NvC-1: What is the premise of Naturalism in Biology?

quote:

---

What is the connection between “Mutations occur by natural law” and “Mutations occur without regard for whether they will be useful or not. Many are not or are even harmful”?

---

Because it’s what we would expect if mutations were produced by the actions of natural law and not by the acts of an intelligence.

And I note that you do not produce the slightest evidence to the contrary.

quote:

---

I asked PaulK(Message 351) and AZPaul3(Message 356) to provide evidences that POINT mutations can produce genetic mutations. Maybe I should ask them for a little detail, that is, to ask them to provide evidences that POINT mutations can produce new genes, new enzymes, improved traits, or even new species, – which is meaningful new genetic information for biological evolution.

---

Perhaps you should actually deal with my response, too.

As I have already pointed out twice, if point mutations can lose information then point mutations can add information. And certainly they can contribute to all the things you mention even if they are not the complete story.

E.g. the diversification in duplication and diversification discussed in my earlier post is likely to involve point mutations.

RLW writes: Yep, those are mutations, but can you provide evidences that those mutations resulted from POINT mutations?

Absolutely.

The first step in explaining the evidence is in my post on transversions and transitions. Naturally occurring point mutations result in a higher rate of transitions compared to transversions, with CpG mutations having the highest rate. Do you agree with this explanation?

Kleinman writes: If you think your understanding of exons and introns can explain the mathematics of DNA evolution, do it. And if you think your understanding of exons and introns can explain mutations and how they relate to genetic information, do it. Taq writes: In case you didn't notice, this isn't a topic on the math of population genetics. One of the signs of a crackpot is that they bring up the same stale topic no matter what the thread is about.

If you understood the subject of population genetics, you would understand how mutations and genetic information is related to this subject. Go back to Message 362 and Message 363 and see that I am right on topic. Instead, you resort to name-calling. I'm presenting empirical and mathematical evidence. You have a superficial understanding of the empirical evidence. You showed that when you computed that it would take 3e9 replications for each beneficial mutation in the Kishony Mega-plate experiment. How does this relate to genetic information? But instead, you are either unwilling or unable to go further. Why won't you attempt to understand this subject?

Kleinman writes: I'm presenting empirical and mathematical evidence.

Evidence of what? What point are you trying to make? Do you have something other than insulting people while demanding that they do math problems?

How does this relate to genetic information?

You tell us. Get to the point.

Kleinman writes: I'm presenting empirical and mathematical evidence. Taq writes: Evidence of what? What point are you trying to make? Do you have something other than insulting people while demanding that they do math problems?

The empirical evidence starts with the Kishony and Lenski experiments. And you started scratching the surface on the math with your calculation of 3e9 replication for each evolutionary step in the Kishony experiment. I already know how to do the math. If you can't do the math and you find that insulting, learn how to do the math.

Kleinman writes: How does this relate to genetic information? Taq writes: You tell us. Get to the point.

Genetic information has to be measured in the context of the environment. So, consider the Kishony experiment. What mutations give increased information (fitness) for that environment? And what is the rate of accumulation of that information? That is your Markov chain calculation. And if you know how to do that calculation, you will understand how DNA evolution works and how it relates to genetic information. Didn't they teach you any of this in your biology class?

Kleinman writes: The empirical evidence starts with the Kishony and Lenski experiments.

Ok. Keep going.

Genetic information has to be measured in the context of the environment. So, consider the Kishony experiment. What mutations give increased information (fitness) for that environment? And what is the rate of accumulation of that information? That is your Markov chain calculation. And if you know how to do that calculation, you will understand how DNA evolution works and how it relates to genetic information.

Then how does DNA evolution work and how does it relate to genetic information? Spit it out.

Edited by Taq, : No reason given.

Kleinman writes: The empirical evidence starts with the Kishony and Lenski experiments. Taq writes: Ok. Keep going. Kleinman writes: Genetic information has to be measured in the context of the environment. So, consider the Kishony experiment. What mutations give increased information (fitness) for that environment? And what is the rate of accumulation of that information? That is your Markov chain calculation. And if you know how to do that calculation, you will understand how DNA evolution works and how it relates to genetic information. Taq writes: Then how does DNA evolution work and how does it relate to genetic information? Spit it out.

I'll say it again and as many times as necessary for you to get it. DNA evolution is a Markov Chain process. From the way you are posting, it appears you have no idea what a Markov Chain process is. Here's a simple introductory video to learn how you do a Markov Chain calculation. This is part 1, it wouldn't hurt for you to watch all three parts.
Markov Chains - Part 1

Kleinman writes: DNA evolution is a Markov Chain process.

