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Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 347 of 452 (877325)
06-12-2020 3:55 PM
Reply to: Message 346 by AZPaul3
06-11-2020 5:43 PM


Re-PaulK/Taq/AZPaul3: let's change a topic
Half a month after I submitted the message RLW(Message 263) on May 27 that Bioinformatic processes don’t obey the natural laws, we’ve posted over 80 messages. I have put all my cards on the table, and you guys still insist that only natural laws play a role in the world. So, I suggest we change a topic, for example, mutations, which PaulK raised ten days ago in PaulK(Message 307).

This message is a reply to:
 Message 346 by AZPaul3, posted 06-11-2020 5:43 PM AZPaul3 has replied

Replies to this message:
 Message 348 by PaulK, posted 06-12-2020 4:02 PM Richard L. Wang has not replied
 Message 349 by Tangle, posted 06-12-2020 4:52 PM Richard L. Wang has not replied
 Message 350 by AZPaul3, posted 06-12-2020 8:42 PM Richard L. Wang has not replied
 Message 351 by PaulK, posted 06-13-2020 9:26 AM Richard L. Wang has replied
 Message 367 by Taq, posted 06-16-2020 11:08 AM Richard L. Wang has not replied

  
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 360 of 452 (877395)
06-15-2020 12:37 PM
Reply to: Message 351 by PaulK
06-13-2020 9:26 AM


PaulK, show evidence for mutations occur by natural law
Richard is here.
As PaulK(Message 307) wrote
quote:
Mutations occur by natural law, ...
How do you know it? What is the evidence to support your assertion?

This message is a reply to:
 Message 351 by PaulK, posted 06-13-2020 9:26 AM PaulK has replied

Replies to this message:
 Message 362 by PaulK, posted 06-15-2020 1:01 PM Richard L. Wang has replied

  
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 361 of 452 (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 seen this message but not replied

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

  
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 374 of 452 (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 replied

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

  
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 375 of 452 (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 replied

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

  
Richard L. Wang
Member (Idle past 1344 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 replied

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

  
Richard L. Wang
Member (Idle past 1344 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 replied

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

  
Richard L. Wang
Member (Idle past 1344 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 replied

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

  
Richard L. Wang
Member (Idle past 1344 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 replied

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

  
Richard L. Wang
Member (Idle past 1344 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 replied

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

  
Richard L. Wang
Member (Idle past 1344 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 replied

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

  
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 408 of 452 (877856)
06-22-2020 4:46 PM
Reply to: Message 404 by AZPaul3
06-19-2020 5:43 PM


Re-Taq & AZPaul3: No evidence for point mutations to make new gene
For the English words with two letters, there are total 26x26=676 different combinations and there are 21 English words with two letters (am, an, as, at, be, by, do, go, he, hi, if, in, is, it, me, my, no, ok, so, us, we). Therefore, start from a two-letter-sequence and change it by point-substitution-mutation, on average it will take 32.2(= 676 / 21) steps to make a new English word with two letters.
Most of the genes are relatively small covering a genomic region of about 3 kb, see Overview of gene structure .
Consider a nucleotide sequence with 1000 bases and estimate how long will it take to produce a new gene by point-substitution-mutation. The 1000-base-sequence contains a total of 4^1000 = 1.15x10^602 or 10^602 different base-sequences. Here and below, all approximations will speed up the evolution.
The total number of protein-coding genes (the Earth's proteome) is estimated to be 5 million sequences, see Just a moment...
Therefore, on average, it will take 10^602 / 5x10^6 = 2x10^595 or 10^595 point-substitution-mutations to produce a new protein-coding gene.
Point-mutations are errors in the process of DNA replication during cell division and reproduction. For E. coli, it takes about 20 minutes to reproduce a new generation, and its DNA duplicates with remarkable precision: less than one error per one billion (10^9) new nucleotides incorporated. If we use Taq(Message 367) data of point substitution rates:
Transition at non-CpG 6.1810^‘9
Transition at CpG 1.1210^‘7
Transversion at non-CpG 3.7610^‘9
Transversion at CpG 9.5910^‘9
Take the rate = 10^-8 for convenience.
For per 20 minutes, one replication takes place, for 1 year, 2.6x10^4(=365x24x60 / 20) time replications occur. For the 1000-base-sequence, 0.26 (= 1000 x 10^-8 x 2.6x10^4) point-substitution-mutation, or approximates to 1 point-substitution-mutation occurs per year.
Therefore, in order for 1000-base-sequence to produce a protein-coding gene, it needs 10^595 point-substitution-mutations, which will take 10^595 years! Consider that life on Earth emerged about 4.5 billion or 4.5x10^9 years ago, 10^595 years is such a long period of time beyond imagination.
RLW(Message 403) provides an example of how genetic novelty is generated through cellular genetic engineering — cells edit their own genome. Taq & AZPaul3, there is no evidence for point mutations to produce genetic novelty in the history of biological evolution.

This message is a reply to:
 Message 404 by AZPaul3, posted 06-19-2020 5:43 PM AZPaul3 has seen this message but not replied

  
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 409 of 452 (877860)
06-22-2020 5:09 PM
Reply to: Message 406 by Taq
06-22-2020 12:16 PM


Re-Taq(406): please check the definition of random processes
What the randomness you understand is very specially defined by Neo-Darwinists that mutations occur randomly with respect to whether their effects are useful.
Please check the definition of random processes, and then you may know that the Neo-Darwinists’ definition of randomness is completely wrong.

