Poll: Does the Theory of Evolution have practical applications?

[pitabread]

Biologists should care that they get the physics and mathematics of evolution correct.

I think biologists studying historical evolution of morphological features should focus on what actually matters (i.e. mapping molecular pathways for evolution of traits) and not worrying about calculating irrelevant probabilities thereof.

You still haven't explained why biologists should care about the probability of feather evolution.

And when did I say evolution should not be taught in schools. I highly support the teaching of evolution in schools. School children need to understand the evolution of drug resistance, herbicide resistance, pesticide resistance, and why cancer treatments fail. Instead, they get stories about reptiles evolving into birds and fish evolving into mammals. All these do is obscure the correct science and truth.

Like it or not, the evolutionary history of life on Earth is part of the biological sciences.

 

[Alan Kleinman]

I think biologists studying historical evolution of morphological features should focus on what actually matters (i.e. mapping molecular pathways for evolution of traits) and not worrying about calculating irrelevant probabilities thereof.

You still haven't explained why biologists should care about the probability of feather evolution.



Like it or not, the evolutionary history of life on Earth is part of the biological sciences.

Morphological features and gross anatomy don't explain evolution. If it did, you could explain the Kishony and Lenski experiments. And the reason why biologists should care about the probability of feather evolution because it requires the correct understanding of DNA evolution. Biologists don't give the correct explanation.

 

[pitabread]

Morphological features and gross anatomy don't explain evolution

By themselves no. Which is why I pointed out how biologists are working out the molecular mechanisms regarding such evolution.

And the reason why biologists should care about the probability of feather evolution because it requires the correct understanding of DNA evolution.

What is specifically "incorrect" about current understanding of feather evolution?

What do you think calculating probabilities of feather evolution is supposed to add here?

 

[Alan Kleinman]

By themselves no. Which is why I pointed out how biologists are working out the molecular mechanisms regarding such evolution.



What is specifically "incorrect" about current understanding of feather evolution?

What do you think calculating probabilities of feather evolution is supposed to add here?

And biologists are not doing the correct mathematics of mechanisms of molecular evolution. Take the Jukes-Cantor model. They try to compute "the genetic distance" using that model. Biologists plug numbers into models they don't understand and they don't know why they are wrong. Calculating feather evolution requires the correct understanding of DNA evolution, that's why biologists can't do it.

 

[pitabread]

And biologists are not doing the correct mathematics of mechanisms of molecular evolution. Take the Jukes-Cantor model.

The Jukes-Cantor model is ~50 years old. There are newer models, so I'm not sure why that one is relevant?

It's also generally recognized that any such models are simplifications and are never going to lead to exact results (re: things like phylogenetic tree construction).

If you have an issue with imprecision in science, well, that just comes with the territory.

Calculating feather evolution requires the correct understanding of DNA evolution, that's why biologists can't do it.

But again, what is this purported "correct" calculation of feather evolution supposed to look like? You're still not explaining exactly what is incorrect about the contemporary understanding of feather evolution and what calculating the historical probability thereof is supposed to solve.

Blindly repeating "correct understanding of DNA evolution" over and over isn't explaining what that "correct understanding of DNA evolution" looks like re: feather evolution.

 

[Alan Kleinman]

The Jukes-Cantor model is ~50 years old. There are newer models.



But again, what is this purported "correct" calculation of feather evolution supposed to look like? You're still not explaining exactly what is incorrect about the contemporary understanding of feather evolution and what calculating the historical probability thereof is supposed to solve.

Blindly repeating "correct understanding of DNA evolution" over and over isn't explaining what that "correct understanding of DNA evolution" looks like re: feather evolution.

They make the same error with the derivative models. You won't compute the behavior of the Kishony and Lenski experiments with any of the derivative models either. And I've published the correct mathematics of DNA evolution and you saying over and over that feathers evolved doesn't explain how it happened.

You should read this paper if you want to understand what's wrong with the Jukes-Cantor and derivative models and how to correct these models so that they do correctly model DNA evolution.
The Kishony Mega-Plate Experiment, a Markov Process

 

[pitabread]

You won't compute the behavior of the Kishony and Lenski experiments with any of the derivative models either.

But again, we're talking about feather evolution here, not bacteria evolving under extreme selection pressures.

Do you think that feathers evolved under the same environmental constraints as the Kishony and Lenski experiments? Do you think the same selective pressures are relevant?

This is what I said earlier when it seems like you assume constant selection pressures and therefore constant fitness effects. Evolution in nature, however, is far more dynamic.

And I've published the correct mathematics of DNA evolution and you saying over and over that feathers evolved doesn't explain how it happened.

What I've said (for like the third or fourth time now) is that scientists are figuring how feathers evolved by tracing the molecular evolution thereof and even performing contemporary genetic experiments thereof.

 

[Alan Kleinman]

But again, we're talking about feather evolution here, not bacteria evolving under extreme selection pressures.

Do you think that feathers evolved under the same environmental constraints as the Kishony and Lenski experiments? Do you think the same selective pressures are relevant?

