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Does Dna Contain A Code?


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#41 Modulous

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Posted 17 April 2005 - 08:38 AM

If agendas are the basis for trust, then most of what people say can't be trusted in this debate.  Are you going to tell me you don't have an agenda?  You believe they are wrong, and I believe they are right about many things, but not all.  That's what the debate is about.  Who's right and who's wrong.

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Good point. However, I wouldn't read a book about genetics written by a white supremist. I would rather read a book about information theory from someone who has no stake in the debate.


Dr. Gitt defines a code system as previously stated in this thread.  There are different definitions of information, and its not purposeful to discuss them all here. 
I believe that the code system used in DNA, and the information stored in DNA, requires a mental origin.  Dr. Gitt has explained this in his book, and I would think that a person who really wants to understand the argument such that he can refute it would read the book, and construct such arguments.  Otherwise, uninformed arguments against the other side's position are like blindly firing randomly directed shots in 3-space, and hopping to hit a target.


That's fair enough. However, I believe it to be the case that Dr Gitt forms his own version of Information Theory, throwing Shannon's out the window, whilst seemingly piggy-backing on it. Information Theory is a fairly hefty subject that seems at first glance counter intuitive (maximum information when disturbance is maximum?? Sounds crazy right?). So it seems Gitt modifies the theory to make it more intuitive.

Now, since I've seen Creationists change mathematical/physical theories before (see Thermodynamics) to suit them, I fail to get to excited about reading through pages and pages of what may well end up being pseudo science.

Of course, I might be wrong, maybe Gitt has just proved an intelligent designer. I am most sceptical about this. I might look into it in a bit more detail as time goes on, but I see nothing contradicting my hypothesis. Maybe I'm wrong, but given the track record of these 'proofs that evolution can't work' I'm not worried just yet.

I'm going to bow out at this point until such time that I can either be bothered to read more about Gitt's claims, from both sides...as well as actually sit down and come to a complete understanding of actual Information Theory.

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Posted 17 April 2005 - 09:57 AM

The computers instructions encoded as "0s" and "1s" direct the operation of the electrical impulses are encoded onto a storage medium, e.g. hard disk or non-volitile RAM.

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I think it's important to understand why this is wrong, because the same mistake applied to biological systems leads to the conclusion that nucleotide bases are 'symbols'.

Computers don't work with "1"s and "0"s.
The processor works with electrical impulses at two different voltages. Storage media have included the use of punched-or-not-punched areas on paper tape or cards, polarity of magnetic particles, and shiny or dull surfaces on plastic disks. In order to grasp the complexity of the computer's function, a conceptual handle is required -- so we chose one of the voltages, or a hole, or a pole, or a dull spot, and call that a "one", and the other voltage, and the no-hole, and the other pole, and the shiny spot we call a "zero".

There is a layer of encoding involved in all this, but it exists between us and the computer. The fact that we call a shiny spot a "zero" doesn't make it a zero. An "adder" doesn't actually add numbers together; it merely directs the pathways of electrical currents -- but if it does so in such a way as to produce results which map perfectly to the results we would obtain by adding two numbers together, we may easily be seduced into thinking that the computer is actually working with numbers.

This may seem like a minor nitpick. Indeed, we may speak of an "angry volcano" with little consequence -- but we commit a serious error if we extend that anthropomorphism to the conclusion that since only sentient agents are capable of anger, our observation that the volcano is angry is evidence that it is sentient (and this very error has had the direst consequences, especially for attractive young virgins living near active volcanos).

#43 Modulous

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Posted 17 April 2005 - 11:27 AM

OK, I sat down and read Gitt's paper and now I understand what he is saying. And I agree with one point. Wouldn't it be wonderful if we could use DNA, or something like it, to store data?

