NvC-1: What is the premise of Naturalism in Biology?

I proposed two new topics, but failed.NvC-2: Information is independent of matter
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I’m used to thinking science issues, but I don’t know how this Forum works. What’s more, I hardly spend time to understand how this Forum works, even after GDR(92) kindly reminded me. I did not reply to Admin(NvC-2-3) in time, while I continued to submit my different posts to this NvC-2 un-threaded topic, so Admin closed it.NvC-3: What is life made of
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After thinking for the past two days, I realized that the premises are unnecessary for both Naturalism and my Creationism (I don’t explain further detail, because I don’t think anyone is interested in it). This is my important result from the discussion/debate here. Thank you all. I’ll revise my book to remove all paragraphs relevant to premise. This proposed topic caused a lot of controversy, and I did not response to Admin(114) in time.I’m sorry to you all for wasting your time because of my mistake.However, we still need a topic in order to set a narrow focus and continue our discussion/debate. Here is my suggestion. Based on the feedback, I’ll decide whether to submit. I don’t want to give Admin any more trouble.NvC-4: Do all biological processes follow the natural laws?
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The mainstream biology claims that all biological processes follow the natural laws. On the other hand, I think that the non-material elements in organisms don’t follow the natural laws, so the biological processes related to non-material elements don’t follow the natural laws.Note 1 — I call the view that all biological processes follow the natural laws as Neo-Darwinian-Naturalism. Anyone can disagree with this name, and call the idea that all biological processes follow the natural laws as Materialism, or Whatever-ism. All biological processes follow the natural laws is a scientific proposition, its correctness can be tested by evidence, and how to name it is just a common agreement;
Note 2 — There is no assumption that all biological processes follow the natural laws is correct or not. One can think of this as a conclusion based on facts, while the other can say no. This is exactly what we are going to discuss/debate;
Note 3 — The non-material elements in organisms include genetic-information, language, knowledge, belief, cognition, mind, etc. If you like, you can discuss about all these non-material elements. I will restrict my discussion/debate to genetic-information, because the research related to genetic-information belongs to empirical science. Genetic-information can be measured, tested, modified and calculated. In a word, all the conclusions related to genetic-information must be supported by evidence. As a result, it is more likely to lead to meaningful discussions/debates.

See Neo-Darwinism — Wikipedia, please. Neo-Darwinism is generally used to describe any integration of Darwin's theory of evolution by natural selection with Gregor Mendel's theory of genetics. Sorry for replying late and thank for your suggestion.

Sorry for replying late. RLW(32) discussed the premise of Naturalism in Biology. Now, I understand that the theoretical structure of my creationism can be simplified by removing this premise, see RLW(202). So, I think it is unnecessary to continue discussing this point. I see you, GDR and others continue discussing many interesting issues, and I like to join your discussion soon. Sorry again.

During the past two decades, with the development of genome sequencing technology and computational methods, bioinformatics, molecular evolution, molecular genetics and genomics have made great progress. The progress of these disciplines deepens the fundamental understanding of basic biological processes, especially the biological evolution, and provides the foundation for their applications in many important fields. In the recent coronavirus pandemic, the analyses of the structures and variation of the covid-19 coronavirus RNA and the relationship with other coronavirus RNA occupy the center position in fighting against covid-19 coronavirus pandemic. All these subjects are included in empirical science, not abstract philosophy.
------As for the biological processes related to non-material elements don’t follow the natural laws, consider an example, 1+1=2 can be operated by electronic circuits in calculators or smartphones and biological circuits in our brains. If only the natural laws play roles, can calculators, smartphones or our brains perform this operation? For reference only, let’s discuss it later.

What I wrote in RLW(215) is

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1+1=2 can be operated by electronic circuits in calculators or smartphones and biological circuits in our brains.
If only the natural laws play roles, can calculators, smartphones or our brains perform this operation?