This is what I said earlier when it seems like you assume constant selection pressures and therefore constant fitness effects. Evolution in nature, however, is far more dynamic.



What I've said (for like the third or fourth time now) is that scientists are figuring how feathers evolved by tracing the molecular evolution thereof and even performing contemporary genetic experiments thereof.

The Kishony and Lenski experiments demonstrate DNA evolution with the mildest environmental constraints, only a single selection pressure acting. Real-world (non-laboratory) conditions have far more selection pressures acting and those pressures are acting simultaneously. If you want to slow down or stop the Kishony and Lenski experiments, add additional selection pressures. Additional selection condition makes for a more complex evolutionary trajectory. That imposes more instances of the multiplication rule simultaneously. The imposition of multiple simultaneous selection pressures is the condition that makes 3 drug combination therapy work for the treatment of HIV.

And biologists are using the wrong models in the wrong way to trace molecular evolution.

 

[Frank Robert]

When it takes a billion replications or more for each evolutionary transitional mutation, you should have vast numbers of transitional fossils. There are about 50 T Rex fossils and I don't think anyone would claim there were a billion T Rex sometime in the past. You can't explain evolution which occurs on a molecular scale using gross anatomy. That's like trying to explain particle physics using classical physics. You have to explain evolution on a molecular level. Misinterpretation of fossils does not explain evolution.

Biologists generally don't like this math. Mathematicians and those interested in understanding the evolution of drug resistance and why targeted cancer treatments fail publish this math.

Again I am not doubting your math as a model, but you have not shown that model reflects the real world of bird evolution. I agree that fossils alone do not explain evolution but they are physical evidence of an 80 million year transition of dinos to birds. Claiming it did not happen does not explain the evidence.

There are many Computational Biologists like Dr.Joshua Swamidass at <A HREF="Peaceful Science">Peaceful Science</A>. Dr. Swamidass most recent book is the The Genealogical Adam and Eve.

 

[Alan Kleinman]

Again I am not doubting your math as a model, but you have not shown that model reflects the real world of bird evolution. I agree that fossils alone do not explain evolution but they are physical evidence of an 80 million year transition of dinos to birds. Claiming it did not happen does not explain the evidence.

There are many Computational Biologists like Dr.Joshua Swamidass at <A HREF="Peaceful Science">Peaceful Science</A>. Dr. Swamidass most recent book is the The Genealogical Adam and Eve.

The Kishony and Lenski experiments are performed under the mildest selection conditions possible, a single selection condition only. Real environments have multiple selection conditions operating simultaneously. Multiple simultaneous selection pressures acting on a population impose multiple instances of the multiplication rule in the evolutionary process. That's why 99% of all species have gone extinct. If selection conditions in evolutionary experiments are made more complex, the experiments don't work. That's why Kishonyl can't get his experiment to work with two drugs.

 

[Speedwell]

And to transform a non-feather producing replicator into a feather producing replicator requires the accumulation of a highly improbable series of mutations. And then these new feather-producing replicators need to accumulate sets of highly improbable series of mutations to give the correct respiratory systems, circulatory systems, excretory systems, musculoskeletal systems,... The ToE has a huge mathematical problem that you are having a hard time seeing and accepting.

Yes, we see it and agree with you: any particular evolutionary outcome is highly improbable. We just don't see why it is a problem for evolution.

 

[Alan Kleinman]

Yes, we see it and agree with you: any particular evolutionary outcome is highly improbable. We just don't see why it is a problem for evolution.

It's not a problem for evolution but it is a problem for the ToE. And have you figured out yet why what you said, "Probability is the ratio of the number of favorable outcomes to the number of all possible outcomes." is wrong?

 

[Speedwell]

It's not a problem for evolution but it is a problem for the ToE. And have you figured out yet why what you said, "Probability is the ratio of the number of favorable outcomes to the number of all possible outcomes." is wrong?

As a informal statement I see nothing wrong with it--it's basically how I learned to calculate probability as an undergraduate math major and I see no reason to change now, your snotty condescension notwithstanding. If I am rolling a die and want to know the probability of rolling a three I divide 1 by 6 because there is one favorable outcome and six possible outcomes altogether. If I want a three or a four I divide 2 by 6 because there are now two favorable outcomes and still six possible outcomes. If I want to know the likelihood of rolling two threes in a row I will multiply 1/6 by 1/6 or 1/36. I don't know where you're coming from on this, but I can support what I say from any math textbook--and from the elementary school sites you linked to. Unless you, yourself, can articulate a cogent reason that I am not correct, I am going to assume that you are merely trying to divert attention from our criticism of your argument--basically that the numerators you choose for your own probability calculations are wrong--which you know you can't defend.

 

[Alan Kleinman]

As a informal statement I see nothing wrong with it--it's basically how I learned to calculate probability as an undergraduate math major and I see no reason to change now, your snotty condescension notwithstanding.

Well, if that is what they taught you, they taught you incorrectly. What happens to your calculation if the probabilities for the outcomes aren't symmetric? Do you even understand what symmetric and asymmetric probabilities are? You ToEists aren't very good at taking correction.

