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Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


(1)
Message 186 of 452 (876528)
05-21-2020 4:58 PM
Reply to: Message 128 by Richard L. Wang
05-18-2020 5:00 PM


Re: Re-RAZD(98): Science articles please
RLW writes:

I submitted only one biological paper, “The Genetic Code was Designed”. As the paper’s conclusion leads to creationism, this paper was rejected by the editors of ten journals, as I expected.

In science, it is experimental results that lead towards conclusions. I'm guessing your paper didn't have a methods section, or even a results section. Am I wrong?

You really don't seem to understand how science is done. It really boils down to one simple rule: If I am right, then you will make these empirical observations and not those empirical observations. That's it. Science doesn't involve a belief that all of nature is just matter, nor does Darwinism or any other theory in science. Just a small note, I think energy is feeling a bit neglected since no one will talk about him.

If you don't think science is a useful tool for describing the universe around us, then create a new method and show how it is better. Until then, we will keep using science.


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Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 267 of 452 (876764)
05-27-2020 5:56 PM
Reply to: Message 263 by Richard L. Wang
05-27-2020 3:18 PM


Re: Bioinformatic processes don’t obey the natural laws
RLW writes:

Yes, information has meaning. In fact, the word “information” itself implies that it contains some meaning. If there is no meaning, why do people make information?

Matter and energy in its own basic form has information. A single quantum particle can have momentum, charge, spin, placement, and size, all of which is information.

"Physical information is a form of information. In physics, it refers to the information of a physical system. Physical information is an important concept used in a number of fields of study in physics. For example, in quantum mechanics, the form of physical information known as quantum information is used in many descriptions of quantum phenomena, such as quantum observation, quantum entanglement and the causal relationship between quantum objects that carry out either or both close and long-range interactions with one another.

In a general sense, information is that which resolves uncertainty, which is due to the fact that it describes the details of that which is associated with the uncertainty. The description itself is, however, divorced from any type of language."
Physical information - Wikipedia

So, information obeys its own rules, not the natural laws.

Natural laws are what creates information.

For example, the gene in DNA is ATG-AAA-CGA-TAG, which is transcribed into mRNA to become AUG-UUU-CGA-UAG. The instructions given to ribosome by DNA through mRNA are:
1. When AUG is found, get an amino-acid Met and start synthesizing
2. When UUU arrives, get an amino-acid Phe and form a peptide bond with Met
3. When CGA arrives, get an amino-acid Arg and form a peptide bond with Phe
4. When UAG arrives, stop.
So, it is the Genetic Code, not the natural laws, to play a role in the translation process.

You need to take a course on biochemistry and genetics. It is the natural laws of hydrogen bonding that governs the binding between the complementary bases in the tRNA and the mRNA codon.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


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 Message 263 by Richard L. Wang, posted 05-27-2020 3:18 PM Richard L. Wang has responded

Replies to this message:
 Message 273 by Richard L. Wang, posted 05-28-2020 12:16 PM Taq has responded

  
Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 268 of 452 (876765)
05-27-2020 6:05 PM
Reply to: Message 262 by WookieeB
05-27-2020 2:55 PM


WookieeB writes:

Being that information is an abstract thing that can be symbolized on matter (yes even outside the brain), I do not see any evidence (unicorn) that it is determined by the matter.

Functioning brains are matter and energy. What we write is matter and energy. What we say is matter and energy. It's all physical.


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Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 270 of 452 (876767)
05-27-2020 6:28 PM
Reply to: Message 269 by WookieeB
05-27-2020 6:14 PM


As for evidence, I have already provided it, with numerous examples. The information that distinctly makes up Macbeth, did exist in the mind of Shakespeare. When he wrote it down the information, it existed on (not as) ink and paper. When it was spoken and acted in a play, it was embedded in the sound waves. Today we can take a written record, have it scanned into some electronic equipment that will then audibly read the play, which can then be heard by yet another device that converts the sound waves to be represented by electromagnetic and/or light symbols and transmitted to yet another device that can receive those signals and convert them to a form that literally imprints the symbols onto a 3D form of matter (via 3d printer) in a language completely different than English. So from Shakespeare's mind to the last iteration, there are at least 8 different symbol systems and just as many different types of matter/energy involved even before another mind "reads" it. There is nothing about the matter in the entire chain that itself defined the symbol system nor the arrangement of matter that conformed to a symbol system. Information, the message, was represented on matter, but it was not the matter that determined the message. That is how information is independent of matter.

