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Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
Richard L. Wang
Member (Idle past 1363 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 271 of 452 (876792)
05-28-2020 12:10 PM
Reply to: Message 264 by PaulK
05-27-2020 3:44 PM


Re-PaulK(264): information does nothing!
PaulK(264) writes:
The translation obeys natural laws. It is a purely chemical process - the abstract information does nothing,
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!

This message is a reply to:
 Message 264 by PaulK, posted 05-27-2020 3:44 PM PaulK has replied

Replies to this message:
 Message 275 by Taq, posted 05-28-2020 12:42 PM Richard L. Wang has not replied
 Message 278 by PaulK, posted 05-28-2020 12:54 PM Richard L. Wang has not replied

  
Richard L. Wang
Member (Idle past 1363 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 272 of 452 (876793)
05-28-2020 12:13 PM
Reply to: Message 266 by Tangle
05-27-2020 4:19 PM


Re-Tangle(266): What’s your logic?
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?

This message is a reply to:
 Message 266 by Tangle, posted 05-27-2020 4:19 PM Tangle has replied

Replies to this message:
 Message 276 by Taq, posted 05-28-2020 12:44 PM Richard L. Wang has not replied
 Message 279 by Tangle, posted 05-28-2020 1:40 PM Richard L. Wang has not replied
 Message 280 by PaulK, posted 05-28-2020 1:53 PM Richard L. Wang has not replied

  
Richard L. Wang
Member (Idle past 1363 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 273 of 452 (876794)
05-28-2020 12:16 PM
Reply to: Message 267 by Taq
05-27-2020 5:56 PM


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

This message is a reply to:
 Message 267 by Taq, posted 05-27-2020 5:56 PM Taq has replied

Replies to this message:
 Message 277 by Taq, posted 05-28-2020 12:50 PM Richard L. Wang has replied

  
ringo
Member (Idle past 431 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 274 of 452 (876795)
05-28-2020 12:24 PM
Reply to: Message 269 by WookieeB
05-27-2020 6:14 PM


Wookie B writes:
Whereas your last prior post stated the subject was about the source of independent information, as I pointed out the subject wasn't about the source, but that independent information exists.
The two are inextricably intertwined. If something exists, it has a source.
Wookie B writes:
The information that distinctly makes up Macbeth, did exist in the mind of Shakespeare.
You have not provided any evidence about how the information got there - i.e. the source. My contention is that it was created in situ, in Shakespeare's brain. Your claim is that it had some abstract existence independent of Shakespeare's brain. You need to support that claim.
Wookie B writes:
There is no evidence that meaningful information is dependent on matter.
Again, you have it backwards. We have no evidence that information is independent from matter. We have no evidence of unicorns. Same thing.
Wookie B writes:
So, if your claim is that there is no evidence that information is 'not dependent' on matter, that means there is evidence that information is not 'not dependent' on matter, or that there is evidence that information is dependent on matter.
Seriously, do you think that pile of multiple negatives makes any sense?

"I'm Fallen and I can't get up!"

This message is a reply to:
 Message 269 by WookieeB, posted 05-27-2020 6:14 PM WookieeB has not replied

  
Taq
Member
Posts: 10028
Joined: 03-06-2009
Member Rating: 5.3


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.

This message is a reply to:
 Message 271 by Richard L. Wang, posted 05-28-2020 12:10 PM Richard L. Wang has not replied

  
Taq
Member
Posts: 10028
Joined: 03-06-2009
Member Rating: 5.3


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.

This message is a reply to:
 Message 272 by Richard L. Wang, posted 05-28-2020 12:13 PM Richard L. Wang has not replied

  
Taq
Member
Posts: 10028
Joined: 03-06-2009
Member Rating: 5.3


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 replied

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

  
PaulK
Member
Posts: 17825
Joined: 01-10-2003
Member Rating: 2.1


Message 278 of 452 (876801)
05-28-2020 12:54 PM
Reply to: Message 271 by Richard L. Wang
05-28-2020 12:10 PM


Re: Re-PaulK(264): information does nothing!
quote:
Frankly, I really don’t know how to answer.
It’s not that different from the example of the player piano. In each case the information is in a form that will produce a particular result when provided in the correct way - through the action of physical law.
quote:
For general concept discussion, I like to take language as an example, because everyone has experience in language.
Arguing by analogy is all very well, but you have to establish a real analogy.
quote:
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!
My logic is based on a basic knowledge of how DNA is transcribed and processed. If you have similar knowledge of how language operates and it tells you that your statement is true then that is your assertion. If you lack such knowledge you are certainly not following MY logic at all.
To add a clarification. For the purposes of this discussion I am not going to go into how the mind operates at all. However, it is a fact that the abstract information plays no role - it is the physical representation of that information interacting with my senses and my mind that does the job. Give me a copy of Hamlet written in Chinese or recorded onto an 8 floppy disk and I won’t be able to read either. It must be in a physical form that I can comprehend.
Edited by PaulK, : No reason given.

