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Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
Richard L. Wang
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Posts: 94
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 361 of 429 (877396)
06-15-2020 12:42 PM
Reply to: Message 356 by AZPaul3
06-13-2020 12:28 PM


PaulK(351)&AZPaul3(356): evidence for point mutations producing genetic information
Can mutations add genetic information? Sure, otherwise, how does biological evolution work?

Can point mutations add genetic information, or produce meaningful genetic information? This is a question. Show experimental evidence, please.


This message is a reply to:
 Message 356 by AZPaul3, posted 06-13-2020 12:28 PM AZPaul3 has not yet responded

Replies to this message:
 Message 363 by PaulK, posted 06-15-2020 1:05 PM Richard L. Wang has not yet responded
 Message 364 by Kleinman, posted 06-15-2020 1:23 PM Richard L. Wang has not yet responded
 Message 366 by Taq, posted 06-16-2020 11:03 AM Richard L. Wang has responded

  
PaulK
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Posts: 16316
Joined: 01-10-2003
Member Rating: 1.7


Message 362 of 429 (877397)
06-15-2020 1:01 PM
Reply to: Message 360 by Richard L. Wang
06-15-2020 12:37 PM


Re: PaulK, show evidence for mutations occur by natural law
quote:
How do you know it? What is the evidence to support your assertion?

For a start the fact that there is no evidence of any guiding force behind mutations. Mutations occur without regard for whether they will be useful or not. Many are not or are even harmful.

But really if you are going to claim the opposite you need evidence. Are we finally going to see you support your claims ?


This message is a reply to:
 Message 360 by Richard L. Wang, posted 06-15-2020 12:37 PM Richard L. Wang has responded

Replies to this message:
 Message 374 by Richard L. Wang, posted 06-16-2020 4:14 PM PaulK has responded

  
PaulK
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Posts: 16316
Joined: 01-10-2003
Member Rating: 1.7


Message 363 of 429 (877398)
06-15-2020 1:05 PM
Reply to: Message 361 by Richard L. Wang
06-15-2020 12:42 PM


Re: PaulK(351)&AZPaul3(356): evidence for point mutations producing genetic information
quote:
Can point mutations add genetic information

This is the same question as “can point mutations lose genetic information?”. What’s your position on that?


This message is a reply to:
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Kleinman
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Posts: 386
From: United States
Joined: 10-06-2016
Member Rating: 1.1


Message 364 of 429 (877399)
06-15-2020 1:23 PM
Reply to: Message 361 by Richard L. Wang
06-15-2020 12:42 PM


Re: PaulK(351)&AZPaul3(356): evidence for point mutations producing genetic information
If you don't mind, let me give the Pauls some help. If you correlate biological fitness with information, here's an experimental example of where a mutation increases biological information.
EXTRA MINUTES - SUPERBBUGS (Harvard Experiment explained)
What you are observing is a Markov Chain which is a second law of thermodynamics process. And of course, information and entropy are related.

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 Message 361 by Richard L. Wang, posted 06-15-2020 12:42 PM Richard L. Wang has not yet responded

  
Taq
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Posts: 8409
Joined: 03-06-2009
Member Rating: 1.9


Message 365 of 429 (877438)
06-16-2020 11:02 AM
Reply to: Message 342 by Richard L. Wang
06-11-2020 4:36 PM


Re: Re-Taq(340)&PaulK(339): regulations refer to rules and implementation
RLW writes:

If all bioinformatic processes could be broken down into a series of chemical and physical processes, people would never know how the basic principle of genetic processes – to produce the right protein at the right time, right place and right quantity – works.

Again, read up on the lac operon:

The lac operon (article) | Gene regulation | Khan Academy

It explains all of the physics and chemistry that allows for beta-lactamase to be expressed at the right time in the right place and in the right quantities.

In that section, I analyzed the transcription regulation of lac operon of E. coli, and demonstrated that the function of regulation is similar to logic circuits in digital circuits, or similar to IF sentences in software.

Where do you demonstrate that the functioning of the lac operon doesn't follow natural laws?


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 Message 342 by Richard L. Wang, posted 06-11-2020 4:36 PM Richard L. Wang has not yet responded

  
Taq
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Posts: 8409
Joined: 03-06-2009
Member Rating: 1.9


Message 366 of 429 (877439)
06-16-2020 11:03 AM
Reply to: Message 361 by Richard L. Wang
06-15-2020 12:42 PM


Re: PaulK(351)&AZPaul3(356): evidence for point mutations producing genetic information
RLW writes:

Can point mutations add genetic information, or produce meaningful genetic information? This is a question. Show experimental evidence, please.

