Poll: Does the Theory of Evolution have practical applications?

Frank Robert said:

Dr. Swamidass offered you an opportunity to produce a stimulation and you suggested the Kishony
Kleinman: Four Questions About Evolution

Kleinman:
What’s so hard for you to understand when I suggest you simulate the Kishony experiment with two drugs? That’s an example that potentially could be tested experimentally and I’ve already predicted the number of replications for each evolutionary step at about one trillion. If you can’t do it with your simulation, that’s your problem.
Swamidass:
As we discussed, you did not demonstrate we are making a different prediction. What is so hard for you to understand?

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Sounds like he's agreeing with me. And I've communicated with Kishony and he told me he tried to do the two drug experiment and it didn't work. The reason why it won't work with two drugs (or if the increase in concentration is too large in a given step) is explained by this paper:
The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance
And a different way of doing the analysis is shown here:
The Kishony Mega-Plate Experiment, a Markov Process

Kishony could get the two drug experiment to work but the colony size would go from 1 billion as seen in the one drug experiment to a colony size of about a trillion (3 orders of magnitude larger) to get a variant with both beneficial mutations (one for each drug) for each step increase in fitness on that evolutionary trajectory. Make the petri dish a thousand times larger and you are good to go.

SelfSim said:

I doubt the simplicity of the reduced model underlying the math. Practical complexity calculations aren't based on ideal normal distibutions.

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Actually, DNA evolution is based on the binomial distribution (does a mutation occur or not on replication) not a normal distribution.

Alan Kleinman said:

Actually, DNA evolution is based on the binomial distribution (does a mutation occur or not on replication) not a normal distribution.

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Ok .. I'm attempting to consume your paper and the follow up papers in your links at the moment. However the question which arises for me, from both your paper and the point you're asserting above is:

SS#1: What other evolutionary influencing factors are specifically excluded by your assertion that DNA evolution is based on the binomial model you've chosen?
SS#2: How do any exclusions from SS#1, above influence (ie: to what degree) the outcomes of a model which assumes a binomial distibution?

Alan Kleinman said:

Sounds like he's agreeing with me.

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Did you miss? "you did not demonstrate we are making a different prediction."

Alan Kleinman said:

Go tell them to figure out the Kishony and Lenski experiment.

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You have not demonstrated that they do not understand the Kishony and Lenski experiments. You are the one that bailed out of the discussion when challenged with your own suggestion for a stimulation missing your best opportunity in a long time to be heard.

BTW, I do appreciate that you are advocating hard for an HIV cure especially when so many Christians couldn't care less.

SelfSim said:

Ok .. I'm attempting to consume your paper and the follow up papers in your links at the moment. However the question which arises for me, from both your paper and the point you're asserting above is:

SS#1: What other evolutionary influencing factors are specifically excluded by your assertion that DNA evolution is based on the binomial model you've chosen?
SS#2: How do any exclusions from SS#1, above influence (ie: to what degree) the outcomes of a model which assumes a binomial distibution?

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Actually, DNA evolution consists of two random trials, the binomial distribution based on a replication as a random trial where the frequency of success is the mutation rate and the mutation itself is a random trial with several different possible outcomes, substitutions, insertions, deletions, etc. The simplest model addresses only substitution mutations since they are most common and insertions and deletions cause frameshifts and are much less likely to be beneficial. What other factor(s) do you think will have a significant effect on DNA evolution? If you think recombination has a significant impact on DNA evolution, it can but only under very specific circumstances. Once you understand the simpler case, I'll show you how to address the mathematic of recombination.

Frank Robert said:

You have not demonstrated that they do not understand the Kishony and Lenski experiments. You are the one that bailed out of the discussion when challenged with your own suggestion for a stimulation missing your best opportunity in a long time to be heard.

BTW, I do appreciate that you are advocating hard for an HIV cure especially when so many Christians couldn't care less.

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I can only demonstrate that they have not presented an explanation for the Kishony experiment. It's up to them to demonstrate they can present an explanation. I've taken the time to write and get peer-reviewed and published my explanation of the Kishony experiment.

Sadly, the antiviral medications only inhibit viral replication and don't completely remove the virus. Where do you get the idea that Christians don't care for people that suffer from HIV? Is it from the Bible that says there are consequences to sin? Most Christians know we are subject to the same judgment for our sins which is why we accept Jesus as our Savior. There still may be consequences, but we trust in His forgiveness.

Frank Robert said:

For the most part yes, one difference was substantial. Swamidass offered him an opportunity to produce a specification for a simulation to test who is correct, Kleinman withdrew.

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Yes; I also noticed that his question on mutations with population doubling, that he claims was answered wrongly, was a self-admitted trap, and was actually answered correctly, with the assumption of low probability (beneficial) mutations.

It seems to be an exercise in ego-massage.

FrumiousBandersnatch said:

Yes; I also noticed that his question on mutations with population doubling, that he claims was answered wrongly, was a self-admitted trap, and was actually answered correctly, with the assumption of low probability (beneficial) mutations.

It seems to be an exercise in ego-massage.

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So it seems.
It takes massive ego to really-really think ones
mark magic is so strong it proves all the Evos
to be fools, AND, not least, it disproves the ToE,
God, and is withal the most amazing discovery of
all time.
Google found a review of the review of one of
Behe's books, which quickly devolved into the same
rant.

Its odd to me anyway how many people go
bonkers with numbers. Cube root of the pyramid
reveals the Bible code, etc.

