Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
1 online now:
Newest Member: popoi
Post Volume: Total: 915,817 Year: 3,074/9,624 Month: 919/1,588 Week: 102/223 Day: 0/13 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   NvC-1: What is the premise of Naturalism in Biology?
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 301 of 452 (877023)
06-01-2020 3:37 PM
Reply to: Message 298 by Richard L. Wang
06-01-2020 3:12 PM


Re: Re-Taq(286)&PaulK(287): Why the anticodon loop of tRNA determines the acceptor stem
quote:
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.
The symbols are the bases, and it is their chemical properties that determine their interactions. Your last sentence denies that - it even denies that we have argued that. If you insist they the bases are inert symbols, that their chemical properties are irrelevant then it is for you to provide evidence.
quote:
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.
I suggest that you read my prior posts, but I’ll repeat my point. All we can say is that a simplistic application of natural law without adequate knowledge Of the circumstances is insufficient to explain it. As our knowledge and understanding grows progress may be made. As the authors would agree.

This message is a reply to:
 Message 298 by Richard L. Wang, posted 06-01-2020 3:12 PM Richard L. Wang has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


(1)
Message 302 of 452 (877026)
06-01-2020 3:46 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
quote:
I find that you deny that rules other than natural laws work in the world. Isn’t it?
If you want to introduce other laws - and show that they are not natural laws or supervenient on natural law - it’s up to you to provide the evidence. The point you are responding to is a fact. The circuits of a cellphone function according to natural law. If you want to argue otherwise it’s for you to provide evidence.
quote:
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.
But it does mean that any other laws in the processes of life will be supervenient on natural law.
quote:
The translation process obeys the Genetic Code, not the natural laws.
A false dichotomy as you have implicitly admitted in your previous point. The translation process works according to natural law to follow the genetic code.
quote:
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.
It’s funny how you said that you wanted to focus on genetic information but you keep talking about the mind instead. I don’t propose to argue about that here since it is contentious and neither side can prove it’s case.
However, I will point out that law in the legal sense is quite different from natural law and confusing the two is folly and nothing more,
Edited by PaulK, : No reason given.

This message is a reply to:
 Message 299 by Richard L. Wang, posted 06-01-2020 3:16 PM Richard L. Wang has replied

Replies to this message:
 Message 303 by Richard L. Wang, posted 06-02-2020 2:57 PM PaulK has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 304 of 452 (877050)
06-02-2020 3:19 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
quote:
But you skip my question in RLW(Message 298)
Your question was a response to an assertion made by someone else. It’s hardly relevant to my points.
Since you fail to produce any evidence that the bases of DNA are merely inert symbols, or that translation is not accomplished by processes following natural law, I presume that you have none,
quote:
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
So you say, but your evidence is lacking.
quote:
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
If we are talking about genetic information, that does not concern us. Only when we get to language - and then, again, we are talking about the mind. I will anticipate your point below by pointing out that Google Translate has a more difficult task than DNA translation because it must preserve meaning - and cope with idiom and other aspects of natural language that make it difficult (and it does so imperfectly, in my experience). A human translator can do better than Google Translate, but DNA translation is too mechanical for humans to have an advantage there,
quote:
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.
We cannot currently explain it in terms of natural law, but that does not mean that it is impossible in principle. We should not expect to understand an immensely complex history with many unknown contingencies - at least not without a huge amount of work.
Nevertheless in the cases where we can study and do have good knowledge we do not see any sign that your claims are true of genetic information. Genetic information is changed and added by natural processes obeying natural law.

This message is a reply to:
 Message 303 by Richard L. Wang, posted 06-02-2020 2:57 PM Richard L. Wang has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 307 of 452 (877080)
06-03-2020 5:09 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
quote:
Now, we are discussing the core of whether naturalism is correct or not: the natural laws govern the info-carrier, not the info-content. Such evidence is everywhere that the natural laws don’t work when it comes to info-content.
On the contrary, the evidence is wholly lacking.
quote:
The natural laws cannot explain why the liquid in river is called as WATER in English, but EAU in French. The natural laws cannot explain why pain means uncomfortable feeling in English, while in French it means Bread, a food made of wheat flour; and the English word "gift" means "poison" in German.
I note again that you are not talking about genetic information at all.
Nevertheless the fact that historical contingencies play a major role is not sufficient to prove a violation of natural law.
quote:
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.
I have already addressed this point. While it cannot be explained by a simplistic application of natural laws, made without adequate understanding of history and circumstances, that does not mean that it is beyond natural law.
I don’t need to address the following paragraph other than to note that it confirms that you are referring to exactly the simplistic application of natural law that I reject as obviously inadequate.
quote:
Can your guys provide just one example of how the natural laws control info-content?
Mutations occur by natural law, and it is mutations that change and add to the info-content.

