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Author Topic:   coded information in DNA
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.3


Message 106 of 334 (510696)
06-02-2009 3:51 PM
Reply to: Message 105 by Stile
06-02-2009 3:14 PM


Re: Communication Mediums - Talk with dead DNA!
Well, if you've learned a tiny, little bit about DNA you'll have learnt that it codes for proteins with arbitary codons which are translated into amino acids to make a protein. Creationists are usually pretty simplistic in their understanding of Biology so I'm guessing that's as far as they got. If you think that's all there is to DNA then you've got a code for a sequence of amino acids to make a protein that you could represent in any form you like and still have it work* so if DNA was as simple as that then it would meet WordAsLogos's notion of a code.
So, like most Creationism, you begin with a sloppy version of a scientific fact, stir it up with some dubious quotes and season with some questionable logic and there you go: proof evolution didn't happenGod created the universe in six days.
* - and, thinking about it, this is actually done with synthetic polypeptides.

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Replies to this message:
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Taq
Member
Posts: 10033
Joined: 03-06-2009
Member Rating: 5.3


Message 107 of 334 (510699)
06-02-2009 5:50 PM
Reply to: Message 106 by Dr Jack
06-02-2009 3:51 PM


Re: Communication Mediums - Talk with dead DNA!
Mr Jack writes:
Creationists are usually pretty simplistic in their understanding of Biology so I'm guessing that's as far as they got.
Indeed.
Another fact worth mentioning is DNA tertiary structure as it relates to DNA binding. A good example is the Arabinose operon. In this example two proteins bind to the DNA creating a loop in the DNA. This tertiary shape blocks access to the promoter.
What happens when you fold a page of code? Nothing.

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WordBeLogos
Member (Idle past 5413 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 108 of 334 (510700)
06-02-2009 6:37 PM


