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Author Topic:   Do you really understand the mathematics of evolution?
Kleinman
Member (Idle past 34 days)
Posts: 528
From: United States
Joined: 10-06-2016


Message 1 of 239 (876413)
05-16-2020 1:37 PM


If you think you understand the mathematics of evolution, please explain the mathematics of the Kishony Mega-Plate experiment and the Lenski Long Term Evolutionary Experiment and what is the significant mathematical difference between the two experiments.

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Admin
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Message 2 of 239 (876414)
05-17-2020 8:59 AM
Reply to: Message 1 by Kleinman
05-16-2020 1:37 PM


Please describe the Kishony Mega-Plate and Lenski Long Term Evolutionary experiments and their mathematics. Provide links as references.

--Percy
EvC Forum Director

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Kleinman
Member (Idle past 34 days)
Posts: 528
From: United States
Joined: 10-06-2016


Message 3 of 239 (876415)
05-18-2020 2:49 AM
Reply to: Message 2 by Admin
05-17-2020 8:59 AM


Sorry, I thought the bloggers on this forum would be familiar with these two experiments. You can learn about the Kishony Mega-Plate experiment here:
Spatiotemporal microbial evolution on antibiotic landscapes
and you can watch a video of the experiment here:
EXTRA MINUTES - SUPERBBUGS (Harvard Experiment explained)
Essentially, what these experimenters do is make a large petri dish. And on this petri dish, they put different levels of an antibiotic in bands on the dish. On the left and right edges of the petri dish, no antibiotic. As you move toward the middle of the petri dish, the antibiotic concentration is increased in each band. Bacteria are then inoculated on the petri dish which initially grows only in the drug-free region. But as colonies grow, variants appear which can grow in the next higher drug concentration region. In this experiment, the antibiotic is the selection pressure.

The Lenski Long Term evolution experiment is performed in a different manner. You can read about how this experiment performed here:
E. coli long-term evolution experiment - Wikipedia
There many other publications based on this experiment but this link gives the essential principles. Essentially, what this experiment consists of are vials which contain 10ml of glucose growth solution for bacteria. Each day 5e6 bacteria are introduced into the solution which has sufficient nutrients to support the growth of about 5e8 bacteria (about 6-7 doublings (generations) per day). By the end of the day, the glucose is used up. 1% of the bacteria are then taken from this solution and introduced into a fresh 10ml solution for the next day's growth. Every 500 generations, the bacteria are saved, their genetic sequence determined, mutations identified. In this experiment, the selection pressure is starvation (nutrient limitation). This experiment has been carried out continuously since 1988 until it was paused recently because of the Covid episode.

If you or any members of this forum know how to correctly describe the physics and mathematics of either of these experiments or know of links that do this, please provide that information.


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Admin
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Message 4 of 239 (876416)
05-18-2020 8:03 PM
Reply to: Message 3 by Kleinman
05-18-2020 2:49 AM


Kleinman writes:

If you or any members of this forum know how to correctly describe the physics and mathematics of either of these experiments or know of links that do this, please provide that information.

Were you hoping for a discussion, or is this a question you'd like answered?


--Percy
EvC Forum Director

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Kleinman
Member (Idle past 34 days)
Posts: 528
From: United States
Joined: 10-06-2016


Message 5 of 239 (876417)
05-19-2020 7:52 AM
Reply to: Message 4 by Admin
05-18-2020 8:03 PM


Both.

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Admin
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Message 6 of 239 (876419)
05-19-2020 9:41 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Do you really understand the mathematics of evolution? thread in the Proposed New Topics forum.

  
AZPaul3
Member
Posts: 5404
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.4


(1)
Message 7 of 239 (876421)
05-19-2020 12:20 PM
Reply to: Message 3 by Kleinman
05-18-2020 2:49 AM


If you or any members of this forum know how to correctly describe the physics and mathematics of either of these experiments or know of links that do this, please provide that information.

If this PDF is your work, and I suspect it is, then you already have your answers since you wrote the paper that answered them.

Why are you here?

I suspect there is a deeper point you want to make with your OP.

What would that be?

Edited by AZPaul3, : No reason given.


Factio Republicana delenda est.

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Kleinman
Member (Idle past 34 days)
Posts: 528
From: United States
Joined: 10-06-2016


Message 8 of 239 (876428)
05-19-2020 4:12 PM
Reply to: Message 7 by AZPaul3
05-19-2020 12:20 PM


If this PDF is your work, and I suspect it is, then you already have your answers since you wrote the paper that answered them.

It is. And I've also written a paper on the mathematics of the Lenski paper. You can find that paper here:
(PDF) Fixation and Adaptation in the Lenski E. coli Long Term Evolution Experiment

And yes, I'm pretty sure that I understand the physics and mathematics of DNA evolution.

Why are you here?

I suspect there is a deeper point you want to make with your OP.

What would that be?