So how does that relate to information in genetics, and how does it relate to the role of naturalism in biology?

provide evidences that POINT mutations can produce genetic mutations.

What's this fixation on point mutations? There are a whole big number of vectors to genetic mutations, point mutations being but one.

Or is it you think a point mutation is not a mutation at all? It doesn't count? It doesn't change the genetic information?

An example of a point mutation might be changing a thymine in place of an adenine. That might change a resultant codon from AGA to AGT. That would change the resultant RNA codon from AGA to AGU. That would change the amino acid designated from arginine to serine.

That one point mutation changed the genetic information resulting in a different protein being produced.

By definition the gene has been changed by the point mutation. The resulting protein differs from the one made before the change. Whether that different protein has any kind of effect on the phenotype is a matter for a myriad of other processes in combination with this new change to determine.

Yep, those are mutations, but can you provide evidences that those mutations resulted from POINT mutations?

What does it matter if these mutations were all point mutations, some of them point mutations or very few of them were point mutations? Whether a mutation is the result of a point mutation or a viral insertion or a frame shift, the genetic information has changed and the cumulative result of all these genetic changes is the difference between human and chimp.

Kleinman writes: DNA evolution is a Markov Chain process. Taq writes: So how does that relate to information in genetics, and how does it relate to the role of naturalism in biology?

To understand this, you first need to recognize that DNA evolution is a stochastic process (mutations occur randomly). Then, from this link:
Entropy rate - Wikipedia
"In the mathematical theory of probability, the entropy rate or source information rate of a stochastic process is, informally, the time density of the average information in a stochastic process.

Since a stochastic process defined by a Markov chain that is irreducible, aperiodic and positive recurrent has a stationary distribution, the entropy rate is independent of the initial distribution."
Then, further down in this link, they show you how to compute this value for a Markov chain process:
"For example, for such a Markov chain... (equations from link which don't format correctly here) is the asymptotic distribution of the chain.

A simple consequence of this definition is that an i.i.d. stochastic process has an entropy rate that is the same as the entropy of any individual member of the process."

The problem with trying to apply this equation directly to actual evolutionary examples such as the Kishony and Lenski experiments (and really all examples of evolution) is that these real DNA evolutionary processes are not stationary, that is they don't go to equilibrium. At equilibrium, the distribution of bases at any site in a population no longer changes. If you look at the Markov DNA evolution models from this link:
Models of DNA evolution - Wikipedia
You will find that these models (e.g. Jukes-Cantor, Kimura) are stationary models. That is, after some period of time, the frequencies of A, C, G, and T all go to 0.25. That is 1/4 of the population will have an A base at the given site, 1/4 of the population will have a C base at the given site and likewise for the G and T bases. The Kishony and Lenski experiments get nowhere close to that distribution. What that means is that the transition matrix they are using is incorrect and that real DNA evolutionary process gets nowhere close to equilibrium.

If you want to learn how information and entropy are related, get a copy of the following text:
Equilibrium Statistical Mechanics: Andrews, Frank C.: 9780471031239: Amazon.com: Books
Andrews has a chapter in this book where he derives Shannon's information equation from the Boltzmann's entropy formula.

The way this relates to naturalism is to do your naturalism correctly. Learn how to correlate your math to reality, not to some vision you have. Darwin recognized what the two fundamental phenomena of evolution were, what he called the struggle for existence (and what we call competition), and adaptation (what we call DNA evolution). What Darwin didn't do is quantify these phenomena. As a naturalist, you should want to quantify these concepts correctly because then you can correctly predict things such as the evolution of drug-resistance or the failure of cancer treatments.

Kleinman writes: The way this relates to naturalism is to do your naturalism correctly.

That was assumed from the very start of this thread. Is that all you have as it relates to the topic?

Kleinman writes: The way this relates to naturalism is to do your naturalism correctly. Taq writes: That was assumed from the very start of this thread. Is that all you have as it relates to the topic?

Yep, the correct way to do the naturalism of DNA evolution. You should learn how to do it.

Kleinman writes: You should learn how to do it.

So you would agree that biology can be understood in terms of naturalism?

Kleinman writes: You should learn how to do it. Taq writes: So you would agree that biology can be understood in terms of naturalism?

Yes, but only if you do the mathematics correctly and the link you posted, they don't do the mathematics correctly. And you don't know why.