 

[Speedwell]

Well, if that is what they taught you, they taught you incorrectly.

How, exactly? Show me in detail how you would calculate the probability of rolling a three on a true six-sided die.

What happens to your calculation if the probabilities for the outcomes aren't symmetric? Do you even understand what symmetric and asymmetric probabilities are?

I do, in fact. Do you? Or are you just using big words to try and impress us with your genius?

You ToEists aren't very good at taking correction.

Now you're just projecting.

 

[Alan Kleinman]

How, exactly? Show me in detail how you would calculate the probability of rolling a three on a true six-sided die. I do, in fact. Do you? Or are you just using big words to try and impress us with your genius?Now you're just projecting.

Your math work only for symmetric probabilities. That's why you have to use a "true" six-sided die to get the correct value. If you used a weighted die, you would not get the correct probabilities because the number of possible outcomes would still be six but your probability of success varies based on the particular outcome.

So go back to your example of a coin toss. That's a binomial probability problem with symmetric outcomes, the probability of getting a head or a tail are both 1/2. The DNA evolution process is also a binomial probability problem but in this case, it is highly asymmetric. The replication is analogous to the toss of the coin but the probability of getting a mutation is very low. The other possible outcome is that no mutation occurs. The probability that the mutation occurs in a single replication is the mutation rate. The probability that a mutation doesn't occur in a single replication is (1-mutation rate). The other random trial in the DNA evolutionary process is the mutation itself. Why don't you try to write down the sample space for that random trial?

 

[FrumiousBandersnatch]

Clearly, you don't recognize that those papers give the correct mathematics for the evolutionary adaptation component of Darwinian evolution. Do you understand the difference between competition and adaptation in the evolutionary process? If you think you do understand that difference, tell us whether competition speeds up adaptation or slows adaptation and give us the reason for your answer.

You're missing or ignoring my point. As I already said, I'm no longer competent to check the mathematics.

If you really believe you've proved the genetic mechanisms used in the ToE are wrong, then why don't you publish a paper about that in a relevant peer-reviewed journal? If those dunderhead evolutionary biologists have been getting it wrong for so long, they obviously need it to be spelt out to them.

I'd be fascinated to see what happens.

 

[Alan Kleinman]

You're missing or ignoring my point. As I already said, I'm no longer competent to check the mathematics.

If you really believe you've proved the genetic mechanisms used in the ToE are wrong, then why don't you publish a paper about that in a relevant peer-reviewed journal? If those dunderhead evolutionary biologists have been getting it wrong for so long, they obviously need it to be spelt out to them.

I'd be fascinated to see what happens.

The genetic mechanisms are not wrong, biologists have not quantified the mechanisms correctly. That's why they can't do the mathematical description of the Kishony and Lenski experiments.

I have published this work in relevant peer-reviewed journals. For example, the peer-reviewers at Statistics in Medicine are well experienced in the mathematics of probability theory and are quite aware of the problem of the evolution of drug-resistance. In fact, 3 of these papers are in the National Library of Medicine.
List of my publication in the National Library of Medicine
And my latest paper, which is in peer-review at this time spells out the error biologists and geneticists are doing with their Markov models of DNA evolution. I've corrected their model so that it properly simulates and predicts DNA evolution. I suspect that they will resist this with everything they can.

 

[FrumiousBandersnatch]

The genetic mechanisms are not wrong, biologists have not quantified the mechanisms correctly. That's why they can't do the mathematical description of the Kishony and Lenski experiments.

I have published this work in relevant peer-reviewed journals. For example, the peer-reviewers at Statistics in Medicine are well experienced in the mathematics of probability theory and are quite aware of the problem of the evolution of drug-resistance. In fact, 3 of these papers are in the National Library of Medicine.
List of my publication in the National Library of Medicine
And my latest paper, which is in peer-review at this time spells out the error biologists and geneticists are doing with their Markov models of DNA evolution. I've corrected their model so that it properly simulates and predicts DNA evolution. I suspect that they will resist this with everything they can.

OK - please keep us updated. It will be interesting to see how this plays out.

Incidentally, how many mutations does it take to go from a non-feather producing (filamentous) placode to a feather-producing placode? and what are the timescales from the fossil record?

 

[Alan Kleinman]

OK - please keep us updated. It will be interesting to see how this plays out.

Incidentally, how many mutations does it take to go from a non-feather producing (filamentous) placode to a feather-producing placode? and what are the timescales from the fossil record?

I don't know how many mutations it would take. I've seen papers where they are attempting to identify the control modules for the beta keratin gene and if I recall, so far they've identified 7 or 8. They don't indicate how many bases in these control modules but even if it only requires 1 or 2 mutations in each module, the variant population size for this evolutionary process is already in the range of 7-16 billion. It wouldn't surprise me as further research goes on that it takes many more genes and control modules to make feathers. Going from stem cell to full-grown differentiated adult takes a lot of precise instruction and control. It really takes a wild imagination to think this could happen by evolution once you understand the DNA evolution of bacteria to an antibiotic or to starvation stress.