Take away all matter and energy from all of the things you mention and the information goes away. It is entirely dependent on matter and energy, from the physical structure of the brain to the physical structure of letters on a page.

Human abstractions are still made of matter and energy. They are processed by the brain through matter and energy. Every single step is derived from physical information.


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 Message 269 by WookieeB, posted 05-27-2020 6:14 PM WookieeB has responded

Replies to this message:
 Message 281 by WookieeB, posted 05-28-2020 4:01 PM Taq has responded

  
Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 275 of 452 (876798)
05-28-2020 12:42 PM
Reply to: Message 271 by Richard L. Wang
05-28-2020 12:10 PM


Re: Re-PaulK(264): information does nothing!
RLW writes:

Frankly, I really don’t know how to answer. For general concept discussion, I like to take language as an example, because everyone has experience in language.

Those concepts don't work for DNA, RNA, and proteins. These processes are directly governed by chemistry. For example, we don't equate the word horse and a picture of a horse because the word chemically binds to the picture. However, AUG results in a methionine because the tRNA anti-codon directly binds to the AUG on the mRNA.


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Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 276 of 452 (876799)
05-28-2020 12:44 PM
Reply to: Message 272 by Richard L. Wang
05-28-2020 12:13 PM


Re: Re-Tangle(266): What’s your logic?
RLW writes:

Gene obeys the Genetic Code, not the natural laws.

False. The entire process follows natural laws. If you think we are wrong, then point to the processes in DNA replication, RNA transcription, and protein translation that do not obey natural laws.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


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Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 277 of 452 (876800)
05-28-2020 12:50 PM
Reply to: Message 273 by Richard L. Wang
05-28-2020 12:16 PM


Re: Re-Tag(267): Does H-bond govern the whole translation process?
RLW writes:

As you wrote that “It is the natural laws of hydrogen bonding that governs the binding between the complementary bases in the tRNA and the mRNA codon.” Well, in your opinion, is this the whole translation process?

There are other processes, but they are all governed by natural laws. The enzymes that attach the amino acid to the tRNA follow natural laws. Which enzymes attach which amino acid to different tRNA's is governed by the chemical and physical interactions between the enzymes, amino acids, and tRNAs. The structure of a tRNA is governed by the natural laws for hydrogen bonding which is again due to complementary bases.

A and U bind to one another and G and C bind to one another, and that is what produces the shape of the tRNA. The bases in the anticodon loop determine where it will bind on the mRNA, which again is through complementary bases.

ALL of it is natural laws. If you disagree, then look through all of the molecular interactions and find one that violates natural laws.


This message is a reply to:
 Message 273 by Richard L. Wang, posted 05-28-2020 12:16 PM Richard L. Wang has responded

Replies to this message:
 Message 285 by Richard L. Wang, posted 05-29-2020 12:30 PM Taq has responded

  
Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 282 of 452 (876810)
05-28-2020 5:46 PM
Reply to: Message 281 by WookieeB
05-28-2020 4:01 PM


WookieB writes:

That is true, but it is not much of an argument. Take all matter and energy away and the information is gone too. But so is the matter and energy. So you're basically saying that if there is nothing, there is nothing.

I am saying that we only take away matter and energy. It just so happens that information also disappears when you do so. If information is independent of matter and energy then information should remain after matter and energy have been removed.

Meaningful information is not dependent on matter or energy.

Then it should still be around if we remove matter and energy.

But the physical structure of the brain does not determine the information.

Where is your evidence for this?

A message on a piece of paper needs the physical structure of the paper and ink to reside on, but the physical structure of the paper or ink does not determine the message.

Umm, yes it does. Change the physical structure of the ink and you change the message.


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Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


(1)
Message 284 of 452 (876836)
05-29-2020 11:05 AM
Reply to: Message 261 by WookieeB
05-27-2020 2:35 PM


WookieeB writes:

A codon of three nucleotides, that is part of a symbol system, that interacts with a different set of molecules that also involve a distinctly separate symbol system is all chemistry.

What symbols? What codes?

A specific tRNA binds to a specific mRNA codon because of hydrogen bonding, not because of a code. You might as well say that oxygen creates water using a code to bind two hydrogens, or that water molecules use a code to make hexagonal ice crystals. Is H2O a code?

But why x? Why that particular arrangement of matter?