Do the genetic differences between the chimp and human genomes give each species meaningful genetic information? Yep. Those are the mutations you are looking for.


This message is a reply to:
 Message 361 by Richard L. Wang, posted 06-15-2020 12:42 PM Richard L. Wang has responded

Replies to this message:
 Message 375 by Richard L. Wang, posted 06-16-2020 4:17 PM Taq has responded

  
Taq
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Posts: 8409
Joined: 03-06-2009
Member Rating: 1.9


Message 367 of 429 (877440)
06-16-2020 11:08 AM
Reply to: Message 347 by Richard L. Wang
06-12-2020 3:55 PM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
RLW writes:

So, I suggest we change a topic, for example, mutations,

Ok. Let's first look at transversion and transition mutations.

A transition is a point mutation where similar bases are switched out for each other. Cytosine and thymine have one ring while adenine and guanine have two rings. A transition is a switch between C and T or A and G. A transversion is a point mutation where dissimilar bases are switched out for one another, such as an A being switched out by a C or T.

The proteins that copy DNA have a harder time distinguishing between similar bases as compared to dissimilar bases. Therefore, we should see more transitions than transversions. That's exactly what we see. Below is the per base human mutation rate for transitions and transversions taken from Kong et al. (2013):

Transition at non-CpG 6.18×10−9
Transversion at non-CpG 3.76×10−9

So transitions are about twice as common as transversions even though there are two possible transversions at each base compared to just one transition. These are de novo mutations measured in humans using genome sequence of parents and their offspring. In nature, we see exactly what we would expect to see from natural processes producing mutations.

It goes even farther.

There is another type of substitution mutation called a CpG mutation.

When there is a CG in a sequence the C is susceptible to methylation. Subsequent deamination of the methylated C results in a T. Let's include CpG mutations to our list from Kong et al. (2013):

Transition at non-CpG 6.18×10−9
Transition at CpG 1.12×10−7
Transversion at non-CpG 3.76×10−9
Transversion at CpG 9.59×10−9

Notice how the rate of CpG transitions is so much higher than the others. Again, this is the hallmark of naturally occurring point mutations.

Are we on the same page so far?

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 347 by Richard L. Wang, posted 06-12-2020 3:55 PM Richard L. Wang has not yet responded

Replies to this message:
 Message 368 by Kleinman, posted 06-16-2020 11:50 AM Taq has responded

  
Kleinman
Member
Posts: 386
From: United States
Joined: 10-06-2016
Member Rating: 1.1


Message 368 of 429 (877445)
06-16-2020 11:50 AM
Reply to: Message 367 by Taq
06-16-2020 11:08 AM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
RLW writes:

So, I suggest we change a topic, for example, mutations,

Taq writes:

Ok. Let's first look at transversion and transition mutations.


Why? You don't understand how this changes the mathematics of DNA evolution. I've given you a link which introduces you to Markov models of DNA evolution:
Models of DNA evolution - Wikipedia
The Jukes-Cantor model assumes the mutation rate for transversions and transitions are equal. The Kimura model takes into account that transversions and transitions have different mutation rates. But there is a fundamental assumption that is made when deriving these models that makes these models incorrect. You should study these models and try to figure out why. Then you might actually understand something about DNA evolution and the mathematics which governs this process.

This message is a reply to:
 Message 367 by Taq, posted 06-16-2020 11:08 AM Taq has responded

Replies to this message:
 Message 369 by Taq, posted 06-16-2020 12:59 PM Kleinman has responded

  
Taq
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Posts: 8409
Joined: 03-06-2009
Member Rating: 1.9


Message 369 of 429 (877450)
06-16-2020 12:59 PM
Reply to: Message 368 by Kleinman
06-16-2020 11:50 AM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
Kleinman writes:

Why? You don't understand how this changes the mathematics of DNA evolution.

You are wearing out your hobby horse.


This message is a reply to:
 Message 368 by Kleinman, posted 06-16-2020 11:50 AM Kleinman has responded

Replies to this message:
 Message 370 by Kleinman, posted 06-16-2020 1:35 PM Taq has responded

  
Kleinman
Member
Posts: 386
From: United States
Joined: 10-06-2016
Member Rating: 1.1


Message 370 of 429 (877452)
06-16-2020 1:35 PM
Reply to: Message 369 by Taq
06-16-2020 12:59 PM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
Kleinman writes:

Why? You don't understand how this changes the mathematics of DNA evolution.

Taq writes:

You are wearing out your hobby horse.