I'm just finishing another paper. I'm using a different approach to solve the mathematics of DNA evolution. Rather than doing the math as a simple probability problem using the "at least one rule", I'm using a Markov Chain. If you are not familiar with that math, you can read about it here: Models of DNA evolution - Wikipedia . I'm in the process of writing the discussion section and since I'm not in academia, I'm looking to discuss the subject before I submit it to the peer reviewers.

So, do you really understand the mathematics of evolution, in particular, DNA evolution?


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AZPaul3
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Posts: 5404
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.4


Message 9 of 239 (876431)
05-19-2020 5:09 PM
Reply to: Message 8 by Kleinman
05-19-2020 4:12 PM


First, if you are looking for some pre-review help on the mathematical efficacy of this new analysis of yours then you are in the wrong forum. A math or a biology forum would seem to be more beneficial.

Second, if this isn't to be a rehash of the discussion in Explaining the pro-Evolution position from years ago then what differences from that discussion are you offering?


Factio Republicana delenda est.

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Kleinman
Member (Idle past 34 days)
Posts: 528
From: United States
Joined: 10-06-2016


Message 10 of 239 (876434)
05-19-2020 7:59 PM
Reply to: Message 8 by Kleinman
05-19-2020 4:12 PM


First, if you are looking for some pre-review help on the mathematical efficacy of this new analysis of yours then you are in the wrong forum. A math or a biology forum would seem to be more beneficial.
Second, if this isn't to be a rehash of the discussion in Explaining the pro-Evolution position from years ago then what differences from that discussion are you offering?

So you don't really understand the mathematics of evolution. Maybe someone else wants to try and explain the Kishony and Lenski experiments. What is the correct explanation for why it takes a billion replications for each evolutionary step in the Kishony experiment? Perhaps someone wants to try and explain why drug-resistant variants appear in Lenski's founder's population despite the fact that these bacteria were never exposed to antibiotics? Or perhaps you want to explain why competition slows evolutionary adaptation?


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nwr
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Posts: 5631
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.0


(2)
Message 11 of 239 (876436)
05-19-2020 8:53 PM
Reply to: Message 10 by Kleinman
05-19-2020 7:59 PM


So you don't really understand the mathematics of evolution.

I am puzzled by your repeated references to "mathematics of evolution."

What is the correct explanation for why it takes a billion replications for each evolutionary step in the Kishony experiment?

Under what definition of "correct"?

It takes as many replications as it takes. This was an empirical experiment to observe how organisms behave.

Perhaps someone wants to try and explain why drug-resistant variants appear in Lenski's founder's population despite the fact that these bacteria were never exposed to antibiotics?

Why does that need explaining? Again, this was an empirical investigation to see how biological organisms behave.

I'm completely puzzled about what you are looking for. I do not see any point to the questions that you are asking.


Fundamentalism - the anti-American, anti-Christian branch of American Christianity

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AZPaul3
Member
Posts: 5404
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.4


(3)
Message 12 of 239 (876437)
05-19-2020 9:58 PM
Reply to: Message 10 by Kleinman
05-19-2020 7:59 PM


What is the correct explanation for why it takes a billion replications for each evolutionary step in the Kishony experiment?

Does it? Unless I missed something I don't see that in Kishony's paper.

Even if that were the case is that significant in some way?

You did see the part where they describe

quote:
Hence, as compensatory mutations often occur behind the front, they are spatially restricted from contributing to the ultimate evolutionary course of the population.
Source

In other words because of the experimental setup the more resistant bugs often got blocked and had they not been the population would have entered the next gradient much more quickly.

Perhaps someone wants to try and explain why drug-resistant variants appear in Lenski's founder's population despite the fact that these bacteria were never exposed to antibiotics?

You don't understand random mutation? You don't understand evolution.

What makes you think exposure is necessary to develop a resistance capability in an individual or a small subset of a population? Do you not know why genetic diversity is so powerful an evolutionary tool? You don't understand evolution.

Or perhaps you want to explain why competition slows evolutionary adaptation?

Since both of these experiments were set up in highly restrictive environments for highly restrictive purposes, trying to conclude this is a general feature within the global biosphere of evolution's reality is not just bogus it is dishonest.

You're trying to use your math manipulations (mathnipulations ) as a sword to strike at the windmill of evolution?

My advice is go learn something about the subject first.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : No reason given.


Factio Republicana delenda est.

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jar
Member
Posts: 33012
From: Texas!!
Joined: 04-20-2004
Member Rating: 3.2


Message 13 of 239 (876446)
05-20-2020 7:36 AM
Reply to: Message 12 by AZPaul3
05-19-2020 9:58 PM


But this attempt is much better so far
So far there have only been 5 content free posts from the OP in this thread compared to 135 in the older thread.