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

Replies to this message:
 Message 311 by Richard L. Wang, posted 06-04-2020 12:49 PM PaulK has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 315 of 452 (877108)
06-04-2020 1:08 PM
Reply to: Message 311 by Richard L. Wang
06-04-2020 12:49 PM


Re: Re-PaulK(307): Discuss mutations later
quote:
Of course, I focus on biology and genetic information.
Of course you don’t.
quote:
However, we first need to understand information in general, then we can understand genetic information in special. We all have experiences in math, language, etc., so it is easy for us to discuss the general properties of information from these aspects.
No, we don’t. In fact these topics actively obscure the issues. The operation of the mind is contentious and not adequately understood.
[quote]
quote:
Of course, I focus on biology and genetic information.
Of course you don’t.
quote:
However, we first need to understand information in general, then we can understand genetic information in special. We all have experiences in math, language, etc., so it is easy for us to discuss the general properties of information from these aspects.
No, we don’t. In fact these topics actively obscure the issues. The operation of the mind is contentious and not adequately understood.
quote:
Apart from the natural laws, you even dare not even mention any other rules that exist in the world. The bioinformatic processes are usually controlled by regulations rather than natural laws. These regulations are discovered by biologists (I believe most of them are traditional biologists). But you don't dare even to mention these regulations.
Why aren’t you mentioning them? Apart from the absurd idea that legislation is the same as natural law you haven’t exactly been forthcoming. And wouldn’t all those rules in biology ultimately rely on natural law anyway?
quote:
You didn’t explain anything, because the natural laws cannot answer these questions.
Well they can’t answer them in the simplistic way you want to do it. But as I did explain we shouldn’t expect them to, nor should we expect to know the actual answers yet. But you don’t address that point.
quote:
You mentioned that mutations occur by natural laws. This is a good topic, we can discuss later.
It would seem to be an essential point if you actually wanted to discuss genetic information. But then you are largely avoiding that topic.

This message is a reply to:
 Message 311 by Richard L. Wang, posted 06-04-2020 12:49 PM Richard L. Wang has replied

Replies to this message:
 Message 320 by Richard L. Wang, posted 06-05-2020 3:04 PM PaulK has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 323 of 452 (877151)
06-05-2020 3:18 PM
Reply to: Message 320 by Richard L. Wang
06-05-2020 3:04 PM


Re: Re-PaulK(315): natural laws or special devices?
quote:
So, what is the answer to the question Why are the results different for different operations +, -, * and /?
Answer 1: because all these operations follow the natural laws.
Answer 2: because different operations go through different logical circuits.
This seems a pretty pointless question, not least because answer 1 is an obvious strawman - although I must point out that the circuits only work because they obey physical laws But also because answer 2 doesn’t get us anywhere, unless it’s sole purpose is to ignore the fact that it is the physical circuits obeying natural law that do the real work. The logical circuits are simply higher level descriptions of the physical circuits used for convenience.
quote:
As for the translation process, what is the answer to the question why codon AAA on mRNA corresponds to amino acid Lys, while codon AAU on mRNA to Asn?
Answer 1: because the translation process follows the natural laws.
Answer 2: because the Genetic Code is embodied in tRNAs. The tRNA with anticodon UUU (H-bonded with the complementary codon AAA on the mRNA) has an acceptor stem connected to amino acid Lys, and the tRNA with anticodon UUA (H-bonded with the complementary codon AAU on mRNA) has an acceptor stem connected to amino acid As
And this is just a repeat of the same errors.

This message is a reply to:
 Message 320 by Richard L. Wang, posted 06-05-2020 3:04 PM Richard L. Wang has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 328 of 452 (877224)
06-08-2020 4:49 PM
Reply to: Message 326 by Richard L. Wang
06-08-2020 4:11 PM


Re: Re-PaulK, Taq, AZPaul3: What physics can do, what physics cannot do
Essentially all you have is assertions without any actual evidence.
So, let us look at genetic information, which is the one we know most about (for the others you always end up talking about the mind - and if you did not you’d have to concede the point)
The genetic information is entirely supervenient on the physical structure of the DNA. All changes to the information are made by changes to the DNA, and we have no evidence (even indirect evidence) of any violation of natural law in those changes. The translation process proceeds by chemistry, following natural law.
So, is there any reason to believe that any bioinformatic laws - at least with respect to DNA are simply higher level representations of processes founded in natural law, and that aspects not immediately dictated by natural law are the product of historical contingencies?
Remember also that natural laws do not have to produce deterministic behaviour. Spontaneous radioactive decay is predictable only statistically.