This message is a reply to:
 Message 406 by Taq, posted 06-22-2020 12:16 PM Taq has replied

Replies to this message:
 Message 410 by Taq, posted 06-22-2020 5:15 PM Richard L. Wang has replied

  
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 411 of 452 (877951)
06-23-2020 4:27 PM
Reply to: Message 410 by Taq
06-22-2020 5:15 PM


Re-Taq(410): random processes and description of random processes
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. For this random process, what characteristics do we need to describe? Each rolling will generate a number on the up side, which can take 1, 2, 3, 4, 5 and 6. While one does not know in advance what number on the up side is after the rolling, one does know that if the dice is made very uniformly, the chance for each number to show on the up side is equal.
Let us describe this random process of rolling dice in mathematics. We assign a random variable x to represent the number shown on the up side after rolling. This random variable can take the following values: x = 1, 2, 3, 4, 5, and 6, and in the case of that the dice is made very uniformly, the probability of each number showing on the up side is equal: P(1) = P(2) = P(3) = P(4) = P(5) = P(6) = 1/6. Note that the sum of all possible probabilities is equal to 1 or 100%, which means that after rolling the number shown on the up side must be one of the following six numbers: 1, 2, 3, 4, 5 and 6.
Now, consider the point mutation of a DNA molecule consisting of 10,000 nucleotides. If a point mutation occurs, what are the uncertainties of this event? 1) Where does the point mutation occur in the DNA molecule? 2) What kind of point mutation is this mutation, substitution, insertion or deletion? 3) If it is a point substitution mutation, what base replaces the original base? 4) If it is a point insertion mutation, what base is inserted into the DNA molecule?
Therefore, to describe this random process, we need four random variables. As shown in the example of rolling dice, for each random variable, we must determine three characteristics: what kind of random process it describes, what are all possible outcomes of the random variable, and the probability that the random variable takes each possible outcome. For simplicity, we assume that the probabilities of a random variable taking all possible values is equal.
Random Variable 1: w describes the base number, where the point mutation occurs, w = 1, 2, , 10000, and P(w) = 0.0001, where w = 1, 2, , 10000;
Random Variable 2: x describes what kind of point mutation occurs, x = substitution / insertion / deletion, and P(substitution) = P(insertion) = P(deletion) = 1/3;
Random Variable 3: y describes what base is used to replace the originating base when a point substitution mutation occurs. If the original base on the w site nucleotide is A, then y = G or C or T, and P(G) = P(C) = P(T) = 1/3. If the original base on the w site nucleotide is G or C or T, the values of the random variable y and the probabilities P(y) can be obtained similarly;
Random Variable 4: z describes what base is inserted between the w-site nucleotide and the (w+1)-site nucleotide when a point insertion mutation occurs. z = A or G or C or T, and P(A) = P(G) = P(C) = P(T) = 1/4. The distribution of a random variable is not necessarily uniform. For human being, the probabilities of a base taking the values A, G, C and T are equal to 0.293, 0.207, 0.200 and 0.300, respectively; therefore, for more precise cases, we can set P(A) = 0.293, P(G) = 0.207, P(C) = 0.200, and P(T) = 0.300, respectively (Bansal M., 2003. DNA structure: Revisiting the Watson-Crick double helix. Current Science. 85 (11): 1556—1563.)
In summary, if a point mutation occurs during DNA replication, in order to accurately determine the point mutation, we must know where the point mutation occurs and what kind of mutation is: substitution or insertion or deletion. If it is a substitution, we have to know what base substitutes the originate base; if it is an insertion, we have to know what base is inserted. Obviously, point mutation is a random process and it happens naturally.
Taq, can you describe transposition mutation to be a random process by the above method?

This message is a reply to:
 Message 410 by Taq, posted 06-22-2020 5:15 PM Taq has replied

Replies to this message:
 Message 412 by Taq, posted 06-25-2020 12:24 PM Richard L. Wang has replied

  
Richard L. Wang
Member (Idle past 1344 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 413 of 452 (878158)
06-26-2020 11:56 AM
Reply to: Message 412 by Taq
06-25-2020 12:24 PM


Re-Taq(412): Is transposition random or non-random?
You have performed random transposon mutagenesis experiments in bacteria, which must be very interesting.
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.
The first step of the generation of anti-freezing gene AFGP in RLW(Message 403): 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.
In order for fish to live normally in the process of creating a new gene, the inserted copy of trypsinogen must not damage the original genome. Although insertion sites can be spread all over the genome, they cannot be any site on the genome. The choice of insertion site of the trypsinogen’s copy is controlled by the condition that it cannot damage the original genome. Therefore, this is not a random process.
The third step of the generation of anti-freezing gene AFGP in RLW(Message 403): Duplication — copy the mutated segment of the original gene over and over again for forty-one times.
Coping Abc on the already existing sequence AbcAbc will result in the sequence AbcAbcAbc. Obviously, it is not random. Random insertion of Abc will produce the sequence AbcAAbcbc, AbcAbAbcc, , that is not a copy.
Returning back to the randomness defined by Neo-Darwinists that mutations occur randomly with respect to whether their effects are useful. In the third step, coping the mutated segment may be beneficial, neutral or deleterious, so according to Neo-Darwinian definition, coping a mutated segment is a random mutation.
There are two related and different things: coping, and the effect of coping. Coping a mutated segment may be beneficial, neutral or deleterious, which means the effect of coping is uncertain, so the correct statement should be that the effect of coping is random, but the coping itself is non-random. The question is why Neo-Darwinists insist that coping is random, because the effect of coping is uncertain?

This message is a reply to:
 Message 412 by Taq, posted 06-25-2020 12:24 PM Taq has replied

Replies to this message:
 Message 414 by AZPaul3, posted 06-26-2020 4:53 PM Richard L. Wang has replied
 Message 419 by Taq, posted 06-29-2020 1:38 PM Richard L. Wang has replied

  
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