleinman
Member (Idle past 949 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

  
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