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

Replies to this message:
 Message 332 by Richard L. Wang, posted 06-09-2020 3:21 PM PaulK has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 333 of 452 (877260)
06-09-2020 3:34 PM
Reply to: Message 332 by Richard L. Wang
06-09-2020 3:21 PM


Re: Re-PaulK(328): bioinformatic laws
quote:
Essentially all you have is assertions without any actual evidence. Well, one of my assertion is that Physics cannot calculate numbers.
If the mind is supervenient on the operations of the physical brain then any calculations it performs are ultimately being performed by physics. As I have said before this is a contentious issue which cannot be shown to be true or false at present.
quote:
why don’t you guys try to explain Translate genetic information AAA on mRNA to amino acid information Lys to make protein? WATER in English is translated to EAU in French, or vice versa?
Why do you waste time with these. For the first the actual prices of translation is chemical as I have said, and the origins are not available to us, or should we expect them to be. The second concerns the mind and I have repeatedly given my reasons for avoiding that topic.
The real question is why you repeatedly keep talking about areas where we are ignorant - and where you cannot prove your point because of that ignorance.
quote:
Bioinformatic laws. Of course. The Genetic Code is the bioinformatic law of translation process. There is always regulation for bioinformatic process. The following is the content of Chapter 16: Gene Expression of the textbook, Biology / OpenStax
Chapter 16: Gene Expression
16.1 Regulation of Gene Expression
16.2 Prokaryotic Gene Regulation
16.3 Eukaryotic Epigenetic Gene Regulation
16.4 Eukaryotic Transcription Gene Regulation
16.5 Eukaryotic Post-transcriptional Gene Regulation
16.6 Eukaryotic Translational and Post-translational Gene Regulation
16.7 Cancer and Gene Regulation
There are no such regulations in chemistry, because chemical processes involve only matter, not information.
Since all of them are based in - very complex - chemistry your assertion is obviously incorrect. It seems that your bioinformatics laws are merely higher level descriptions of physical processes.

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

Replies to this message:
 Message 336 by Richard L. Wang, posted 06-10-2020 4:42 PM PaulK has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 338 of 452 (877278)
06-10-2020 4:50 PM
Reply to: Message 336 by Richard L. Wang
06-10-2020 4:42 PM


Re: Re-PaulK(333): Your statement is against logic
quote:
Your statement is against logic: as I pointed out in what physics can do, what physics cannot, physics cannot calculate numbers, how can any calculations are ultimately being performed by physics?
I would expect a scientist to understand the difference between logic and his personal opinion. It seems that you do not.
quote:
The same is WATER in English is translated to EAU in French, or vice versa: physics and chemistry don’t know languages at all, how physicochemical processes in brain can translate language?
When science discovers how the mind operates we can revisit this question. Until then any answer would be speculative.
And I note that once again you evade the whole issue of genetic information to try to talk about the mind. It’s amazing how often you repeat this tactic, despite the fact that it cannot work.

This message is a reply to:
 Message 336 by Richard L. Wang, posted 06-10-2020 4:42 PM Richard L. Wang has replied

Replies to this message:
 Message 341 by Richard L. Wang, posted 06-11-2020 4:34 PM PaulK has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 339 of 452 (877279)
06-10-2020 4:59 PM
Reply to: Message 337 by Richard L. Wang
06-10-2020 4:48 PM


Re: Re-PaulK(333)&Taq(335): Regulations control bioinformatic processes
quote:
It seems that you know physical processes cannot explain these regulations, so you suggest higher level descriptions of physical processes.
On the contrary, I know that physical processes can and do explain them. However for convenience more abstract explanations are used in this context, since the details are complex. For comparison consider logic circuits - they are typically described in terms of inputs and outputs, not the arrangement of transistors. Or the use of gas pressure rather than listing the motions of individual molecules,
quote:
What does it mean? If you could explore and find the higher level descriptions of physical processes which can explain these regulations, you would win Nobel prize.
The higher level descriptions are those in the textbook you cited. Repeating those won’t win me a Nobel.

This message is a reply to:
 Message 337 by Richard L. Wang, posted 06-10-2020 4:48 PM Richard L. Wang has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 343 of 452 (877310)
06-11-2020 4:43 PM
Reply to: Message 341 by Richard L. Wang
06-11-2020 4:34 PM


Re: Re-PaulK(338): Logic is a powerful tool in science
quote:
For the translation between English and French, there must be a table of corresponding vocabulary, such as WATER in English < = > EAU in French. Obviously, this is not a chemical or physical process, but an information process. There is no need to discover the detail of how the mind operates, people can make the judgement.
You seem to be saying that physics can do it, just as physics translates the genetic code. But of course the question was not about the translation, it was the explanation for the differences, which really will involve the mind.

