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Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
Taq
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Posts: 9973
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Message 382 of 452 (877485)
06-16-2020 5:56 PM
Reply to: Message 381 by Kleinman
06-16-2020 5:53 PM


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

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 Message 381 by Kleinman, posted 06-16-2020 5:53 PM Kleinman has replied

Replies to this message:
 Message 383 by Kleinman, posted 06-16-2020 6:28 PM Taq has replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 384 of 452 (877488)
06-16-2020 6:41 PM
Reply to: Message 383 by Kleinman
06-16-2020 6:28 PM


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

This message is a reply to:
 Message 383 by Kleinman, posted 06-16-2020 6:28 PM Kleinman has replied

Replies to this message:
 Message 386 by Kleinman, posted 06-17-2020 9:50 AM Taq has replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 387 of 452 (877523)
06-17-2020 11:59 AM
Reply to: Message 386 by Kleinman
06-17-2020 9:50 AM


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

This message is a reply to:
 Message 386 by Kleinman, posted 06-17-2020 9:50 AM Kleinman has replied

Replies to this message:
 Message 388 by Kleinman, posted 06-17-2020 12:42 PM Taq has replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 389 of 452 (877528)
06-17-2020 1:12 PM
Reply to: Message 388 by Kleinman
06-17-2020 12:42 PM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
Kleinman writes:
You should learn how to do it.
So you would agree that biology can be understood in terms of naturalism?

This message is a reply to:
 Message 388 by Kleinman, posted 06-17-2020 12:42 PM Kleinman has replied

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 Message 390 by Kleinman, posted 06-17-2020 1:26 PM Taq has not replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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 - BioLogos
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 replied

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

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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 replied

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 Message 398 by Richard L. Wang, posted 06-18-2020 3:52 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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.

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 Message 397 by Richard L. Wang, posted 06-18-2020 3:49 PM Richard L. Wang has not replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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 replied

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

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 406 of 452 (877832)
06-22-2020 12:16 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
RLW writes:
I did not say that. What I pointed out is Translocation or Transposition is non-random mutation.
Then you are saying that translocation and transposition can only ever be beneficial and can never be neutral or deleterious. That's what non-random mutation means.
You need to explain how the mechanisms that cause translocation and transposition know to only cause beneficial mutations.

This message is a reply to:
 Message 403 by Richard L. Wang, posted 06-19-2020 4:24 PM Richard L. Wang has replied

Replies to this message:
 Message 409 by Richard L. Wang, posted 06-22-2020 5:09 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 407 of 452 (877834)
06-22-2020 12:20 PM
Reply to: Message 402 by Richard L. Wang
06-19-2020 4:21 PM


Re: Taq & RLW comment on Taq(399) & AZPaul3(401)
RLW writes:
What are the EXPERIMENTAL evidences?
The experimental evidences are in posts 367 and 395.

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 Message 402 by Richard L. Wang, posted 06-19-2020 4:21 PM Richard L. Wang has not replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 410 of 452 (877861)
06-22-2020 5:15 PM
Reply to: Message 409 by Richard L. Wang
06-22-2020 5:09 PM


Re: Re-Taq(406): please check the definition of random processes
RLW writes:
What the randomness you understand is very specially defined by Neo-Darwinists that mutations occur randomly with respect to whether their effects are useful.
When we say mutations are random, that is the randomness we are talking about. If you want to debate evolution and natural processes, then those are the concepts you are arguing against.
Please check the definition of random processes, and then you may know that the Neo-Darwinists’ definition of randomness is completely wrong.
The map is not the territory. Definitions should reflect how the words are used, and in biology that is the usage of the word random.
More to the point, you use the same definition all of the time. Is the lottery random? If your answer is yes, then you are using the same definition as biologists are using. The tickets are not bought at random places, but at specific places. The range of numbers are not completely random numbers, but are restricted to a set range. The drawings do not happen at random times, but at set times each week. The only thing that is random is that the process that picks the numbers is blind to the tickets being held by the players. You would use the same definition in the game of craps. There is a much higher chance of rolling a 7 than there is a 2 or 12. However, the game is still random because the dice aren't affected by the placement of chips on the table.

This message is a reply to:
 Message 409 by Richard L. Wang, posted 06-22-2020 5:09 PM Richard L. Wang has replied

Replies to this message:
 Message 411 by Richard L. Wang, posted 06-23-2020 4:27 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 412 of 452 (878059)
06-25-2020 12:24 PM
Reply to: Message 411 by Richard L. Wang
06-23-2020 4:27 PM