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While what you quoted in AZPaul3(217) of what I wrote in RLW(215) is

quote:

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1+1=2 can be operated by electronic circuits in calculators or smartphones and biological circuits in our brains.
can calculators, smartphones or our brains perform this operation?

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Have you found the difference?

When designing/making player piano, do only natural laws play a role?The 1+1=2 is just for a question: do only natural laws play a role in our daily life? In fact, many issues will cause the same question.
When you write your posts in English, do only the natural laws play a role? What about English vocabulary and grammar?
When you decide to travel to A or B, do only the natural laws play a role? What do you think of these factors: schedule, transportation, weather, meal, These examples come from our daily life, everyone has experience. I use these issues just for asking questions. Human neural network of humans is so complex that we cannot obtain clear answers on these questions. Therefore, I’ll discuss genetic information in detail, because the processes of genetic information are essentially understood.

It seems to me that this thread NvC-1 is a site to discuss with your guys at present, although the topics are far beyond the NvC-1 original topic.I’m interested in reading the recent messages of PaulK, WookieeB, AZPaul3, ringo, GDR, Tangle and Ben!. Let me first outline my general idea.AZPaul3(252) well analyzes Shannon’s theory of information communication, and points that

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This discussion, however, is heavily concerned with the meaningful content of the information especially as to its origination and use.

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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?Why do people make information? It’s for communication. A person produces a message because she/he wants to tell a story, or give someone an instruction, or describe a fact, or ask someone or herself/himself a question.In order to that information communicates successfully, that is, the info-receiver knows the meaning of the info-sender, the information must follow certain rules. The messages in this Forum are written in English. You write your message according to the rules of English vocabulary and grammar. I read your message according to the same rules: English vocabulary and grammar, so I understand your message and can discuss it with you.So, information obeys its own rules, not the natural laws.Furthermore, the bioinformatic processes in our brain should not follow the natural laws. These bioinformatic processes include all processes related to language, math operation 1+1=2, and thinking about how to make PaulK(219)’s player piano, but these bioinformatic processes are too complex to discuss further.Let’s discuss gene, the protein-coding sequence in DNA.1. Gene contains information about how to make the right protein;
2. Gene information is used for communication: DNA instructs ribosome to synthesize the right protein through mRNA;
3. The communication follows the rule — The Genetic Code;
4. It is clear that the bioinformatic process — translation — obeys the Genetic Code, not the natural laws.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.

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.Well, according to your logic, in writing your message, it is a purely chemical process, the abstract information — your knowledge of English, English vocabulary and grammar, and your idea on this message — does nothing!

English obeys its vocabulary and grammar, not the natural laws;
Gene obeys the Genetic Code, not the natural laws.Are these conclusions terrible non sequitur? What’s your logic?

The word information is widely used. We have to carefully distinguish what it really means.The information I use in my discussion belongs to Information - Wikipedia: In information theory, information is taken as an ordered sequence of symbols from an alphabet, say an input alphabet , and an output alphabet ‘.Therefore, information is taken as an ordered sequence of symbols from an alphabet. All the messages in this forum, all the messages in a smartphone, and genetic information are such information, but your Physical information is not.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? Please explain the following questions from the natural laws, or your course on biochemistry and genetics, or hydrogen bonding:
- Why does ribosome read three bases on the mRNA strand at a time?
- In your figure, the tRNA with the bases UUU carries an amino-acid Lys, but not other amino-acid. Why?