As for the rest, I agree with Chance on this one, its just clever wordplay. He boldly portrays information as needing a code. He defines information in a communications perspective and so the whole thing boils down to "Is there a communication going on here? Well, since communication requires a code, and we have a code, we have communication"

If we define information differently (since there are many different definitions) his whole theory falls down. So, what I'm saying is, I disagree with the premise being "Information implies communication". If it can be proven that it does, we can move ahead.

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Posted 17 April 2005 - 01:16 PM

Given corect cell function, a given codon always produces the same amino-acid.

Give correct structure, a molecule of water is always H2O. You speak as if the codon has some choice and agrees to be consistent.

This is like saying that the process of speech is just an electro-acoustic process, and has nothing to do with the language convention involved.

Where did I say that there is no "convention" with DNA? I agree that DNA is encoded. The question is whether other things are, too.

The only problem for evlutionists, atheists really, is that its observable that DNA has precisely the same characteristics. Consequently, its a logical conclusion that the code system implemented in DNA has a mental origin.

It's a problem for atheists? You mean I have to believe in a deity for this too make sense? Now, how do you come to the conclusion that it has a mental origin? I don't get that part.

I should also add that its funny that you accuse me, Dr. Gitt really, of rigging the definition, when you are trying to do the very same thing.

I'm not trying to rig any definition, because I have not specified a definition. I agree that you can define code so that DNA is encoded and nothing else is. Perhaps that's a good definition, perhaps it's not useful. But it's rigged one way or the other.

~~ Paul

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Posted 17 April 2005 - 04:22 PM

If we define information differently (since there are many different definitions) his whole theory falls down.


The paper only scratches the surface of what he's proposing. His book covers everything in much more detail. Defining information differently does not counter his theory. You have to show where his theories are wrong to counter them.

Terry

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Posted 17 April 2005 - 05:23 PM

There is a layer of encoding involved in all this, but it exists between us and the computer.


That's exacly the point. There was a layer of encoding the data into DNA that allows cells to function. That was obviously not mankind. So then the question becomes who was it?

Some argue that it was an alien, and some argue that it was God. Either way, it had to be an intelligent being since codes require a mental origin, and so does the data that is stored in it. I believe it was between God and the life he created.

Terry

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Posted 17 April 2005 - 06:16 PM

Some argue that it was an alien, and some argue that it was God. Either way, it had to be an intelligent being since codes require a mental origin, and so does the data that is stored in it.

Why?

~~ Paul

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Posted 17 April 2005 - 06:17 PM

Where did I say that there is no "convention" with DNA? I agree that DNA is encoded. The question is whether other things are, too.


It doesn't matter if other things are coded to. You may be able to argue that a code exists in the atomic structure, or whatever it is your suggesting, but I doubt it.

It's a problem for atheists? You mean I have to believe in a deity for this too make sense?


The origin of the gentic code certainly makes more sense from the standpoint of an intelligent source, than it does anything else. Whether that source is a diety or not, is a little bit of a seperate topic, but its certainly what the logical conclusion would seem to be.

Now, how do you come to the conclusion that it has a mental origin? I don't get that part.


Coding systems are not created arbitraliy. They are optimized for thier use. Dr. Gitt has shown that the gentic code is optimal for space storage and redundancy.

In chains of symbols conveying information, the stringing-together of symbols to form words as well as the joining of words to form sentences are subject to specific rules, which, for each language, are based on consciously established conventions. At the syntactical level, we require a supply of symbols (code system) in order to represent the information. Most written languages employ letters; however, an extremely wide range of conventions is in use for various purposes: Morse code, hieroglyphics, semaphore, musical notes, computer codes, genetic codes, figures in the dance of foraging bees, odour symbols in the pheromone languages of insects, and hand movements in sign language.

The field of syntax involves the following questions:

Which symbol combinations are defined characters of the language (code)?

Which symbol combinations are defined words of the particular language (lexicon, spelling)?

How should the words be positioned with respect to one another (sentence formation, word order, style)? How should they be joined together? And how can they be altered within the structure of a sentence (grammar)?


