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Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
Taq
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Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 318 of 452 (877128)
06-05-2020 10:37 AM
Reply to: Message 312 by Richard L. Wang
06-04-2020 12:50 PM


Re: Re-Taq(308): explain one question, please
RLW writes:
The rocks’ photo has nothing to do with what we discussed about.
It has EVERYTHING to do with we are discussing. There is no natural law that says a rock must have a specific shape or a specific composition. This is just like tRNAs. The shape and composition of a rock is the result of historical contingencies and natural laws, and the very same thing is true of tRNAs and the genetic code.
Well, please explain one of my questions, for example, 1+1=2, or The natural laws cannot explain why the liquid in river is called as WATER in English, but EAU in French.
Why can't natural laws explain those? This is your claim, you need to support it with evidence.

This message is a reply to:
 Message 312 by Richard L. Wang, posted 06-04-2020 12:50 PM Richard L. Wang has replied

Replies to this message:
 Message 322 by Richard L. Wang, posted 06-05-2020 3:12 PM Taq has replied

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 319 of 452 (877129)
06-05-2020 10:40 AM
Reply to: Message 314 by Richard L. Wang
06-04-2020 12:52 PM


Re: Re-Tangle(310): understand the facts first
RLW writes:
The conclusion is drawn from the analyses of facts.
You haven't offered any facts. All you do is assert that something can't be produced by natural laws without any facts to back it.
My conclusion is that God created life on Earth and gave life the ability to survive and evolve.
Based on what evidence?

This message is a reply to:
 Message 314 by Richard L. Wang, posted 06-04-2020 12:52 PM Richard L. Wang has not replied

  
Taq
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Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 324 of 452 (877154)
06-05-2020 4:32 PM
Reply to: Message 322 by Richard L. Wang
06-05-2020 3:12 PM


Re: Re-Taq(318)&PaulK(315): natural laws cannot explain language and tRNA
RLW writes:
The vocabulary of a language is a common agreement of the population who use the language. The recently prevalent coronavirus, known as COVID-19, is named by WHO. Many professional words are named by special professional committee. Imagine that in an ancient English speaking population, someone pointed to the liquid in a river and at the same time pronounced WATER, and others accepted it, then WATER means the liquid in river. The same thing happened for the ancient French speaking population, but the person pointed to the liquid in a river and at the same time pronounced EAU.
All of this is the product of natural brains operating through natural processes.
As for the Genetic Code or the tRNA that embodied it , as the authors of the review paper Origin and evolution of the genetic code: The universal enigma pointed out, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. It seems that the two-pronged fundamental question: ‘Why is the genetic code the way it is and how did it come to be?’, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years.
Not knowing the exact history of a process does not mean it violates natural laws. Do you know what an argument from ignorance is?
Therefore, the meaning of a word is assigned by common agreement, not due to the word itself. This is very easy to understand from the information point of view. The meaning of a word has nothing to do with natural laws.
Those words and agreements are the product of natural laws as described by neurobiology.

This message is a reply to:
 Message 322 by Richard L. Wang, posted 06-05-2020 3:12 PM Richard L. Wang has not replied

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 327 of 452 (877223)
06-08-2020 4:16 PM
Reply to: Message 326 by Richard L. Wang
06-08-2020 4:11 PM


Re: Re-PaulK, Taq, AZPaul3: What physics can do, what physics cannot do
Richard L. Wang writes:
However, physics is not everything, because physics only governs all physicochemical processes of matter, physics cannot govern all processes of non-material elements.
Physics cannot calculate numbers;
Cavendish calculated the gravitational constant in his famous experiments. Maxwell and others were able to measure the permitivity and permiability of space which allowed them to calculate the speed of light. Einstein was able to calculate the distortion of spacetime due to velocity. You sure you know what you are talking about?
Physics has no sense of humor;
Physics is the underlying process that gives rise to humor. The brain is matter, after all.
Physics cannot think, it does not know how to write messages for this Forum;
Physics has no purpose;
Physics cannot design any hardware and/or software;
Physics has no language function, because materials do not need to communicate with each other;
Physics cannot make decision as physics does not understand logic;
Physics cannot produce any non-material elements;
Physics underlies neurobiology which produces all of those things.

This message is a reply to:
 Message 326 by Richard L. Wang, posted 06-08-2020 4:11 PM Richard L. Wang has replied

Replies to this message:
 Message 331 by Richard L. Wang, posted 06-09-2020 3:16 PM Taq has replied

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


(1)
Message 334 of 452 (877262)
06-09-2020 3:40 PM
Reply to: Message 331 by Richard L. Wang
06-09-2020 3:16 PM


Re: Re-Taq(327): You sure you know what you are talking about?
RLW writes:
Cavendish, Maxwell and Einstein are PHYSICISTS, not PHYSICS.
Thank you for the entertainment. A giggle in the middle of the day always cheers me up.