This message is a reply to:
 Message 271 by Richard L. Wang, posted 05-28-2020 12:10 PM Richard L. Wang has not replied

  
Tangle
Member
Posts: 9503
From: UK
Joined: 10-07-2011
Member Rating: 4.6


Message 279 of 452 (876803)
05-28-2020 1:40 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:
English obeys its vocabulary and grammar, not the natural laws;
What is unnatural about language?
Gene obeys the Genetic Code, not the natural laws.
Genes are chemicals, organic chemicals; the genetic code follows the laws of chemical bonding.
Are these conclusions terrible non sequitur? What’s your logic?
It's not logic, it's scientific observation.
Just out of interest, are you saying that language and DNA recombination are supernatural?

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.

This message is a reply to:
 Message 272 by Richard L. Wang, posted 05-28-2020 12:13 PM Richard L. Wang has not replied

  
PaulK
Member
Posts: 17825
Joined: 01-10-2003
Member Rating: 2.1


Message 280 of 452 (876804)
05-28-2020 1:53 PM
Reply to: Message 272 by Richard L. Wang
05-28-2020 12:13 PM


Re: Re-Tangle(266): What’s your logic?
quote:
English obeys its vocabulary and grammar, not the natural laws; Fun
Gene obeys the Genetic Code, not the natural laws.
Are these conclusions terrible non sequitur? What’s your logic?
They are certainly terrible.
You have to follow the rules of vocabulary and grammar to write correct English, but the information doesn’t have to obey those laws. The information can exist in other forms than written English. You can even communicate it with incorrect English. Many spelling mistakes, for instance, can be easily glossed over - indeed, standardised spelling is itself a relatively recent addition.
Likewise the genetic code merely describes how the genes are interpreted - and that interpretation is carried out by chemistry which follows natural law. It is not something that genes obey. How could they?

This message is a reply to:
 Message 272 by Richard L. Wang, posted 05-28-2020 12:13 PM Richard L. Wang has not replied

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


Message 281 of 452 (876809)
05-28-2020 4:01 PM
Reply to: Message 270 by Taq
05-27-2020 6:28 PM


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.
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.
The fact is we have matter, and we have energy, and we have information. Meaningful information is not dependent on matter or energy. Information may need the physical structure of the brain for it to reside on. But the physical structure of the brain does not determine the information. 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.
Human abstractions are still made of matter and energy.
Ok, then someone should be able to demonstrate how matter and energy form an abstraction. Until that is done, it is merely an assertion.
But what about non-human abstractions. Like mathematics or logic. Are those determined by matter and energy too?

This message is a reply to:
 Message 270 by Taq, posted 05-27-2020 6:28 PM Taq has replied

Replies to this message:
 Message 282 by Taq, posted 05-28-2020 5:46 PM WookieeB has not replied

  
Taq
Member
Posts: 10028
Joined: 03-06-2009
Member Rating: 5.3


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.

This message is a reply to:
 Message 281 by WookieeB, posted 05-28-2020 4:01 PM WookieeB has not replied

  
AZPaul3
Member
Posts: 8527
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


(1)
Message 283 of 452 (876818)
05-29-2020 12:47 AM
Reply to: Message 261 by WookieeB
05-27-2020 2:35 PM