FrumiousBandersnatch said:

Yes; I also noticed that his question on mutations with population doubling, that he claims was answered wrongly, was a self-admitted trap, and was actually answered correctly, with the assumption of low probability (beneficial) mutations.

It seems to be an exercise in ego-massage.

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So, if the probability of a beneficial mutation occurring for a population size "n" is 0.6, doubling the population size to "2n" gives a probability of 1.2???? It is easy to trap ToEists with their limited understanding of introductory probability theory. Swamidass also bungled the question about whether microevolutionary changes add up to a macroevolutionary change. Until you ToEists learn that microevolutionary changes are random events where the joint probabilities are computed using the multiplication rule, you will make all kinds of mathematically irrational claims about evolution. And you do that to the detriment of those suffering drug-resistant infections and failed cancer treatments.

Alan Kleinman said:

Until you ToEists learn that microevolutionary changes are random events where the joint probabilities are computed using the multiplication rule, you will make all kinds of mathematically irrational claims about evolution. .

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We know that already. We also know that the joint probabilities thus calculated only apply to specific evolutionary pathways.

Speedwell said:

We know that already. We also know that the joint probabilities thus calculated only apply to specific evolutionary pathways.

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Which DNA evolutionary pathways don't occur by random mutations? Are those the imaginary DNA evolutionary pathways that evolve reptiles into birds and fish into mammals? Were you really a math major in college and did you get your degree?

SelfSim said:

You really need to study up on where people like Kauffman have come from and are going to. Your model would be regarded as a toy model compared with his. Not only has he spent extraordinary time and efforts working on computer simulations on both Evolution and Abiogenesis, he has also spent large amounts of time on testing them out in the lab (and entire lifetime, in fact).

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Sorry I missed this post. So where is Kauffman's "real" model of evolution that explains the evolution of drug resistance? The "toy" model that I've presented very accurately predicted the population sizes needed for the Kishony experiment to operate with a single drug. This model also predicts the population sizes needed for the two drug experiment to work and explains why Kishony can't get his two drug experiment to work in his experimental petri dish. He needs a vastly larger carrying capacity petri dish for the two drug experiment to work. And the Markov model that I've presented for the Kishony experiment does as well. And Markov models are commonly used to model phylogenetic trees though biologists use the wrong Markov models and use those models incorrectly to generate their phylogenetic trees. Biologists need to learn how to play with toys correctly, otherwise, they break things. It hasn't taken me a lifetime to figure out the physics and mathematics of evolution. At least Kauffman has figured out that natural selection doesn't explain the ToE. That should be obvious to anyone that recognizes that the joint probability of random processes is computed by multiplying the individual probabilities. It doesn't take a lifetime to figure that out when you are dealing with events that occur at the frequency of the mutation rate, those joint probabilities become vanishingly small unless the lineage can amplify a billion times at each evolutionary step. My models may be toys but they quite nicely predict real evolutionary processes. The models that biologists use don't.

Alan Kleinman said:

Which DNA evolutionary pathways don't occur by random mutations? Are those the imaginary DNA evolutionary pathways that evolve reptiles into birds and fish into mammals? Were you really a math major in college and did you get your degree?

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They all occur by random mutations. That's not the point. The point is that the probabilities you are calculating are for specific evolutionary pathways. You calculate the odds for a specific mutation, followed by another specific mutation, and so on. That is not the same as calculating the probability that some evolutionary pathway will succeed. Nothing in evolution requires that reptiles evolved into birds or fish into mammals. That's just what happened. Reptiles and fish could have evolved into something entirely different.

Speedwell said:

They all occur by random mutations. That's not the point. The point is that the probabilities you are calculating are for specific evolutionary pathways. You calculate the odds for a specific mutation, followed by another specific mutation, and so on. That is not the same as calculating the probability that some evolutionary pathway will succeed. Nothing in evolution requires that reptiles evolved into birds or fish into mammals. That's just what happened. Reptiles and fish could have evolved into something entirely different.

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So any old mutation will transform reptiles into birds and fish into mammals. Reptiles and fish could have evolved into Wookies, Orcs, and Hobbits, all they need is some mutations. You still haven't told us whether you actually got a degree in mathematics.

Alan Kleinman said:

So any old mutation will transform reptiles into birds and fish into mammals.

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Why does it have to be birds and mammals?

Reptiles and fish could have evolved into Wookies, Orcs, and Hobbits, all they need is some mutations.

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Some favorable mutations. More mutations will produce a favorable outcome of some kind than will produce a single favorable outcome of a specific kind.

When I play poker I realize (despite my inadequate mathematics education) that the probability of being dealt any particular hand is low. But I don't need a particular hand, all I need is a winning hand and there are many of those--one in each game, in fact.

Alan Kleinman said:

So any old mutation will transform reptiles into birds and fish into mammals. Reptiles and fish could have evolved into Wookies, Orcs, and Hobbits, all they need is some mutations. You still haven't told us whether you actually got a degree in mathematics.

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If someone has a pair of red kings, a pair of black queens and an ace and their opponent beats them with three aces, you can't treat the odds of them having three aces as synonymous with the odds of them winning... which seems to be what you are doing with your probability of a particular chain of evolution idea.

Shemjaza said:

If someone has a pair of red kings, a pair of black queens and an ace and their opponent beats them with three aces, you can't treat the odds of them having three aces as synonymous with the odds of them winning... which seems to be what you are doing with your probability of a particular chain of evolution idea.

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And I don't do that.

So what do you who believe in the ToE want to be called? If you say "scientist", I'm going to ask you to explain the physics and mathematics of the Kishony and Lenski experiments because that is what real scientists do.