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Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
Richard L. Wang
Member (Idle past 0 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 391 of 452 (877536)
06-17-2020 4:24 PM
Reply to: Message 378 by Taq
06-16-2020 4:33 PM


Taq: what you wrote in Taq(378) did not answer what ...
what I asked in RLW(375): "Yep, those are mutations, but can you provide evidences that those mutations resulted from POINT mutations?"

This message is a reply to:
 Message 378 by Taq, posted 06-16-2020 4:33 PM Taq has responded

Replies to this message:
 Message 395 by Taq, posted 06-17-2020 6:29 PM Richard L. Wang has responded

  
Richard L. Wang
Member (Idle past 0 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 392 of 452 (877537)
06-17-2020 4:26 PM
Reply to: Message 385 by AZPaul3
06-16-2020 7:00 PM


Re-PaulK(377)&AZPaul3(385): point mutations are random, while …
While all other mutations such as translocation are non-random.

This message is a reply to:
 Message 385 by AZPaul3, posted 06-16-2020 7:00 PM AZPaul3 has responded

Replies to this message:
 Message 393 by PaulK, posted 06-17-2020 5:12 PM Richard L. Wang has not yet responded
 Message 394 by AZPaul3, posted 06-17-2020 5:56 PM Richard L. Wang has not yet responded
 Message 396 by Taq, posted 06-17-2020 6:33 PM Richard L. Wang has responded

  
PaulK
Member
Posts: 16570
Joined: 01-10-2003
Member Rating: 2.4


Message 393 of 452 (877538)
06-17-2020 5:12 PM
Reply to: Message 392 by Richard L. Wang
06-17-2020 4:26 PM


Re: Re-PaulK(377)&AZPaul3(385): point mutations are random, while …
Non-random in what sense and how does it help your argument ?

Noting that you have yet again ignored my points and yet again have failed to produce any evidence that anything other than natural law is involved.


This message is a reply to:
 Message 392 by Richard L. Wang, posted 06-17-2020 4:26 PM Richard L. Wang has not yet responded

  
AZPaul3
Member
Posts: 5365
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.4


Message 394 of 452 (877541)
06-17-2020 5:56 PM
Reply to: Message 392 by Richard L. Wang
06-17-2020 4:26 PM


Re: Re-PaulK(377)&AZPaul3(385): point mutations are random, while …
While all other mutations such as translocation are non-random.

What makes you think ANY mutation is non-random?


Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 392 by Richard L. Wang, posted 06-17-2020 4:26 PM Richard L. Wang has not yet responded

  
Taq
Member
Posts: 8438
Joined: 03-06-2009
Member Rating: 6.4


Message 395 of 452 (877545)
06-17-2020 6:29 PM
Reply to: Message 391 by Richard L. Wang
06-17-2020 4:24 PM


Re: Taq: what you wrote in Taq(378) did not answer what ...
RLW writes:

hat I asked in RLW(375): "Yep, those are mutations, but can you provide evidences that those mutations resulted from POINT mutations?"

I am providing that evidence. The first part of that evidence is that non-CpG transitions occur at a higher rate per site compared to non-CpG transversions. CpG transitions occur at the highest rates. This is what natural mutations look like, and we can observe them happening in living populations.

If we chart the non-CpG mutations that differ between humans, this is what they look like:



It is the same pattern as what we see happening in real time. Transitions outnumber transversions. This is evidence that the differences between humans is due to the observed natural mechanisms that cause mutations.

What happens when we compare the human and chimp genomes? THE EXACT SAME PATTERN!!!!



When we compare the chimp and human genomes the transitions outnumber the transversions. This means the differences between the chimp and human genomes is due to the observed mechanisms that cause mutations in living populations, the ones we see occurring in experiments every day.

How far does it go?

The same pattern is seen when comparing many different primate genomes:



The same thing is seen in different groups of vertebrate species:



This pattern is everywhere in nature, and it is smoking gun evidence that the difference between species is due to the known and observed mechanisms that cause mutations.