Because it became part of a replicating system. It's a feedback system. Why does a certain sound frequency become dominant in a container (i.e. resonance)? Feedback systems. If a chemical reaction becomes part of a self replicating system then it is amplified.

There is nothing in the properties of the matter itself that account for that arrangment.

That could be said for every single molecule in the universe. There is nothing inherent in a molecule of water in Earth's atmosphere that says it has to be there with its specific placement and temperature. That water molecule is a product of history, just as the molecules of life are a product of history.


This message is a reply to:
 Message 261 by WookieeB, posted 05-27-2020 2:35 PM WookieeB has responded

Replies to this message:
 Message 296 by WookieeB, posted 05-31-2020 10:50 PM Taq has responded

  
Taq
Member
Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 286 of 452 (876849)
05-29-2020 12:36 PM
Reply to: Message 285 by Richard L. Wang
05-29-2020 12:30 PM


Re: Re-Taq(275&276&277), PaulK(278&280), Tangle(279): How does the Genetic Code work?
RLW writes:

The question is where is the genetic information? The process is called as TRANSLATION, can natural laws translate genetic information into protein information? Have you guys thought about it?

Natural laws can transmit information through biological processes in exactly the same way they transmit information in inorganic chemical processes. If you start with hydrogen and oxygen you get the information passed through combustion that produces water, H2O. As temperature decreases you get information passed along through the process of crystallization, which results in hexagonal formations:

Biology works with the same exact type of information as every other physical and chemical process occurring throughout the universe.

Back to DNA translation. The biological device or biological processor of DNA translation is shown in the Figure of peptide synthesis in Taq(267). (Thank Taq for your two wonderful Figures, which are very useful for our discussion). Maybe there will be videos on YouTube showing how DNA translation works. What would a person think if she/he did not take biology course and saw such a video? I guess she/he would think it may be an automatic assembly line. This device can be called as DNA-Protein-Translator. If one links the input and output to screen, this device would work exactly as Google Translator: input gene information and translate it into protein structure information. Can natural laws do this?

Natural laws are doing that.

The most important component of the device is tRNA. The Genetic Code is directly reflected in tRNA. As shown in the Figure in Taq(277), the anticodon portion and the amino acid linked portion are located at both ends of the tRNA, respectively. A tRNA contains typically 76-90 nucleotides in length, so the two portions are separated by about 30-40 nucleotides. If only natural laws work, then the anticodon portion is unlikely to affect what type amino acid will be attached for a tRNA.

The other loops on the tRNA are recognized by enzymes that attach the amino acid, all through natural laws that govern chemical interactions. The specific base sequences offer different chemical structures. The specific structure of an enzyme, as defined by the physical interaction of amino acids in the protein, binds to specific sequences on those loops. That's what specifies an amino acid to a specific tRNA. It is a similar process to the codon/anti-codon relationship.

Read more here:
Aminoacyl tRNA synthetase - Wikipedia

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 285 by Richard L. Wang, posted 05-29-2020 12:30 PM Richard L. Wang has responded

Replies to this message:
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Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 289 of 452 (876866)
05-29-2020 5:03 PM


Artificial is Still Natural
One of the mistakes I often see people make is thinking that whatever humans do violates some natural law. We humans have arbitrarily divided the world into what humans do and what humans don't do, but it is just an arbitrary and subjective border. What humans do is as natural as what birds do, or what rivers do. We humans follow all the same natural laws as the rest of nature.

If humans didn't have to follow natural laws then we could freely ignore the laws of thermodynamics and create free energy. We could just decide that we have negative mass and start floating through the air.


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Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 297 of 452 (877014)
06-01-2020 1:48 PM
Reply to: Message 296 by WookieeB
05-31-2020 10:50 PM


WookieeB writes:

Some examples of information not relying on matter - mathematics, rationality

How is math and rationality "information"?

When speaking of the physical structure, we're talking about the physics of each compound. How the compounds are arranged to make a message is not determined by those physics.

How the compounds are arranged is determined by physics, such as the physics and chemistry of a human writing with a pen.

How ink reacts on paper may be chemical, but where ink is concentrated on paper (to do it's chemistry) is not chemically determined.

It isn't determined by brain chemistry, or biochemistry?

But that a particular chemistry is invoked is due to a code. That a specific tRNA binds to a specific mRNA is due to chemistry. But why that specific tRNA, why that specific mRNA.

How is it not due to chemistry?