This message is a reply to:
 Message 341 by Richard L. Wang, posted 06-11-2020 4:34 PM Richard L. Wang has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


(1)
Message 344 of 452 (877311)
06-11-2020 4:50 PM
Reply to: Message 342 by Richard L. Wang
06-11-2020 4:36 PM


Re: Re-Taq(340)&PaulK(339): regulations refer to rules and implementation
quote:
If all bioinformatic processes could be broken down into a series of chemical and physical processes, people would never know how the basic principle of genetic processes — to produce the right protein at the right time, right place and right quantity — works.
On the contrary, that is the only way to fully understand how it works. And yes, it can be broken down in that way. However there are contexts where the details of how it works is of little relevance and a high-level view of what happens is far more useful.
quote:
It you have time, you can read p.103 — p.108 of my book Darwinian-Naturalism is Pseudoscience: Science Studies What God Created. In that section, I analyzed the transcription regulation of lac operon of E. coli, and demonstrated that the function of regulation is similar to logic circuits in digital circuits, or similar to IF sentences in software.
I have reasons for not paying money for your book. And really a similarity at the level of high level descriptions hardly seems relevant. It still boils down to chemistry.

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

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 348 of 452 (877326)
06-12-2020 4:02 PM
Reply to: Message 347 by Richard L. Wang
06-12-2020 3:55 PM


Re: Re-PaulK/Taq/AZPaul3: let's change a topic
Eighty messages in which you have produced no real evidence of bioinformatic processes violating natural law. So what do you expect? That we should just accept your opinion? That certainly isn’t how it works in science.
But yes, let’s discuss how mutations change and add information, since that would be an actually relevant discussion.

This message is a reply to:
 Message 347 by Richard L. Wang, posted 06-12-2020 3:55 PM Richard L. Wang has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 351 of 452 (877339)
06-13-2020 9:26 AM
Reply to: Message 347 by Richard L. Wang
06-12-2020 3:55 PM


Mutations can add information
In the context of reproductive biology, the information in a DNA molecule is entirely determined by the sequence of bases. Thus, changes to the information - including additions - must be changes to that sequence.
Mutations do change that sequence, adding to it, removing from it, changing bases and even swapping one part of the sequence to another.
Creationists have tried to argue that mutations cannot add information, but those arguments generally founder on the lack of a suitable measure of information. Typically no measure is given, but even when one is showing that it is relevant and actually applying it properly are serious difficulties.
I believe, however, that there are two arguments which make a case that mutation can add information.
The first relies on the simple fact that point mutations - the replacement of one base with another - are reversible - any change made by one such mutation can be done by another. Unless we assume that all sequences of a given length have the same amount of information then point mutations can change the information content - and if any mutation causes a loss the reverse mutation must cause a gain of information.
The second relies on multiple mutations. The addition of a new, distinct gene to a genome - differing from the other genes, at least slightly - is surely a gain of information. Certainly it is if the protein that the gene codes for is produced and is useful to the organism. Mutation can and does do this, although it takes multiple steps. First an existing gene is duplicated, then - in some cases - subsequent mutations change one of the copies, making it distinct. With the aid of selection that version can become adapted to a particular use - which may or may not have been served by the original gene. For instance a gene involved in blood clotting could evolve to produce a venom. This is called duplication and diversification
While these arguments as I have presented them fall short of proof they still represent a very good reason to think that mutations can add information. Unless they can be overcome it is not at all reasonable to insist that mutations cannot add information.

This message is a reply to:
 Message 347 by Richard L. Wang, posted 06-12-2020 3:55 PM Richard L. Wang has replied

Replies to this message:
 Message 352 by Kleinman, posted 06-13-2020 10:38 AM PaulK has replied
 Message 360 by Richard L. Wang, posted 06-15-2020 12:37 PM PaulK has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 353 of 452 (877344)
06-13-2020 11:03 AM
Reply to: Message 352 by Kleinman
06-13-2020 10:38 AM


Re: Mutations can add information
quote:
Information like beauty is in the eye of the beholder.
An assertion that does more to undermine Richard Wang’s arguments than mine.

This message is a reply to:
 Message 352 by Kleinman, posted 06-13-2020 10:38 AM Kleinman has replied

Replies to this message:
 Message 354 by Kleinman, posted 06-13-2020 12:07 PM PaulK has replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024