Credit goes to Dr. Steve Schaffner for putting this info together. You can read his article over at BioLogos:

Testing Common Ancestry: It’s All About the Mutations - Articles

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 391 by Richard L. Wang, posted 06-17-2020 4:24 PM Richard L. Wang has responded

Replies to this message:
 Message 397 by Richard L. Wang, posted 06-18-2020 3:49 PM Taq has responded

  
Taq
Member
Posts: 8438
Joined: 03-06-2009
Member Rating: 6.4


Message 396 of 452 (877546)
06-17-2020 6:33 PM
Reply to: Message 392 by Richard L. Wang
06-17-2020 4:26 PM


Re: Re-PaulK(377)&AZPaul3(385): point mutations are random, while …
RLW writes:

While all other mutations such as translocation are non-random.

Bare assertions may work in church, but they don't work well in science.


This message is a reply to:
 Message 392 by Richard L. Wang, posted 06-17-2020 4:26 PM Richard L. Wang has responded

Replies to this message:
 Message 398 by Richard L. Wang, posted 06-18-2020 3:52 PM Taq has responded

  
Richard L. Wang
Member (Idle past 0 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 397 of 452 (877572)
06-18-2020 3:49 PM
Reply to: Message 395 by Taq
06-17-2020 6:29 PM


Taq(366) & Taq(395) are irrelevant to my question
My question for PaulK, AZPaul3 and you, Taq, in RLW(375) is “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.”

What do your show in Taq(Message 366) is that different point substitution mutations and their rates.

What do your show in Taq(Message 395) is that there is common feature of point substitution mutations among humans, chimps and vertebrate species that transitions outnumber the transversions.

Have you provided evidence to show that POINT mutations can produce new genes, new enzymes, improved traits, or even new species? No.


This message is a reply to:
 Message 395 by Taq, posted 06-17-2020 6:29 PM Taq has responded

Replies to this message:
 Message 399 by Taq, posted 06-18-2020 5:06 PM Richard L. Wang has not yet responded
 Message 401 by AZPaul3, posted 06-18-2020 10:19 PM Richard L. Wang has responded

  
Richard L. Wang
Member (Idle past 0 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 398 of 452 (877573)
06-18-2020 3:52 PM
Reply to: Message 396 by Taq
06-17-2020 6:33 PM


Translocation or Transposition is non-random mutation
In the process of transposition, transposable-elements or transposons, which are DNA sequences, possess a mechanism that permits them to move around within the genome. Some of these transposable-elements are excised from their original sites and then inserted into new sites in DNA, while other transposable-elements are duplicated first and then the copies are relocated, leaving behind the originals.

Transposition mutation takes place in a similar way to that one copies or cuts a word or sentence in a draft and then pastes it into a proper place when editing a file by using Microsoft Word. It is definitely non-random. After copying a sentence, she/he pastes it as a new paragraph, or at the beginning of an existing paragraph or after a sentence; She/he does not randomly paste it into the middle of a sentence to destroy the original manuscript. For example, if there is a word Mutation, she/he copies a word Genetic from somewhere and pastes it to form Genetic Mutation, but she/he cannot randomly paste it into the middle of the word Mutation, such as MutGenetication, which damages the original information.


This message is a reply to:
 Message 396 by Taq, posted 06-17-2020 6:33 PM Taq has responded

Replies to this message:
 Message 400 by Taq, posted 06-18-2020 5:10 PM Richard L. Wang has responded

  
Taq
Member
Posts: 8438
Joined: 03-06-2009
Member Rating: 6.4


Message 399 of 452 (877579)
06-18-2020 5:06 PM
Reply to: Message 397 by Richard L. Wang
06-18-2020 3:49 PM


Re: Taq(366) & Taq(395) are irrelevant to my question
RLW writes:

My question for PaulK, AZPaul3 and you, Taq, in RLW(375) is “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.”

The point mutations that separate chimps and humans are exactly those mutations. Chimps and humans are separate species because of those random point mutations. Humans have improved traits because of those random point mutations, combined with natural selection.


This message is a reply to:
 Message 397 by Richard L. Wang, posted 06-18-2020 3:49 PM Richard L. Wang has not yet responded

  
Taq
Member
Posts: 8438
Joined: 03-06-2009
Member Rating: 6.4


Message 400 of 452 (877580)
06-18-2020 5:10 PM
Reply to: Message 398 by Richard L. Wang
06-18-2020 3:52 PM


Re: Translocation or Transposition is non-random mutation
RLW writes:

Transposition mutation takes place in a similar way to that one copies or cuts a word or sentence in a draft and then pastes it into a proper place when editing a file by using Microsoft Word. It is definitely non-random.