That information is not like water, or even water crystals. Even if we assume the law of physics, water forming from oxygen and hydrogen and then water crystals is easy to explain as the result of a necessary (lawlike) process.

Using your argument, there is nothing in physics or chemistry that requires snow to be found on a specific mountain. So is that information?

But the arrangment of the nucleotides is not due to lawlike chemistry.

How so?

Would you also say that the shape of a rock is not due to lawlike chemistry?

Edited by Taq, : No reason given.


This message is a reply to:
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Taq
Member
Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


(1)
Message 300 of 452 (877022)
06-01-2020 3:26 PM
Reply to: Message 299 by Richard L. Wang
06-01-2020 3:16 PM


Re: Re-PaulK(287): There are rules other than natural laws in the world
RLW writes:

The translation process obeys the Genetic Code, not the natural laws.

How does the Genetic Code violate the natural laws?

As my previous message shows, the research reveals that the natural laws cannot explain why is the Genetic Code the way it is.

Why can't natural laws explain the Genetic Code?

The natural laws cannot design those electronic circuits in smartphone.
The natural laws cannot decide how you plan your travel.
The natural laws cannot tell you how to write your message.
There are many rules in the world besides the natural laws!

All of those processes are the product of neurochemistry which is natural laws.


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Taq
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Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


Message 305 of 452 (877053)
06-02-2020 4:03 PM
Reply to: Message 303 by Richard L. Wang
06-02-2020 2:57 PM


Re: Re-Taq(300)&PaulK(301&302): Information and info-carrier obey different rules
RLW writes:

But the natural laws cannot explain information processes, or bioinformatic processes in biology, because information obeys its own rules.

Where is your evidence for any of these claims? You seem to just assert them as true without anything to back them up.

Neurochemistry follows the natural laws, but neuro-informatic process does not follow the natural laws: the natural laws cannot explain how the math rule 1+1=2 works in the brain.

Again, where is your evidence that thought processes violate natural laws?

Suppose that I download an English eBook Hamlet to my smartphone by wireless. At this time, the carrier is electromagnetic wave containing countless 0s and 1s codes. The transmission of electromagnetic wave is controlled by Maxwell equation of electromagnetic field. However, how these 0s and 1s codes express Hamlet depends on encoding rule, English vocabulary and grammar, and has nothing to do with Maxwell equation of electromagnetic field. Information and information-carrier obey different rules.

Gravity obeys different rules than electromagnetism, but they are both natural processes that follow natural laws. Humans obey all natural laws when constructing all of those files and computers.


This message is a reply to:
 Message 303 by Richard L. Wang, posted 06-02-2020 2:57 PM Richard L. Wang has responded

Replies to this message:
 Message 306 by Richard L. Wang, posted 06-03-2020 4:47 PM Taq has responded

  
Taq
Member
Posts: 8470
Joined: 03-06-2009
Member Rating: 6.0


(2)
Message 308 of 452 (877081)
06-03-2020 5:42 PM
Reply to: Message 306 by Richard L. Wang
06-03-2020 4:47 PM


Re: Re-PaulK(304)&Taq(305): Natural laws don’t govern info-content
RLW writes:

the natural laws govern the info-carrier, not the info-content.

Based on what evidence?

Very simple, the natural laws cannot explain why 1+1=2.

So natural laws can not explain why you can add 1 gram to 1 gram and get 2 grams at the end? Pretty sure natural laws can explain that.

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 that?

For the translation bioinformatic process, the natural laws work for the info-carriers: the H-bond between codon on mRNA and anticodon on tRNA, the binding between acceptor stem and amino acid; but the natural laws cannot explain the info-content: why a tRNA with the anticodon UUU is linked to an amino acid Lys.

Why can't natural laws explain that?

Here is a simple example. The rocks below have different chemical and physical structures. How are they all different? They each experienced different conditions during their formation, and natural laws governed the formation of all the rocks even though they had different outcomes. The same applies to everything you are discussing. History plays out differently in different places and times, and this results in different outcomes, and all of it is governed by natural laws. tRNAs could have been different if conditions and historical contingencies were different, but that doesn't exclude natural laws from the process that formed them to begin with.


This message is a reply to:
 Message 306 by Richard L. Wang, posted 06-03-2020 4:47 PM Richard L. Wang has responded

Replies to this message:
 Message 312 by Richard L. Wang, posted 06-04-2020 12:50 PM Taq has responded

  
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