Re: Re-Taq(410): random processes and description of random processes
RLW writes:
Let us use the simplest example of rolling dice to explain how to describe random process in mathematics. Roll a dice and look at the number on the up side. One does not know in advance what number will appear, so this is a random process.
In the same way, before a child is born you can not predict which mutations they will have.
Taq, can you describe transposition mutation to be a random process by the above method?
Can you show us how to predict where a transposon will insert?
I have personally done random transposon mutagenesis experiments in bacteria, and the result was insertions all over the bacterial genome. There were short sequences that the transposon preferred to insert into, but those potential insertion sites are spread throughout the genome and there is no way to determine which site will be used for a specific insertion.
quote:
The results indicate that random transposon mutagenesis causing growth-delayed phenotype results in identification bacterial virulence genes, and attenuated strains with transposon interrupted virulence genes could be used as vaccine to activate fish immune system.
Transposon mutagenesis and identification of mutated genes in growth-delayed Edwardsiella ictaluri | BMC Microbiology | Full Text

This message is a reply to:
 Message 411 by Richard L. Wang, posted 06-23-2020 4:27 PM Richard L. Wang has replied

Replies to this message:
 Message 413 by Richard L. Wang, posted 06-26-2020 11:56 AM Taq has replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 419 of 452 (878365)
06-29-2020 1:38 PM
Reply to: Message 413 by Richard L. Wang
06-26-2020 11:56 AM


Re: Re-Taq(412): Is transposition random or non-random?
RLW writes:
From the point of view of molecular mechanics — bond broking and binding -, transposon insertion should be similar to point insertion, that is, each site on the genome should be approximately the same. In fact, they are different.
That's like saying the lottery is not random because the drawing happens at predictable times.
There are short sequences that transposons like to insert into, but those short sequences are found throughout the genome and the transposon will insert randomly among them.
The choice of insertion site of the trypsinogen’s copy is controlled by the condition that it cannot damage the original genome.
That's false. Transposons can insert into genes and knock them out. In fact, that is exactly what I used transposons for in the lab. I screened thousands of clones to find the one that lacked the activity I was focused on. This told me the trasposon had inserted into the gene responsible for the activity I was interested in.
There is nothing stopping transposons from inserting into functional DNA and doing away with that function. Nothing.

This message is a reply to:
 Message 413 by Richard L. Wang, posted 06-26-2020 11:56 AM Richard L. Wang has replied

Replies to this message:
 Message 423 by Richard L. Wang, posted 06-30-2020 12:21 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 420 of 452 (878366)
06-29-2020 1:47 PM
Reply to: Message 415 by Tanypteryx
06-26-2020 8:15 PM


Re: Re-Taq(412): Is transposition random or non-random?
Tanypteryx writes:
This got me wondering, are retro-viral insertions considered to be mutations? And are their insertion points random?
Any change in the base sequence of a stretch of DNA is a mutation, so retroviral insertions would most definitely be a mutation. Their insertion points are also random with respect to fitness since they can be neutral, beneficial, or deleterious. Certain viruses do prefer different motifs, such as AT repeats or transcriptional units, but when biologists mean random they mean random with respect to fitness.
Also, are genetic modifications using tools like CRISPR considered mutations, and are they random or specific as far insertion point?
CRISPR/Cas9 would be the big exception. Those are mutations and they are non-random. This would be a case of purposefully changing DNA to get a specific beneficial outcome.
As a general rule, if mutations were non-random with respect to fitness then (at the most extreme) we would expect to see the same beneficial mutation suddenly appear in every new offspring when exposed to the same environmental challenge. For example, we would expect all bacteria to get the same mutation for antibiotic resistance right after being exposed to antibiotics. Instead, it is only about 1 in 200 million bacteria that get the needed mutation (for select antibiotics), and this happens whether or not they have been exposed to antibiotics.

This message is a reply to:
 Message 415 by Tanypteryx, posted 06-26-2020 8:15 PM Tanypteryx has replied

Replies to this message:
 Message 421 by Tanypteryx, posted 06-29-2020 2:10 PM Taq has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 425 of 452 (878460)
06-30-2020 1:18 PM
Reply to: Message 423 by Richard L. Wang
06-30-2020 12:21 PM


Re: Re-Taq(419): transposon insertions involve two types of forces
RLW writes:
Transposon insertion involves two types of forces: natural force and X force related to bioinformatic process.
It's all natural forces, from start to finish. The function of the enzymes, DNA binding, and so forth are all natural processes and forces.
Because information, including genetic information, does not follow the natural laws, but follows its own rules.
This is something you have made up from whole cloth. It simply isn't true.
Why those short sequences are found throughout the genome?
Base matching. Complementary bases on the genome and transposon sequences physically stick to each other because of their charges and shape.
Under the regulation, the transposon will insert randomly among them, but this RANDOM of mutation is different from the RANDOM of mutation insisted by Neo-Darwinists.
They are one in the same.
First, why Neo-Darwinists insist that genetic mutations are random is because they want to emphasize that mutations are driven by natural forces.
Mutations are observed to be the result of natural forces. Mutations are observed to be random.
but your experiments show that there are regulations at work other than the natural laws.
Again, that is something you have made up from whole cloth.
Second, Neo-Darwinian randomness should occur without any additional conditions, but in your experiments, the randomness of transposon insertions is controlled by regulations.
It's controlled by natural forces.

This message is a reply to:
 Message 423 by Richard L. Wang, posted 06-30-2020 12:21 PM Richard L. Wang has replied

Replies to this message:
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