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Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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 replied

Replies to this message:
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PaulK
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Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 287 of 452 (876852)
05-29-2020 1:39 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?
quote:
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
You have already agreed that the answer to the sensible interpretation of that question is yes - since the translation process obeys natural law.
quote:
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.
Of course the circuits are designed according to natural law, otherwise they wouldn’t work.
The more accurate description is that the mathematical operations supervene on the physical operations. There is no violation of natural law.
Of course, DNA is different in a significant way - the chemistry is everything. There is no associated meaning beyond the chemical. There is a translation within the realm of chemistry but the outputs are as chemical as the inputs and the machinery (I will note that the diagrams are purely illustrative and bear little resemblance to the actual chemicals).
quote:
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?
I hope that Google Translate can do better. This is closer to a simple substitution cipher than translating natural language - a much, much easier problem. And again, by any sensible interpretation natural laws are doing it. Even the machinery is assembled by natural operations. So long as we stay in the realm of the known that remains true.
quote:
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.
I suspect you are trying to apply natural law without understanding the conditions, which is a basic error. There isn’t even an analytical solution for the three-body problem, so to think you can understand what will happen in a complex chemical environment without understanding it is clearly foolish.
quote:
- 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?
Why is that an important question? I suppose other systems are conceivable but surely we would be getting deeply into unproductive speculation in considering that here.
quote:
- 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?
I don’t see why that is an important question either, for much the same reason.
Note also that the answers to both may well involve a degree of historical contingency - from a history that is beyond our knowledge.
Again, you are seeking to step beyond the bounds of knowledge, which is certainly not where you want to go if you are trying to make a string scientific case.

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

Replies to this message:
 Message 299 by Richard L. Wang, posted 06-01-2020 3:16 PM PaulK has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 288 of 452 (876853)
05-29-2020 1:59 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:
This is the most important issue, so I’ll not discuss other issues at present.
I think this is far more important than you trying to overcomplicate a fairly simple question
Tangle writes:
Just out of interest, are you saying that language and DNA recombination are supernatural?
Your answer is?

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London.I am Finland. Soy Barcelona
"Life, don't talk to me about life" - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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.

Replies to this message:
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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 290 of 452 (876868)
05-29-2020 5:16 PM
Reply to: Message 289 by Taq
05-29-2020 5:03 PM


Re: Artificial is Still Natural
Yes. The natural versus supernatural dichotomy shouldn’t be confused with the natural versus artificial. The former is the usual concern here.

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dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 291 of 452 (876886)
05-30-2020 1:28 AM
Reply to: Message 289 by Taq
05-29-2020 5:03 PM


Re: Artificial is Still Natural
One of the mistakes I often see people make is thinking that whatever humans do violates some natural law. ... 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.
A couple decades ago, I knew a PhD Chemistry. One day I asked him whether we could make things happen that could not happen naturally -- ie, change or act in violation of natural law. He assured me that we could not. All we can do is to set up the conditions for a reaction or a natural process to occur and, if that reaction or process could not happen naturally, then it would not happen.
So, no, humans cannot violate natural law. The most that we could do would be to create conditions for reactions or other processes to occur -- conditions that would not normally arise on their own in the wild -- , but if those reactions or processes would not naturally occur under those conditions, then they will not occur.
 

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Admin
Director
Posts: 12998
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.3


Message 292 of 452 (876909)
05-30-2020 12:23 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?
Hi Richard,
Could you please use the dBCodes. Your first line:
Richard L. Wang writes:
Taq(277) explains in detail that All of it is natural laws. And PaulK(264)...
Should instead be:
Richard L. Wang writes:
Taq (Message 277) explains in detail that All of it is natural laws. And PaulK (Message 264)...
Creating those links to messages is extremely easy. In your original message simply type this:
Richard L. Wang writes:
Taq ([msg=277]) explains in detail that All of it is natural laws. And PaulK ([msg=264])...
If you'd like to see how any message was composed, just click on the "peek" button in the lower right of any message and you'll be shown the original text.

--Percy
EvC Forum Director

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

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


Message 293 of 452 (876926)
05-30-2020 12:58 PM
Reply to: Message 292 by Admin
05-30-2020 12:23 PM


Re-Admin: Thanks
for your message. I'll try.

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 Message 292 by Admin, posted 05-30-2020 12:23 PM Admin has seen this message but not replied

  
Admin
Director
Posts: 12998
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.3


Message 294 of 452 (876958)
05-31-2020 7:51 AM
Reply to: Message 89 by WookieeB
05-11-2020 4:42 PM


Moderator Suggestion
It would be nice to begin your message with, "In this message I'll be replying to both Dr Adequate's Message 65 and RAZD's Message 11. I'll address RAZD's Message 11 first."
Then further down in your post it would be nice to say, "Now, shifting to Dr Adequate's Message 65..."
These are just suggestions to make it less likely that someone will miss a reply from you. You're under no obligation to follow them.