The syntax of a language, therefore, comprises all the rules by which individual elements of language can or must be combined. The syntax of natural languages is of a much more complex structure than that of formalised or artificial languages. Syntactical rules in formalised languages must be complete and unambiguous, since, for example, a compiler has no way of referring back to the programmer’s semantic considerations. At the syntactical level of information, we can formulate several theorems to express empirical principles:

Theorem 4: A code is an absolutely necessary condition for the representation of information.

Theorem 5: The assignment of the symbol set is based on convention and constitutes a mental process.Theorem 6: Once the code has been freely defined by convention, this definition must be strictly observed thereafter.

Theorem 7: The code used must be known both to the transmitter and receiver if the information is to be understood.

Theorem 8: Only those structures that are based on a code can represent information (because of Theorem 4). This is a necessary, but still inadequate, condition for the existence of information.

These theorems already allow fundamental statements to be made at the level of the code. If, for example, a basic code is found in any system, it can be concluded that the system originates from a mental concept.


What a code is


Look at Calipithicus's example. He says the the encoding of data into a computer is a mental process. This is always the case, even with regards to the data encoded into DNA.

I'm not trying to rig any definition, because I have not specified a definition. I agree that you can define code so that DNA is encoded and nothing else is. Perhaps that's a good definition, perhaps it's not useful. But it's rigged one way or the other.


I think this is a good way of looking at it. There are many ways of defining information, and I suppose you could do the same thing with a code. Other definitions do not matter. What matters is whether a given definition is correct, and if so what does it mean.

The coding system implemented in DNA, and used by the cell for life function and procreation has all of the characteristics of any other known code that has a mental origin. There is no reason to assume that the code in DNA is in principle any different.

Terry

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Posted 17 April 2005 - 06:26 PM

Do we agree that if DNA is a code, the correspondence between DNA codons and amino acids should be arbitrary? If it is not arbitrary, but instead has an underlying chemical explanation, then it is less compelling to consider it an intelligently-designed code.

There is some evidence that the correspondence is not arbitrary:

http://64.233.161.10... triplets&hl=en

~~ Paul

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Posted 17 April 2005 - 11:24 PM

There is a layer of encoding involved in all this, but it exists between us and the computer.

That's exacly the point. There was a layer of encoding the data into DNA that allows cells to function.

"There is, in addition to the layer of encoding between the computer and the human, a layer of encoding between the computer and the external storage medium (the disk, tape, whatever) in which the holes or shiny spots or whatever are mapped to electrical impulses -- and, similarly, there is a layer of encoding between the cell and its internal storage medium, the DNA".

(You should have said. In which case I would have said):

"Yes, I see your point, and as much as I hate to admit it, it looks as though you are right, and I am wrong. It does seem reasonable to refer to that mapping as a code. Thanks for helping me see that correctly. I stand by what I said about the ones and zeros, though."

Look at Calipithicus's example. He says the the encoding of data into a computer is a mental process.

I'm not sure where you think I said that, but I won't dispute it. What I take issue with is the practice of making comparisons between that and what happens in a living cell, and presenting the percieved similarities as evidence for intelligent design of biological systems.

#51 Modulous

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Posted 17 April 2005 - 11:39 PM

The origin of the gentic code certainly makes more sense from the standpoint of an intelligent source, than it does anything else. 


Therein lies the problem. What does 'makes sense' mean? I would say it means 'conforms to our notions'. I invite you to look at quantum physics and try to say that 'makes sense', becuase it really goes against the grain of everything we think we know.

You look at the world and you see lots of codes. All of them are man-made. You say 'All codes are from man, except one. In all cases of man-made code, the code has an intelligent source, therefore a natural code fall into the same category'. Unfortunately that's one heck of an assumption. Especially if you consider that, if our ancestors evolved from some other species of ape then all man-made codes are ultimately natural anyway...but that way leads to philosophy and madness.