What accounts for that "arrangement" or 'specificity' is the question
But where that code symbol system comes from is what has to be explained
Appealing to just "physics" is not an explanatory answer.
Appealing to just "physics" is not just *an* explanation, it is *the* explanation, and is the only explanation with any explanatory power at all in this universe.
Where did the various nucleotides and amino acids come from?
How did the various groupings of 3 nucleobases achieve their connections to the various amino acids?
How did any millions of molecules and their reactions to others come to exist?
Physics. Specifically, quantum field theory. More specifically, chemistry. And a good deal of evolution which is even more physics piled on that.
When we look out into space we find thousands of molecules just floating around naturally formed in the interstellar medium. Of the thousands of molecules we have detected out there the vast majority of them are organic molecules, and include a couple simple amino acids, partial ribo- and dioxyribo- phosphate groups and amino and nucleotide precursors.
From our lab experiments we KNOW with certainty that these molecules on an early earth could combine into ever more complex molecular structures by the force of chemistry alone.
If you want specific atom-by-atom bond-by-bond details of these experiments and their results then consult a chemist.
List of interstellar and circumstellar molecules - Wikipedia
We do not know, yet, how the first replicators came to be. I certainly don’t and neither do you. Since every solved we don’t know, yet problem that humans have ever come across was resolved by a physical system there is no reason to pre-suppose otherwise for all our remaining ignorance.
But we do know how evolution works. We understand the physics of replication and selection. We understand the power of trillions upon trillions of trials and failures each moment over billions of years of evolution. All naturally achieved. All by the natural processes of chemistry. All by nothing but physics.
Other than the personal incredulity of the ignorant there is no reason to conclude that the aminos, nucleobases and all the chemistry cascades associated with each that we have been talking about came to be by any other than natural physical means.
Of all the trillions upon trillions of trials and failures each moment over billions of years of evolution, finding a few dozen chemical cascades that grew to work well and consistently in the complex life systems we see on this planet is not difficult to justify. Evolution works. So does physics.
Once the chemical processes are in place and operating consistently in every cell in every living thing it should be no surprise that some smart monkeys would come along with test tubes and pipettes and charts and graphs to document each of the molecules, their interactions and the consistent nature of their operations.
Bobo make’t information.
It may be more difficult than rocket surgery owning to the complexity involved but we really are super smart monkeys.
Once all the monkeys stopped arguing over the forms, names and numbering of the charts and graphs, the consistent repetitious pattern of nucleobase codons and their chemistry became clear.
quote:
What accounts for that "arrangement" or 'specificity' is the question
But where that code symbol system comes from is what has to be explained
At Percy's request I accept the word code and accept that information has more popular connotations than it should.
In the end what Bobo found was a genetic code, information that symbolically reduces to specific chemical results.
The chemistry did not create the code. The code is mere description of the chemistry as perceived by Bobo.
That code was born from the charts and graphs Bobo made observing the physical chemistry in action. And that chemistry in action was born from the physics of evolution. Nowhere else.
quote:
Where did the various nucleotides and amino acids come from?
How did the various groupings of 3 nucleobases achieve their connections to the various amino acids?
How did any millions of molecules and their reactions to others come to exist?
Physics. Only physics. Exclusively physics. Nothing more. There is no reason to suggest otherwise.
But the symbol system is integral to the process ...
No, it is not.
Adenine came from natural chemical processes. The codon AUG results in a methionine amino added to the protein chain. The symbology of the code means nothing. The process is purely rote chemistry and came about from trillions of trials over billions of years.
... and for answering the "why", and physics doesnt explain the symbol system, nor where the configuration of x came from
The "why" is because after trillions of trials over billions of years *that* is what worked.
Physics doesn't need to explain the the symbol system. The symbol system is a direct picture of the physics. The symbol system explains the physics.
So you are here at least admitting that there are external copies of something (form matters not) that carries a symbolic meaning. This is all external to the mind.
I never denied symbology external to the mind. But I insist that symbology be embedded in a physical system. And while I will allow such symbology to be popularly called "information" I further insist that all symbology can only represent and be copied from that which originates in the mind.
Edited by AZPaul3, : No reason given.

Factio Republicana delenda est.

This message is a reply to:
 Message 261 by WookieeB, posted 05-27-2020 2:35 PM WookieeB has not replied

  
Taq
Member
Posts: 10028
Joined: 03-06-2009
Member Rating: 5.3


(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 replied

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

  
Richard L. Wang
Member (Idle past 1363 days)
Posts: 104
From: Ottawa, ON, Canada
Joined: 04-27-2020


Message 285 of 452 (876847)
05-29-2020 12:30 PM
Reply to: Message 277 by Taq
05-28-2020 12:50 PM


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

This message is a reply to:
 Message 277 by Taq, posted 05-28-2020 12:50 PM Taq has replied

Replies to this message:
 Message 286 by Taq, posted 05-29-2020 12:36 PM Richard L. Wang has replied
 Message 287 by PaulK, posted 05-29-2020 1:39 PM Richard L. Wang has replied
 Message 288 by Tangle, posted 05-29-2020 1:59 PM Richard L. Wang has not replied
 Message 292 by Admin, posted 05-30-2020 12:23 PM Richard L. Wang has replied

  
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