Gentlemen,
First off, I would like to take most of the blaim here for being unable to make myself as clear as need be. It's obvious that we are all describing different codes. In order to make sure we are on the same page, I would like to start from the beginning and try to shed more light on how code is being defined here.
*Note* - this is in reference to Mr. Marshalls current material.
Code = a communication between an encoder a writer / speaker" and a decoder a reader / listener using agreed upon symbols.
Using Claude Shannon’s model, which is THE definitive model of engineering communication theory. And we are going to narrow down this definition to digital communication using symbols. Shannon’s approach is the simplest available structure for defining digital communication. Note that Shannon’s paper was written in 1948, a decade before DNA was discovered.
pmarshall writes:
This definition is Shannon’s, and Shannon’s accurately describes all communication systems. Years after Shannon wrote his paper, we also discovered that DNA matches his model 100%. Shannon’s definition has been working just fine for 61 years.
All definitions are restrictive, otherwise we couldn’t have meaningful communication about anything at all.
There are no contradictions. DNA fits Shannon’s model. As does everything on the Internet, and human languages.
Snowflakes, rocks, volcanos and hurricanes do not fit Shannon’s model.
AM radio does not fit this definition because it's analog. We are going to use digital comunication instead of analog because digital is completely black and white, and totally unambiguous. By using black and white, 1 and 0, a specific definition of information, we are able to put our finger on the distinct difference between information and non information. In defining things we want to use terms that allow us to make important distinctions between seemingly similar things.
In this discussion "information" and "code" are interchangable terms being as obvious as "all bachelors are unmarried."
In Shannon’s model there is a encoder that sends a digital message that is decoded by a decoder using agreed upon symbols. When this process is complete with all three parts, we have digital communication. This definition makes a clear distinction between things that are communication systems and things that are not.
According to Shannon’s model, in oder for communication to take place, a encoder, decoder and a transmitted code must be in place. We can look at any system and see if it has an encoder, decoder and a message or not. DNA is a communication system. Pebbles and gravity etc., are not. The definitions are black and white.
For ease, I'll post pmarshall here if that's ok, this part is in reply to a question way down in the middle of a page...
pmarshall writes:
If you press the button on your garage door opener and the garage door opens, this happens because a code has been successfully transmitted and received.
The opening of the garage door is real.
Therefore the information that was passed between the transmitter and the receiver was also real.
Communication is real. It’s physically measurable.
Communication systems are real. They are also physically measurable.
We can make a judgment as to whether the code was successfully transmitted and received. If you push the button and the garage door doesn’t open, then transmission was unsuccessful.
It could be unsuccessful because the battery was dead. It could be unsuccessful because the I set the DIP switches wrong in the transmitter and it was transmitting the wrong code or using the wrong frequency.
It could be unsuccessful because you were too far away or because there was interference from electrical noise.
In any case there is an implicit definition of success or failure based on the INTENT of the code - and the intended consequences of pushing the button. The fact that the right transmitter is supposed to open my garage (notice the teleology here) and that all other transmitters in the neighborhood are not supposed to open my garage door.
We can describe this in terms of the OSI 7-layer model - physical layer, data link layer, transport layer, application layer, etc.
In the garage example there are only a few of layers in use. There’s the radio transmission (physical layer), and there is a code that is transmitted (transport layer). Then there is the application layer, which is the command to open the garage door (i.e. pushing the button).
In any communication system, there is ALWAYS at least one additional implied layer, on top of the ones that are physically present. In this example it’s the INTENT to open the garage; and also the INTENT to build a system that performs this task in the first place. All communication systems imply intent. DNA implies intent to convert GGG triplets to Glycine.
This implied intent is posteriori analytic. We can infer that this system existed as a thought experiment before it existed as a physical system. We make this inference from our observation that the system uses agreed-upon symbols. Symbols are abstract.
In DNA, the tables that map triplets to mRNA to proteins are not physical but the tables describe ideas that accurately describe the rules of a real coding system.
I think you are trying to ask the question, are symbols real? Are the rules of a communication system real?
(BTW I recognize the distinction between a physical object and the labels we attach to it. Glycine is a label we attach to a certain amino acid. As the Neuro Linguistic Programming people say, the territory is not the map.)
The rules of a communication system are not physically real. You cannot weigh them on a scale.
However the fact that we can MEASURE whether the rules were followed or not; whether the symbols were properly decoded or not; proves that they are still real. We could not talk sensibly about them if they were not.
We can measure whether the rules of a communication were followed or not just as accurately as we can measure a tree.
Correct programming of a garage door opener is real because the garage door opens. A measurable event.
Incorrect programming of a garage door opener is real because the garage door does not open. Also a measurable event.
Therefore communication is real; communication systems are real; the information in those systems is real; and the rules that govern them are real.
The fact that these words on this blog have appeared on your screen, properly decoded by your PC and in turn properly decoded by you, is proof of the reality of multiple layers information. And intent. Even on a purely mechanical level, ie your Wi-Fi sending this information to your computer.
Our judgment of proper or improper decoding is not a physical object. But the judgment exists and it is still measurably true or false.
This is proof that Norbert Weiner was right: Information is information, neither matter nor energy.
So information is on solid footing on priori analytic, posteriori synthetic, and posteriori analytic grounds.
This brings us to the priori synthetic - my metaphysical proposition of God.
Communication systems are built using rules that are arbitrary. The choice of 1000001 meaning the letter A in ASCII is arbitrary. The choice of GGG coding for Glycine in DNA is arbitrary.
Neither the rules of ASCII nor the rules of the genetic code can be derived from the laws of physics (Yockey, 2005). The rules of any particular coding system are not properties of pure matter and energy. Rather, these rules organize the movement of matter and energy.
In the OSI model, these rules operate in the upper layers, not at the physical layer. The physical layer simply obeys the instructions of the layers above it.
Since physical laws can never be disobeyed, the rules of codes are fundamentally different from the laws of physics. Why? Because they can fail. The intended outcome can fail to occur. The decoder can fail to properly decode.
The only place that rules of this kind originate, so far as we have ever observed, is from conscious intelligent minds. We have 100% inference from millions of codes supporting this statement and 0% inference to the contrary.
Rocks do not talk. Therefore the rules of communication systems come from consciousness and not from matter or energy.
Information is a separate entity from matter and energy and therefore has a separate source.
Since information exists and does not come from unconscious material sources, it must come from an immaterial conscious source that exists.
Therefore an immaterial conscious source exists, and information has a metaphysical origin.
Therefore God exists.
I have not formally proven this; such a thing is inherently unprovable in the formal mathematical sense. As Gdel said, all knowledge rests on axioms that you know are true but cannot be proven.
I have shown that all human knowledge provides 100% inference to this. Based on current knowledge and the scientific method of induction, we can be just as certain that God exists as we are certain about the laws of thermodynamics.
Gotta run for now guys, hope this sheds more light on how I'am using the terms "code" and "information." Peace.
-Word

Replies to this message:
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 Message 111 by Blue Jay, posted 06-02-2009 8:28 PM WordBeLogos has not replied
 Message 116 by Taq, posted 06-03-2009 12:14 AM WordBeLogos has not replied
 Message 117 by Dr Adequate, posted 06-03-2009 2:00 AM WordBeLogos has not replied
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Percy
Member
Posts: 22479
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.7