You are trying to demonstrate that DNA has all the properties of a man-made code, including an intelligent source. Whilst you have had varying levels of success in demonstrating it has most of the properties of a man-made code, you have yet to demonstrate an intelligent source.

To me, making lots of little changes makes a big change. That makes sense to me. However, whilst you accept little changes you cannot accept they add up to big ones. That makes no sense to you, you need to have it demonstrated.

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Posted 18 April 2005 - 02:31 AM

(You should have said. In which case I would have said):

"Yes, I see your point, and as much as I hate to admit it, it looks as though you are right, and I am wrong. It does seem reasonable to refer to that mapping as a code. Thanks for helping me see that correctly. I stand by what I said about the ones and zeros, though."


What I should have said is, "that I think there is a misunderstanding, as I've never meant to imply that a cell, or any other machine that functions with encoded information, has the mental capaicty to interpret symblos".

I'm not sure where you think I said that, but I won't dispute it. What I take issue with is the practice of making comparisons between that and what happens in a living cell, and presenting the percieved similarities as evidence for intelligent design of biological systems.


IMO, unless you can show how a coding sytem can arise by chance in nature from statistical matterialistic processes, all known cases have a mental source behind them, then you have in essence admitted to exactly that.

Terry

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Posted 18 April 2005 - 02:36 AM

Do we agree that if DNA is a code, the correspondence between DNA codons and amino acids should be arbitrary? If it is not arbitrary, but instead has an underlying chemical explanation, then it is less compelling to consider it an intelligently-designed code.


I don't know. If I was smart enough to use chemicals to design living beings and encode the information needed in them to make them work correctly, then I might very well choose codons that had affinities for the amino acids they code for.

Terry

#54 Modulous

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Posted 18 April 2005 - 02:47 AM

IMO, unless you can show how a coding sytem can arise by chance in nature from statistical matterialistic processes, all known cases have a mental source behind them, then you have in essence admitted to exactly that.



So once again it all comes down to abiogenesis? If we can get abiogenesis to occur, creating self replicating inherited things, merely by creating the right conditions and allowing the system to take over, then we have demonstrated that the genetic code is not a message, and there was no sender? Or at least we would have demonstrated that it need not have come about by an intelligent source.

So - to prove there is need for a source, a designer, a sender of some kind, you need to demonstrate that abiogenesis is impossible

To prove there is no need for a source/designer/sender, we need to demonstrate that abiogenesis is possible.

So far, abiogenesis is still considered a possibility - though it is still in the realms of maybes and don't knows.

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Posted 18 April 2005 - 05:20 AM

I don't know. If I was smart enough to use chemicals to design living beings and encode the information needed in them to make them work correctly, then I might very well choose codons that had affinities for the amino acids they code for.

Well, if it's going to be a designed code even when it can be shown to have its origin in chemical affinities, it's more or less unfalsifiable.

Again, I'm at a loss to understand why something that happens to look like a code needs to have been designed by an intelligent agent. The fact that every example of a designed code we have happens to have been designed is not compelling.

So - to prove there is need for a source, a designer, a sender of some kind, you need to demonstrate that abiogenesis is impossible.

Which means you need to do serious scientific research into all possible scenarios for abiogenesis and show them all to be impossible.

This rings a bell. Oh yes, now I remember. This is similar to what Dembski has to do to show that the flagellum could not have evolved. He needs to uncover all possible evolutionary pathways for the flagellum and calculate the probabilities of those pathways, showing that they are all below the probability bound.

It's ironic that IDers have to do real evolution research in order to show that evolution is not the answer. I wonder if they have the stomach for it?

~~ Paul

#56 Method

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Posted 18 April 2005 - 12:59 PM

What I should have said is, "that I think there is a misunderstanding, as I've never meant to imply that a cell, or any other machine that functions with encoded information, has the mental capaicty to interpret symblos".


Then who is interpretting the code?