Then please explain how transposons are able to only make changes that are beneficial to the organism, and how that same mechanism prohibits transposon insertions that are either neutral or deleterious.

When we say mutations are random we mean random with respect to fitness. The processes that produce mutations have no way of determining what the organism needs. Mutations are blind to the needs of the organism.

After copying a sentence, she/he pastes it as a new paragraph, or at the beginning of an existing paragraph or after a sentence; She/he does not randomly paste it into the middle of a sentence to destroy the original manuscript.

We are talking about transposons, not humans. Just because humans behave that way doesn't mean transposons behave that way.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 398 by Richard L. Wang, posted 06-18-2020 3:52 PM Richard L. Wang has responded

Replies to this message:
 Message 403 by Richard L. Wang, posted 06-19-2020 4:24 PM Taq has responded

  
AZPaul3
Member
Posts: 5365
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.4


Message 401 of 452 (877585)
06-18-2020 10:19 PM
Reply to: Message 397 by Richard L. Wang
06-18-2020 3:49 PM


Re: Taq(366) & Taq(395) are irrelevant to my question
Have you provided evidence to show that POINT mutations can produce new genes, new enzymes ...

Yes. Message 385

A point mutation changes the gene. In English that is called a "new" gene.

Depending on the specifics of the nucleobase changed and where, a point mutation has the capability of altering the sequence of the amino acids used in forming the protein. A difference in amino structure means a difference in protein fold which means a difference in electrochemical properties which *can* mean a novel function. And if the function of the protein is to catalyze other reactions then this new protein is a new enzyme.

So, yes, Richard, a point mutation does make a novel gene and may make a novel protein and the evidence you asked for has been provided.

... improved traits, or even new species?

As for making new traits or species, the genetics involved in larger phenotypic changes is dependent on the complex interplay of more than a few genes. And some point mutation or series of point mutations needs to be assessed in regard to the larger system. Point mutations in HOX and other control genes can have significant effects on phenotype depending on the interplay of that change with the rest of the developmental environment.

Asking for proof that point mutations create new species shows a lack of knowledge in the way genetics and evolution work.


Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 397 by Richard L. Wang, posted 06-18-2020 3:49 PM Richard L. Wang has responded

Replies to this message:
 Message 402 by Richard L. Wang, posted 06-19-2020 4:21 PM AZPaul3 has responded

  
Richard L. Wang
Member (Idle past 0 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 402 of 452 (877658)
06-19-2020 4:21 PM
Reply to: Message 401 by AZPaul3
06-18-2020 10:19 PM


Taq & RLW comment on Taq(399) & AZPaul3(401)
For what Taq wrote in Taq(Message 399)
The point mutations that separate chimps and humans are exactly those mutations. Chimps and humans are separate species because of those random point mutations. Humans have improved traits because of those random point mutations, combined with natural selection.

and what AZPaul3 wrote in AZPaul3(Message 401)
A point mutation changes the gene. In English that is called a "new" gene.
Depending on the specifics of the nucleobase changed and where, a point mutation has the capability of altering the sequence of the amino acids used in forming the protein. A difference in amino structure means a difference in protein fold which means a difference in electrochemical properties which *can* mean a novel function. And if the function of the protein is to catalyze other reactions then this new protein is a new enzyme.
So, yes, Richard, a point mutation does make a novel gene and may make a novel protein and the evidence you asked for has been provided.

Taq comments in Taq(Message 396)

Bare assertions may work in church, but they don't work well in science.

RLW’s comment is

What are the EXPERIMENTAL evidences?

This message is a reply to:
 Message 401 by AZPaul3, posted 06-18-2020 10:19 PM AZPaul3 has responded

Replies to this message:
 Message 404 by AZPaul3, posted 06-19-2020 5:43 PM Richard L. Wang has responded
 Message 407 by Taq, posted 06-22-2020 12:20 PM Richard L. Wang has not yet responded

  
Richard L. Wang
Member (Idle past 0 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 403 of 452 (877660)
06-19-2020 4:24 PM
Reply to: Message 400 by Taq
06-18-2020 5:10 PM


Re-Taq(400): an example of how genetic novelty is generated
Taq(400) writes:

Then please explain how transposons are able to only make changes that are beneficial to the organism, and how that same mechanism prohibits transposon insertions that are either neutral or deleterious.