--Percy
EvC Forum Director

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 Message 89 by WookieeB, posted 05-11-2020 4:42 PM WookieeB has not replied

  
Admin
Director
Posts: 12998
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.3


Message 295 of 452 (876959)
05-31-2020 9:06 AM
Reply to: Message 252 by AZPaul3
05-26-2020 2:30 PM


Re: Moderator Suggestion Regarding Information
AZPaul3 writes:
A second issue with Shannon is that he had no concern for the meaningful content of the message,...
Exactly. I quoted that portion. Science has so far been unable to quantify meaning. It feels to me that the way information is being discussed in this thread requires quantification, so unless the discussion shifts from meaning to Shannon information the discussion is bound to become like comparing different genera of fruit.

--Percy
EvC Forum Director

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WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 296 of 452 (876973)
05-31-2020 10:50 PM
Reply to: Message 284 by Taq
05-29-2020 11:05 AM


Taq writes:
Message 282I 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.
It basically comes down to an ontology. Information has two attributes, an arrangement (that is not determined by matter) and something (99.999--% of the time matter) that it is instantiated on. So no, if a particular arrangement is of matter, and the matter goes away, then the information does not remain.
Some examples of information not relying on matter - mathematics, rationality
You should probably define information. Or use the Shannon definition, though it also doesnt rely on matter. Either way, it is the arrangement attribute of information that needs explaining.
Change the physical structure of the ink and you change the message.
You misunderstand or are changing the context. 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 ink reacts on paper may be chemical, but where ink is concentrated on paper (to do it's chemistry) is not chemically determined.
Taq writes:
Message 284A 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?
Yes, that chemistry works is not due to a code. 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. For the chemistry to occur you have to assume that the specific chemicals, not just any chemicals, are present. Why those specific chemicals? If you go to the DNA, the specific arrangement is not due to any known chemistry. The symbol convention that DNA is following cannot logically be due to the DNA itself. It's easy to point to the chemistry doing it all when you assume all the parts are there. But the parts themselves need to be explained, as that is the root of the information for the whole genetic process. (and we're not even touching epigenetic items which adds on layers of different information processing systems to the whole system of life)
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. That the DNA ((A), cytosine (C), guanine (G), and thymine (T)) bind together in a dual fashion and react with the sugar backbone of the DNA is all due to lawlike chemistry. But the arrangment of the nucleotides is not due to lawlike chemistry. The same could be said for the makeup of tRNA, the tRNA synthetase, RNA polymerase, and the ribosome.

This message is a reply to:
 Message 284 by Taq, posted 05-29-2020 11:05 AM Taq has replied

Replies to this message:
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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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.

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


Message 298 of 452 (877020)
06-01-2020 3:12 PM
Reply to: Message 286 by Taq
05-29-2020 12:36 PM


Re-Taq(286)&PaulK(287): Why the anticodon loop of tRNA determines the acceptor stem
Taq(286) writes:
If you start with hydrogen and oxygen you get the information passed through combustion that produces water, H2O. Biology works with the same exact type of information as every other physical and chemical process occurring throughout the universe. Natural laws are doing that (that here means natural laws translate genetic information into protein information).
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.
Taq(286) writes:
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.
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.

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 Message 286 by Taq, posted 05-29-2020 12:36 PM Taq has not replied

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 Message 301 by PaulK, posted 06-01-2020 3:37 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 299 of 452 (877021)
06-01-2020 3:16 PM
Reply to: Message 287 by PaulK
05-29-2020 1:39 PM


Re-PaulK(287): There are rules other than natural laws in the world
PaulK(287) writes:
the translation process obeys natural law.
Of course, the circuits are designed according to natural law, otherwise they wouldn’t work.
The more accurate description is that the mathematical operations supervene on the physical operations. There is no violation of natural law.
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.

This message is a reply to:
 Message 287 by PaulK, posted 05-29-2020 1:39 PM PaulK has replied

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 Message 300 by Taq, posted 06-01-2020 3:26 PM Richard L. Wang has not replied
 Message 302 by PaulK, posted 06-01-2020 3:46 PM Richard L. Wang has replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(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.

This message is a reply to:
 Message 299 by Richard L. Wang, posted 06-01-2020 3:16 PM Richard L. Wang has not replied

  
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