Taq(277) explains in detail that All of it is natural laws. And PaulK(264) states that The translation obeys natural laws. It is a purely chemical process - the abstract information does nothing, it is the actual chemical sequence and it’s interaction with the other chemicals surrounding it that does the work. All according to natural law. And Taq(276) points out that The entire process follows natural laws.In this sense, I agree with both of you that each step follows natural laws.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?If you input numbers 3 and 2 into a calculator. The results for the operations +, -, * and / are 5, 1, 6 and 1.5, respectively. No matter what operation the calculator does, every step follows natural laws. Why are the results different? Because electronic signals go through different electronic circuits for different operations. Therefore, the math operation rules embodied in the electronic circuits or electronic devices. The electronic devices of these math operations are designed according to the math operation rules, rather than natural laws. Therefore, math operations follow the math operation rules, not natural laws. No one can get 3+2=5 from natural laws.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?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. So, the questions are:
- Why all 61 tRNA (3 codons for STOP removed from the total 64 codons) can only carry one type of amino acid, but not more than one type of amino acid?
- For a tRNA, such as the tRNA in the Figure of Taq(267) with an anticodon UUU, why does it carry Lys instead of other amino acid?This is the most important issue, so I’ll not discuss other issues at present. Sorry Taq, PaulK and Tangle.

for your message. I'll try.

The physical information of hydrogen and oxygen is exactly different from the genetic information. The genetic information is an ordered sequence of symbols from an alphabet, A/C/G/T for DNA or A/C/G/U for RNA. Does the physical information of hydrogen and oxygen have an alphabet and present as an ordered sequence of symbols from the alphabet? No. Therefore, your conclusion Natural laws are doing that is not supported by evidence or arguments. This is your key point: the specific base sequences of a specific tRNA determines the specific amino acid that bind to that specific tRNA (through the interaction with a specific enzyme).Your general description does not answer my question in RLW(Message 285) that
- Why does ribosome read three bases on the mRNA strand at a time?
- In your figure, the tRNA with the bases UUU carries an amino-acid Lys, but not other amino-acid. Why?PaulK(Message 287) asked me what this means? My questions are, in the Figure of Taq (Message 277), why must the anticodon be three bases instead of two? Why does the anticodon loop determine the acceptor stem by the natural laws? In other words, why is the Genetic Code as we see it now? Can the laws of nature explain it? I suggest you read a review article:Koonin, EV. and Novozhilov, AS., 2009. Origin and evolution of the genetic code: The universal enigma. International Union of Biochemistry and Molecular Biology Life, 61, 99-111.They pointed out that The fundamental question is how these regularities of the standard code came into being, considering that there are more than 10^84 possible alternative code tables if each of the 20 amino acids and the stop signal are to be assigned to at least one codon. More specifically, the question is, what kind of interplay of chemical constraints, historical accidents, and evolutionary forces could have produced the standard amino acid assignment, which displays
many remarkable properties.Their conclusion is considerable skepticism. 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.This means that the natural laws cannot answer these questions.

I find that you deny that rules other than natural laws work in the world. Isn’t it?
There is no doubt that all the processes of life, including human beings, can be decomposed into a series of physical/chemical processes, which follow the natural laws, but this does not mean that there are no other rules in the world except the natural laws.
The translation process obeys the Genetic Code, not 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.
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!
Our society is governed by law, not by the natural laws. Law is the product of intellectual activity, not the natural laws.

But you skip my question in RLW([msq=298]) As you wrote As our knowledge and understanding grows progress may be made, many of today’s mysteries will have answers. For example, I expect that in the future, human being will interpret the dark matter and dark energy by natural laws, since this is natural phenomena.But the natural laws cannot explain information processes, or bioinformatic processes in biology, because information obeys its own rules. Information needs material as its carrier. Info-carrier follows the natural laws. Therefore, the natural laws can explain how information processes are executed, but not the meaning of information.You, Taq and PaulK both emphasize is that the EXECUTION of information processes follows the natural laws, but the natural laws cannot explain why 1+1=2.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.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.Back to the Genetic Code. The natural laws cannot explain it, because it is a bioinformatic process, as the word CODE shows. My English is very poor, I often use Google translate to translate English to Chinese or Chinese to English, when I write my replies. The natural laws determine the EXECUSION of the translation processes, but it cannot decide how to translate English to Chinese or Chinese to English.PaulK, sometimes my discussion might be too far away from genetic information which should be my focus. I will pay attention on it.