Message 109 of 334 (510703)
06-02-2009 7:37 PM
Reply to: Message 108 by WordBeLogos
06-02-2009 6:37 PM


WordBeLogos,
At least when you were passing off other other people's words as your own the mistakes were not as bad, but I'll comment on your errors later. For now I'll just comment on this:
For ease, I'll post pmarshall here if that's ok, this part is in reply to a question way down in the middle of a page...
No, it is not okay. It wasn't okay before, and it's still not okay. This is from the Forum Guidelines that I quoted to you just a short while ago:
  1. Avoid lengthy cut-n-pastes. Introduce the point in your own words and provide a link to your source as a reference. If your source is not on-line you may contact the Site Administrator to have it made available on-line.
What is your problem with following a few simple rules? Members are asked to put things in their own words because otherwise we find that some people, like yourself, take advantage and cite arguments they don't understand, as you've just demonstrated by failing to express Perry Marshall's ideas in your own words. You can't even copy his mistakes right.
I'm returning to my TV program, more later.
--Percy

This message is a reply to:
 Message 108 by WordBeLogos, posted 06-02-2009 6:37 PM WordBeLogos has replied

Replies to this message:
 Message 110 by WordBeLogos, posted 06-02-2009 7:52 PM Percy has replied

WordBeLogos
Member (Idle past 5413 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 110 of 334 (510704)
06-02-2009 7:52 PM
Reply to: Message 109 by Percy
06-02-2009 7:37 PM


Percy,
He's the problem. If I provide you a link, to material burried way down in the middle of a page, I doubt anyone will seriously hunt for it, muchless read the complete portion intended. Second, I feel Mr. Marshall articulates his ideas perfect, if I were to use my own words, we are probably going to keep arguing about different meanings of information and codes. This argument is very subtle and nuanced. That's why we keep arguing over what has not been meant, implied or suggested. Can we at least let him speak until we can agree on his definition and the point he's making so we don't continue to sit here and say gravity and pebbles are coded information as is Shannon's comunication model?
-Word
Edited by WordBeLogos, : No reason given.
Edited by WordBeLogos, : No reason given.

This message is a reply to:
 Message 109 by Percy, posted 06-02-2009 7:37 PM Percy has replied

Replies to this message:
 Message 112 by Son, posted 06-02-2009 9:55 PM WordBeLogos has replied
 Message 114 by Percy, posted 06-02-2009 10:18 PM WordBeLogos has not replied

Blue Jay
Member (Idle past 2718 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 111 of 334 (510706)
06-02-2009 8:28 PM
Reply to: Message 108 by WordBeLogos
06-02-2009 6:37 PM


Hi, WordBeLogos.
Welcome to EvC (in case I haven’t done that already)!
I’ve been watching this debate, but the usage of information in the evolution/creation debate confuses the crap out of me, so I always just end up watching from the sidelines.
But, today is going to be different: I thought it prudent to insert a couple comments of my own.
First, you’ve put up a definition that groups DNA with artificial codes. This is fine with me: I’m no expert, so I’ll let you have it.
But, it seems to me that you’re ignoring the complexity of the issue. Definitions, while convenient for discourse, are subject to all kinds of inaccuracies when applied to nature.
For instance, you could define life to include viruses and prions; to exclude viruses and include prions; to exclude prions and include viruses; or to exclude both, depending on the traits that you deem appropriate for defining "life."
But, so what? What have you proven? Nothing really. The real task of a scientist is to show that his or her definition is meaningful in the real world.
To that end, let me present a different system of classifying codes:
While genomics has an encoder, a decoder and a message, thus making it compatible with a grouping based on these characteristics, it is different from other things that you have grouped it with in other ways.
For example, computers, radios and human languages are not inextricably tied to their substrates. You can download information onto a computer, adjust the reception of a radio and interpret several different languages, all without changing the chemical composition of your computer, radio or eardrum.
However, you cannot change the information content of DNA without changing the chemical composition of the DNA. This suggests that the information content of DNA is just a chemical property of the molecule, and not an externally-enforced "message."
This constitutes evidence that DNA is more appropriately grouped with those codes that are simply an expression of the physical and chemical nature of their source---such as gravity and pebbles---than it is with artificial codes.
What is the difference between my system and yours? My system groups things by basal, fundamental characteristics, while yours groups them based on functional, derived characteristics. My system is like grouping people based on their ancestry; yours is like grouping people based on their profession.
Now, which of these two systems do you think is more appropriate for determining the origin of something?
Edited by Bluejay, : No reason given.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 108 by WordBeLogos, posted 06-02-2009 6:37 PM WordBeLogos has not replied