I did not say that. What I pointed out is “Translocation or Transposition is non-random mutation”.

Here, I just provide you an example of how genetic novelty was generated: molecular evolution of new antifreeze protein gene.

C.-H. Christina Cheng, a Professor at the University of Illinois at Urbana–Champaign, Urbana, IL, US, spent two decades exploring how fishes swimming in the chilly waters of the Antarctica and Arctic Ocean survive by producing similar antifreeze proteins to prevent ice from forming when the ocean began to freeze over 10-14 million years ago. Based on molecular biology, advanced genome sequencing technology and bioinformatics, Cheng’s team deduced how the new antifreeze glycoprotein (AFGP) gene has evolved step-by-step.

The antifreeze protein is very simple. It consists of many repeating basic tripeptide units: threonine-alanine-alanine or Thr-Ala-Ala. Through blood circulation, the protein is able to effectively combine with ice crystals, prevent ice crystals from growing and thereby keep their blood from freezing. The questions are how antifreeze genes had arisen.

Cheng and her partner, Arthur DeVries at the University of Illinois Urbana-Champaign as well, studied the notothenioid fishes, a group of Antarctic fishes. In 1997, they found that the AFGP gene of notothens arose from the existing gene making digestive enzyme, pancreatic trypsinogen through the following steps –
- Duplication - make a copy of trypsinogen. Because the original gene is still valid, fish can live normally in the process of creating a new gene;
- Modification - the original gene contains a right Thr-Ala-Ala building unit, so all other codes except this Thr-Ala-Ala unit have been deleted;
- Duplication – copy the mutated segment of the original gene over and over again for forty-one times.
The duplicated region acts as a powerful antifreeze agent, and the fish thrive in the chilly waters.

Logsdon, Jr. JM. and Doolittle, WF., 1997. Origin of antifreeze protein genes: A cool tale in molecular evolution. Proc. Natl. Acad. Sci. USA Vol. 94, pp. 3485–3487.

Chen L., DeVries AL. and Cheng C-HC., 1997a. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod. Proc. Natl. Acad. Sci. USA 94:3817–3822.

Chen L., DeVries AL. and Cheng C-HC., 1997b. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proc. Natl. Acad. Sci. USA 94:3811–3816.


This message is a reply to:
 Message 400 by Taq, posted 06-18-2020 5:10 PM Taq has responded

Replies to this message:
 Message 405 by AZPaul3, posted 06-19-2020 5:51 PM Richard L. Wang has not yet responded
 Message 406 by Taq, posted 06-22-2020 12:16 PM Richard L. Wang has responded

  
AZPaul3
Member
Posts: 5365
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.4


Message 404 of 452 (877664)
06-19-2020 5:43 PM
Reply to: Message 402 by Richard L. Wang
06-19-2020 4:21 PM


Re: Taq & RLW comment on Taq(399) & AZPaul3(401)
What are the EXPERIMENTAL evidences?

Are you serious?

"A point mutation changes the gene."

Are you saying a point mutation does *not* change the gene?

Do you really need a lab result to evidence this?

Changing a letter changes the word. Do you really need a 3rd grade class exercise to show this as well?

Are you really so lost and so desperate as to deny the obvious?

Also, did you not understand the protein example?

Are you, again, going to try to deny the obvious?

Step up your intellectual game. You're not an idiot.


Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 402 by Richard L. Wang, posted 06-19-2020 4:21 PM Richard L. Wang has responded

Replies to this message:
 Message 408 by Richard L. Wang, posted 06-22-2020 4:46 PM AZPaul3 has acknowledged this reply

  
AZPaul3
Member
Posts: 5365
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.4


Message 405 of 452 (877665)
06-19-2020 5:51 PM
Reply to: Message 403 by Richard L. Wang
06-19-2020 4:24 PM


Re: Re-Taq(400): an example of how genetic novelty is generated
molecular evolution of new antifreeze protein gene.

So how does this show non-random mutations?

Do you think the duplication step was deliberate? Destined? By what evidence?

Edited by AZPaul3, : No reason given.


Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 403 by Richard L. Wang, posted 06-19-2020 4:24 PM Richard L. Wang has not yet responded

  
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