You don't even have a horse in this race. You should stick with posting in the "Coffee House" and "Faith and Belief" forums. You certainly don't have the mathematical skills to be posting in the "Is it Science" and "Biological Evolution" forums. If you did have any mathematical skills, you could explain the Jukes-Cantor and Kimura models of DNA evolution and the differences between those two models. And then you could explain how to apply these models to the Kishony Mega-plate experiment. But you don't have those skills.

This message is a reply to:
 Message 369 by Taq, posted 06-16-2020 12:59 PM Taq has responded

Replies to this message:
 Message 371 by Taq, posted 06-16-2020 1:45 PM Kleinman has responded

  
Taq
Member
Posts: 8409
Joined: 03-06-2009
Member Rating: 1.9


Message 371 of 429 (877453)
06-16-2020 1:45 PM
Reply to: Message 370 by Kleinman
06-16-2020 1:35 PM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
Kleinman writes:

You certainly don't have the mathematical skills to be posting in the "Is it Science" and "Biological Evolution" forums.

So says the person who didn't know what exons and introns are.

If you don't think my posts are worthy of comment then don't respond to them.


This message is a reply to:
 Message 370 by Kleinman, posted 06-16-2020 1:35 PM Kleinman has responded

Replies to this message:
 Message 372 by Kleinman, posted 06-16-2020 2:21 PM Taq has responded

  
Kleinman
Member
Posts: 386
From: United States
Joined: 10-06-2016
Member Rating: 1.1


Message 372 of 429 (877457)
06-16-2020 2:21 PM
Reply to: Message 371 by Taq
06-16-2020 1:45 PM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
Kleinman writes:

You certainly don't have the mathematical skills to be posting in the "Is it Science" and "Biological Evolution" forums

Taq writes:

So says the person who didn't know what exons and introns are.

If you don't think my posts are worthy of comment then don't respond to them.


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.

You had a good start with your posts when you calculated 3e9 replication for a beneficial mutation to occur for the Kishony Mega-plate experiment but then you stopped attempting to understand. Instead, you bring up exons and introns which really have nothing to do with DNA evolution and genetic transformation or recombination which is related to genetic transformation (and therefore phenotype) but has little effect on DNA evolution (but you don't know why). But then you stop when I ask you to explain the mathematics of random recombination. Try studying a little harder and learn and understand the mathematics of genetic transformation and what genetic information is all about. You really don't understand this subject as well as you claim you do.


This message is a reply to:
 Message 371 by Taq, posted 06-16-2020 1:45 PM Taq has responded

Replies to this message:
 Message 373 by Taq, posted 06-16-2020 3:41 PM Kleinman has responded

  
Taq
Member
Posts: 8409
Joined: 03-06-2009
Member Rating: 1.9


Message 373 of 429 (877463)
06-16-2020 3:41 PM
Reply to: Message 372 by Kleinman
06-16-2020 2:21 PM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
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.

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.


This message is a reply to:
 Message 372 by Kleinman, posted 06-16-2020 2:21 PM Kleinman has responded

Replies to this message:
 Message 379 by Kleinman, posted 06-16-2020 4:40 PM Taq has responded

  
Richard L. Wang
Member
Posts: 94
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 374 of 429 (877465)
06-16-2020 4:14 PM
Reply to: Message 362 by PaulK
06-15-2020 1:01 PM


Re-PaulK(362): What is the connection …
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”?

This message is a reply to:
 Message 362 by PaulK, posted 06-15-2020 1:01 PM PaulK has responded

Replies to this message:
 Message 376 by PaulK, posted 06-16-2020 4:21 PM Richard L. Wang has not yet responded

  
Richard L. Wang
Member
Posts: 94
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 375 of 429 (877466)
06-16-2020 4:17 PM
Reply to: Message 366 by Taq
06-16-2020 11:03 AM


Re: PaulK(263)&Taq(366): evidence for POINT mutations producing genetic information
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.

Taq(Message 366) wrote

quote:
Do the genetic differences between the chimp and human genomes give each species meaningful genetic information? Yep. Those are the mutations you are looking for.

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

This message is a reply to:
 Message 366 by Taq, posted 06-16-2020 11:03 AM Taq has responded

Replies to this message:
 Message 377 by PaulK, posted 06-16-2020 4:28 PM Richard L. Wang has not yet responded
 Message 378 by Taq, posted 06-16-2020 4:33 PM Richard L. Wang has responded
 Message 385 by AZPaul3, posted 06-16-2020 7:00 PM Richard L. Wang has responded

  
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