Son
Member (Idle past 3850 days)
Posts: 346
From: France,Paris
Joined: 03-11-2009


Message 112 of 334 (510710)
06-02-2009 9:55 PM
Reply to: Message 110 by WordBeLogos
06-02-2009 7:52 PM


WordBeLogos writes:
Second, I feel Mr. Marshall articulates his ideas perfect
It's funny I used to think the same way when I was copying some author for a French redaction. I always received bad marks from it (because I sucked, not because the teacher saw that I plagiarised). Some years later, I finally understood that the reason I received bad marks was because I didn't understand the author or the subject, that's the reason I couldn't write a good redaction: I couldn't use those authors' texts in the right context. I think that it's maturity that allowed me to see that.
When you grow older and have more experience, you will see that when you really understand a text, you will be able to express it in your own words, there's no such thing as a "perfect way" to express an idea. Depending on the context, there's always a different way to express an idea in order to be better understood. You can either simplify the idea, use analogies or detail the idea more, detail some parts more while simplfying other parts if you want to highlight the parts revelant to the discussion, etc.....
You will notice that other members didn't copy paste their arguments to counter yours, they used their own words because they actually have an understanding of the subject.

This message is a reply to:
 Message 110 by WordBeLogos, posted 06-02-2009 7:52 PM WordBeLogos has replied

Replies to this message:
 Message 113 by WordBeLogos, posted 06-02-2009 10:08 PM Son has replied

WordBeLogos
Member (Idle past 5413 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 113 of 334 (510711)
06-02-2009 10:08 PM
Reply to: Message 112 by Son
06-02-2009 9:55 PM


Hello Son,
Depending on the context, there's always a different way to express an idea in order to be better understood. You can either simplify the idea, use analogies or detail the idea more, detail some parts more while simplfying other parts if you want to highlight the parts revelant to the discussion, etc.....
I agree, some people are just better at it.
Anyway, what say you concerning this discussion?
-Word

This message is a reply to:
 Message 112 by Son, posted 06-02-2009 9:55 PM Son has replied

Replies to this message:
 Message 115 by Son, posted 06-02-2009 10:30 PM WordBeLogos has not replied

Percy
Member
Posts: 22479
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.7


Message 114 of 334 (510713)
06-02-2009 10:18 PM
Reply to: Message 110 by WordBeLogos
06-02-2009 7:52 PM


WordBeLogos writes:
Second, I feel Mr. Marshall articulates his ideas perfect...
Here's the problem - you don't even understand Mr. Marshall's ideas, so in reality you have no idea how well he articulates them. That's why when you try to express them in your own words you only compound his errors. Since you don't understand what Mr. Marshall is saying, you don't understand our rebuttals either, which makes replying to you kind of pointless.
Being able to accurately explain something in your own words is the only way to be sure you understand it. And you should never promote ideas you don't understand, which is what you're doing here.
You've got to stop looking for a way where you can win a debate about something you don't understand. It isn't possible. Why don't you at least read Shannon's Paper so you can discover the magnitude of your errors when you first invoked Shannon, then insisted on definitions that contradict Shannon. In Shannon's time most communication was over analog channels, and he would never have excluded AM radio. He would never have described the terms "information" and "code" as interchangeable.
--Percy
Edited by Percy, : Spelling.
Edited by Percy, : Grammar.

This message is a reply to:
 Message 110 by WordBeLogos, posted 06-02-2009 7:52 PM WordBeLogos has not replied

Son
Member (Idle past 3850 days)
Posts: 346
From: France,Paris
Joined: 03-11-2009


Message 115 of 334 (510714)
06-02-2009 10:30 PM
Reply to: Message 113 by WordBeLogos
06-02-2009 10:08 PM


I feel that the definition of code here seems to obfuscate this discussion more than it helps it. Remember that we are supposed to discuss whether DNA could have originated naturally or not but most of the discussion ended up being about the definition of codes while it should have been a secondary subject.
It would be more meaningful for you to try to rebute the different natural scenarios that could have given rise to DNA. Arguing about codes feels like arguing 100 years ago that humans can only reproduce through sex because it's the only way known at that time. The fact that you've only seen babies born after sex doesn't mean it's the only way.
So even if you were right about DNA being a code and not gravitation and all the stuffs you discussed about, the fact that all the codes you have seen being produced were the results of intelligence wouldn't mean there are no other way of producing codes.
That's why I feel this debate obfucates this discussion more than it helps it and that you should debate the different abiogenesis scenarios proposed instead.
Edited by Son, : No reason given.
Edited by Son, : No reason given.