IMO, unless you can show how a coding sytem can arise by chance in nature from statistical matterialistic processes, all known cases have a mental source behind them, then you have in essence admitted to exactly that.

Terry

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Peptides, nucleotides, and lipids can all form through natural processes. We find amino acids and nucleotides in meteors, for instance. Miller's experiments showed that amino acids can form in very simple chemical reactions that could have taken place on Earth. Your code has been observed to occur naturally.

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Posted 18 April 2005 - 04:30 PM

Then who is interpretting the code?
Peptides, nucleotides, and lipids can all form through natural processes.  We find amino acids and nucleotides in meteors, for instance.  Miller's experiments showed that amino acids can form in very simple chemical reactions that could have taken place on Earth.


Miller's experiments are no help since they lacked chirlality, and most of what they produced were muck.

Your code has been observed to occur naturally.


You keep telling yourself that, and one day, you might just belive it.....

Terry

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Posted 18 April 2005 - 04:31 PM

What I should have said is, "that I think there is a misunderstanding, as I've never meant to imply that a cell, or any other machine that functions with encoded information, has the mental capaicty to interpret symblos".

Then who is interpretting the code?


It isn't interpretation of the code that the ID argument (if I understand it correctly) posits as requiring an intelligence; that process (in either the computer or the cell) can be viewed as completely mechanistic. It is only the origin of the system of encoding/decoding that requires intelligence under ID. The argument reduces to the following syllogism:

1) DNA is a code.
2) All codes are the products of intelligent design.
3) DNA is the product of intelligent design.

Thanks to 92g's patient efforts, I now accept premise one as defensible. Premise two, however still looks pretty dubious:

"The coding system implemented in DNA, and used by the cell for life function and procreation has all of the characteristics of any other known code that has a mental origin. There is no reason to assume that the code in DNA is in principle any different."

I find Gitt's Theorem 5 unconvincing:

"The assignment of the symbol set is based on convention and constitutes a mental process."

Does Gitt make any attempt to support this assertion, or are we expected to accept it at face value?

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Posted 18 April 2005 - 04:42 PM

Well, if it's going to be a designed code even when it can be shown to have its origin in chemical affinities, it's more or less unfalsifiable.


If real time experimentation is ever performed that generates a coding system from completely random process, then the theory would be falsified. Speculation about it falsifies nothing.

There is no reason to believe that will ever happen since random process are devoid of the type of information that life requires.

Again, I'm at a loss to understand why something that happens to look like a code needs to have been designed by an intelligent agent. The fact that every example of a designed code we have happens to have been designed is not compelling.


Its simply becuase coding systems are conceptual things, not material things. A set of symbols means nothing unless someone sits down and makes up the meanings, and how they are going to be implemented in a physical system.

Which means you need to do serious scientific research into all possible scenarios for abiogenesis and show them all to be impossible.


Most of the scientific evidence we have today, e.g. chirality, leads to brick walls for abiogenisis.

Anyway, the purpose of this thread was to discuss if if DNA contains a code. I think there is no doubt that it does.

Terry

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Posted 18 April 2005 - 05:40 PM

If real time experimentation is ever performed that generates a coding system from completely random process, then the theory would be falsified. Speculation about it falsifies nothing.

Of course we're not going to get a coding system from a completely random process. Who said any such thing, except some disingenuous creationists?

Its simply becuase coding systems are conceptual things, not material things. A set of symbols means nothing unless someone sits down and makes up the meanings, and how they are going to be implemented in a physical system.

If this is your definition of code, then DNA is not encoded. Simple.

Tom Schneider's Ev program creates a code from random DNA.

Anyway, the purpose of this thread was to discuss if if DNA contains a code. I think there is no doubt that it does.

There may be no doubt that DNA contains a code, but there is a lot of doubt about what that implies.

To get some interesting papers on the genetic code:

http://www.ncbi.nlm....trez/query.fcgi

and search on 'Landweber LF code'.

~~ Paul




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