Edited by jar, : fix sub-title


My Sister's Website: Rose Hill Studios     My Website: My Website

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Kleinman
Member (Idle past 34 days)
Posts: 528
From: United States
Joined: 10-06-2016


Message 14 of 239 (876454)
05-20-2020 10:53 AM


Responses nwr and AZPaul3
nwr writes:

I am puzzled by your repeated references to "mathematics of evolution."


Are you familiar with the work of Haldane, Kimura, and many other population geneticists?

Kleinman writes:

What is the correct explanation for why it takes a billion replications for each evolutionary step in the Kishony experiment?

nwr writes:

Under what definition of "correct"?

It takes as many replications as it takes. This was an empirical experiment to observe how organisms behave.


So why doesn't it take 10 or 100 replications for each evolutionary step?

Kleinman writes:

Perhaps someone wants to try and explain why drug-resistant variants appear in Lenski's founder's population despite the fact that these bacteria were never exposed to antibiotics?

nwr writes:

Why does that need explaining? Again, this was an empirical investigation to see how biological organisms behave.
I'm completely puzzled about what you are looking for. I do not see any point to the questions that you are asking.


Don't you find this surprising that drug-resistant bacteria would appear in bacterial populations that were never exposed to the antibiotics and there was resistance to many different antibiotics?

Kleinman writes:

What is the correct explanation for why it takes a billion replications for each evolutionary step in the Kishony experiment?

AZPaul3 writes:

Does it? Unless I missed something I don't see that in Kishony's paper.

Even if that were the case is that significant in some way?

You did see the part where they describe

Hence, as compensatory mutations often occur behind the front, they are spatially restricted from contributing to the ultimate evolutionary course of the population.
Source

You are correct, neither Kishony nor any members of the Kishony team have ever published a paper describing the mathematics of their experiment. Kishony only talks about the billion replications in his video which I linked to in Message 3.

However, are you claiming that it takes fewer than a billion replications for compensatory mutations to occur because these variants are appearing behind the front but their migration is inhibited? If so, how many fewer replications are needed?

AZPaul3 writes:

In other words because of the experimental setup the more resistant bugs often got blocked and had they not been the population would have entered the next gradient much more quickly.


When you say more quickly, do you mean fewer replications for each lineage on their particular evolutionary trajectory or just a shorter duration of the experiment if you reduce the migration time of the variants with the compensatory mutations?

Kleinman writes:

Perhaps someone wants to try and explain why drug-resistant variants appear in Lenski's founder's population despite the fact that these bacteria were never exposed to antibiotics?

AZPaul3 writes:

You don't understand random mutation? You don't understand evolution.

What makes you think exposure is necessary to develop a resistance capability in an individual or a small subset of a population? Do you not know why genetic diversity is so powerful an evolutionary tool? You don't understand evolution.


I never said exposure was required for drug-resistance to appear. It is simply a matter of population size and mutation rate which determines the appearance of these variants. So, why don't you tell us how large the population must be for these drug-resistant variants to appear?

Kleinman writes:

Or perhaps you want to explain why competition slows evolutionary adaptation?

AZPaul3 writes:

Since both of these experiments were set up in highly restrictive environments for highly restrictive purposes, trying to conclude this is a general feature within the global biosphere of evolution's reality is not just bogus it is dishonest.

You're trying to use your math manipulations (mathnipulations ) as a sword to strike at the windmill of evolution?

My advice is go learn something about the subject first.


You can't even do the mathematics of these experiments "set up in highly restrictive environments". Why should anyone believe that you can correctly explain the mathematics of evolution in unrestricted environments?

So, when are you going to design an experiment that works more quickly than either the Kishony or Lenski experiments? You should tell them to stop restricting their experiments.


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nwr
Member
Posts: 5631
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.0


(4)
Message 15 of 239 (876460)
05-20-2020 12:40 PM
Reply to: Message 14 by Kleinman
05-20-2020 10:53 AM


Re: Responses nwr and AZPaul3
Are you familiar with the work of Haldane, Kimura, and many other population geneticists?

Somewhat. The mathematics that they use is ordinary mathematical probability theory. Is that what you mean by "mathematics of evolution"?

So why doesn't it take 10 or 100 replications for each evolutionary step?

I puzzled as to why you would think that.

Evolution isn't a mechanical system to grind out a sequence of steps leading to a particular result. Rather, evolution is a system of keeping the population well adapted to a changing environment.

Don't you find this surprising that drug-resistant bacteria would appear in bacterial populations that were never exposed to the antibiotics and there was resistance to many different antibiotics?

No, that is not at all surprising.

Evolution is a system of trial and error, in order to see what works well. If you are using trial and error methods, then you are going to try out things that turn out to not work. So the bacteria population tries mutations that turn out to not be currently helpful. That's what we should expect.

If they could not produce occasional antibiotic resistant variants when not useful, then they also could not produce them when would be useful.


Fundamentalism - the anti-American, anti-Christian branch of American Christianity

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