This message is a reply to:
 Message 113 by WordBeLogos, posted 06-02-2009 10:08 PM WordBeLogos has not replied

Taq
Member
Posts: 10033
Joined: 03-06-2009
Member Rating: 5.3


Message 116 of 334 (510715)
06-03-2009 12:14 AM
Reply to: Message 108 by WordBeLogos
06-02-2009 6:37 PM


WordBeLogos writes:
In Shannon’s model there is a encoder that sends a digital message that is decoded by a decoder using agreed upon symbols. When this process is complete with all three parts, we have digital communication. This definition makes a clear distinction between things that are communication systems and things that are not.
Then please define for us who is the encoder, the decoder, and the symbols that are used in a genetic system, and please show at what point an intelligence is observed as part of the system.

This message is a reply to:
 Message 108 by WordBeLogos, posted 06-02-2009 6:37 PM WordBeLogos has not replied

Dr Adequate
Member (Idle past 305 days)
Posts: 16113
Joined: 07-20-2006


Message 117 of 334 (510721)
06-03-2009 2:00 AM
Reply to: Message 108 by WordBeLogos
06-02-2009 6:37 PM



This message is a reply to:
 Message 108 by WordBeLogos, posted 06-02-2009 6:37 PM WordBeLogos has not replied

Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.3


Message 118 of 334 (510730)
06-03-2009 4:40 AM
Reply to: Message 108 by WordBeLogos
06-02-2009 6:37 PM


Hi WordBeLogos,
For as long as you persist in merely parotting other peoples ideas this discussion is going to go nowhere. Please try to stick to ideas expressed in your own words using arguments and theory that you personally understand.
Anyway, onwards to your new and changed notion of what a code is:
Code = a communication between an encoder a writer / speaker" and a decoder a reader / listener using agreed upon symbols.
Okay. Could you elucidate what the encoder is in DNA? What the decoder is? And how it meets the notion of "agreed upon symbols"?
In this discussion "information" and "code" are interchangable terms being as obvious as "all bachelors are unmarried."
No, no, no, no! You can't do that. Information is a fundamentally different idea to code; especially if you're going to bring Shannon's ideas into it. To see the difference consider the really simple alphabet shifting code (B=A, C=B ... Z=A) - that's the code. Now consider the coded message: bpeft - that message contains information - a different amount of information than the message jogpsnbujpo.

This message is a reply to:
 Message 108 by WordBeLogos, posted 06-02-2009 6:37 PM WordBeLogos has not replied

bluegenes
Member (Idle past 2498 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 119 of 334 (510732)
06-03-2009 5:55 AM
Reply to: Message 108 by WordBeLogos
06-02-2009 6:37 PM


Agreed? By whom?
WordBeLogos writes:
Code = a communication between an encoder a writer / speaker" and a decoder a reader / listener using agreed upon symbols.
Who is the "reader" / "listener" who agrees to the "symbols" in DNA? Your definition excludes all transfers of information that do not have a sentient receiver who can agree to the code. That means that it cannot apply to the chemistry of life.
Try again.

This message is a reply to:
 Message 108 by WordBeLogos, posted 06-02-2009 6:37 PM WordBeLogos has not replied

WordBeLogos
Member (Idle past 5413 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 120 of 334 (510811)
06-03-2009 6:00 PM


Fellas,
Who is the "reader" / "listener" who agrees to the "symbols" in DNA? Your definition excludes all transfers of information that do not have a sentient receiver who can agree to the code. That means that it cannot apply to the chemistry of life.
Try again.
If your computer automatically logs onto Nortons website and downloads antivirus updates, communication takes place, but not between conscious minds. Parts of the machines communicate with other parts, to read and carry out the instructions. Therefore, communication is taking place. It’s just machines communicating via computer languages. By observation, all computer programs, all codes (TCP/IP etc.) and all symbolic communication systems outside the realm of life, (radio, tribal drum beats, thermometers etc) are all ultimately designed by conscious minds.
-Word
Edited by WordBeLogos, : No reason given.

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

Replies to this message:
 Message 121 by Perdition, posted 06-03-2009 6:10 PM WordBeLogos has not replied
 Message 140 by bluegenes, posted 06-04-2009 6:54 AM WordBeLogos has replied
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