This message is a reply to:
 Message 331 by Richard L. Wang, posted 06-09-2020 3:16 PM Richard L. Wang has not replied

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 335 of 452 (877263)
06-09-2020 3:42 PM
Reply to: Message 332 by Richard L. Wang
06-09-2020 3:21 PM


Re: Re-PaulK(328): bioinformatic laws
RLW writes:
16.1 Regulation of Gene Expression
16.2 Prokaryotic Gene Regulation
16.3 Eukaryotic Epigenetic Gene Regulation
16.4 Eukaryotic Transcription Gene Regulation
16.5 Eukaryotic Post-transcriptional Gene Regulation
16.6 Eukaryotic Translational and Post-translational Gene Regulation
16.7 Cancer and Gene Regulation
All of that is controlled by enzyme kinetics and and binding between complementary nucleotide bases. It's all natural processes.

This message is a reply to:
 Message 332 by Richard L. Wang, posted 06-09-2020 3:21 PM Richard L. Wang has replied

Replies to this message:
 Message 337 by Richard L. Wang, posted 06-10-2020 4:48 PM Taq has replied

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 340 of 452 (877281)
06-10-2020 5:25 PM
Reply to: Message 337 by Richard L. Wang
06-10-2020 4:48 PM


Re: Re-PaulK(333)&Taq(335): Regulations control bioinformatic processes
RLW writes:
For Taq(Message 267), the key point is translation, but in your opinion the key point is the H-bond.
For Taq(Message 335), the key point is regulations, the control of these bioinformatic processes, but in your opinion the key point is biochemistry, which doesn’t know control at all.
The key point is basic chemistry. Biomolecules stick to one another because of chemistry and physics.
What regulates the expression of a gene? The binding of transcription factors to the DNA upstream of the gene. What controls the binding of the transcription factors? Chemistry and physics. The physical shape and chemical characteristics of the amino acids across the protein determine what it will bind to. Certain amino acid sequences produce a folded protein that specifically binds to specific DNA sequences. If those sequences are upstream of a gene, those proteins will bind to that region. Other physical and chemical features on the protein then promote the binding of RNA polymerase to the DNA molecule, and what results is RNA transcription. ALL of it is physics and chemistry.
Transcription factor - Wikipedia
You should also study the classic lac promoter found in E. coli:
lac operon - Wikipedia
Let's also look at post-transcriptional regulation by micro-RNA's. How does that work? micro-RNA's bind to a protein complex in the same way that other proteins bind to DNA promoter regions. The micro-RNA has a 7 or 8 base section called a seed sequence, and if a 3' untranslated region (3' UTR) of an mRNA has a sequence complementary the mico-RNA/protein complex will bind to that 3' UTR. The presence of that bound complex prevents the mRNA from being translated into protein. That is how post-transcriptional gene regulation works, and all of it occurs through natural processes.
Atlas of Genetics and Cytogenetics in Oncology and Haematology
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 337 by Richard L. Wang, posted 06-10-2020 4:48 PM Richard L. Wang has replied

Replies to this message:
 Message 342 by Richard L. Wang, posted 06-11-2020 4:36 PM Taq has replied

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 365 of 452 (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?

This message is a reply to:
 Message 342 by Richard L. Wang, posted 06-11-2020 4:36 PM Richard L. Wang has not replied

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 366 of 452 (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 replied

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

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 367 of 452 (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 6.1810‘9
Transversion at non-CpG 3.7610‘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 6.1810‘9
Transition at CpG 1.1210‘7
Transversion at non-CpG 3.7610‘9
Transversion at CpG 9.5910‘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 replied

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

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 369 of 452 (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 replied

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

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 371 of 452 (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 replied

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

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 373 of 452 (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 replied

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

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 378 of 452 (877470)
06-16-2020 4:33 PM
Reply to: Message 375 by Richard L. Wang
06-16-2020 4:17 PM


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

This message is a reply to:
 Message 375 by Richard L. Wang, posted 06-16-2020 4:17 PM Richard L. Wang has replied

Replies to this message:
 Message 391 by Richard L. Wang, posted 06-17-2020 4:24 PM Taq has replied

  
Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 380 of 452 (877472)
06-16-2020 4:48 PM
Reply to: Message 379 by Kleinman
06-16-2020 4:40 PM


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

This message is a reply to:
 Message 379 by Kleinman, posted 06-16-2020 4:40 PM Kleinman has replied

Replies to this message:
 Message 381 by Kleinman, posted 06-16-2020 5:53 PM Taq has replied

  
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