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Does Dna Contain A Code?


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#21 Guest_Calipithecus_*

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Posted 15 April 2005 - 04:20 PM

The sequence in the DNA is what matters...

As I have pointed out repeatedly here, things are not so neatly separable as that. The chemical context of the cell is at least as important.

and it cannot be reduced to chemical or phsyical law.

No more (and no less) than a forest, a hurricane, or a strip of beach -- but on the other hand, neither is it necessary to postulate the violation of any known physical law in order to explain these phenomena.

...the genetic code has the characteristics of proper code...

So it has been asserted.

The basis for this assertion is: "necessary and sufficient conditions". This logical method may be traced to Plato, who believed that things have 'essences', and that it is possible to specify the necessary and sufficient conditions for membership in the class of things denoted by any concept. This basic idea of Plato’s had a profound effect on Western thought; it led people to think we could, just by thinking, say exactly what goodness or beauty or philosophy (or code) is.

Ludwig Wittgenstein revolutionized Western philosophy by arguing that this underlying idea is wrong. He points out that most concepts are open: i.e., that we define concepts in terms of paradigms, and argue that a particular thing either is or is not a member of the class in question on the basis of resemblance or lack of resemblance of the thing in question to the paradigm.

Even if we agreed to use Plato's "necessary and sufficient conditions", who gets to decide what those are? And who gets to determine when they have been met? How can they possibly hope to be met if critical terms remain undefined? It has been proposed that among the N&S conditions for 'code' is that: "A uniquely defined set of symbols is used". In an earlier response to that, I pointed out that the challenge of showing how biological systems utilize symbols (or even defining that term in a non-circular way) has yet to be met. I don't think defining 'code' as: "something which uses symbols", and 'symbols' as: "something used in a code" is going to get it.

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Posted 15 April 2005 - 07:18 PM

I think Fred's post pretty much summed it up, and left little else to be said.

Terry

#23 Guest_Calipithecus_*

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Posted 15 April 2005 - 11:52 PM

This is marvelously, stupendously wrong, and I can't tell you how many places I have encountered this misconception. I believe it originates with the metaphor of DNA as: "the blueprint for life". What this overlooks is that the 'information content' -- a property of the system as a whole -- resides as much with the chemical context of the cell as with the DNA itself.


Does anyone understand this rebuttal to Yockey? It makes no sense!


I'm happy to try to clarify, but I can't guarantee that it will lead to better understanding (only a certain dedication to the study of cellular biology can guarantee that).

The popular metaphor of DNA as "the blueprint for life" is misleading because the notion it invokes -- that of the DNA as a complete set of instructions, "independent of its environment" -- simply couldn't be more wrong. In truth, it is more like a 'list of ingredients'. The nucleotide sequences are primarily protein templates. Inside the nucleus of a cell is a complete set of all the protein templates that cell needs -- as well as those needed by every other cell in the organism. This arrangement isn't as inefficient as it sounds, because many of the same proteins are used in common by different cells. In fact, many of the same proteins are used in common by different organisms -- this is why we see so much similarity in such large portions of the genomes of different organisms; why human DNA has more than 98% in common with that of a chimpanzee, and maybe 60% in common with a banana. By way of analogy, the list of English words used to produce "Catcher In The Rye" is very nearly the same as that used to produce "David Copperfield".

The difference between (say) a human and a chimpanzee then appears to have rather more to do with differences in the ways the proteins are assembled than with differences in the proteins themselves. Notably absent in the DNA, however, are any explicit instructions for how the proteins should be assembled. These instructions aren't explicitly specified anywhere; the 'choice' as to what protein to make and when to make it emerges as an implicit feature of the chemical context of the cell. It is the cell itself, and not the DNA, that directly performs the critical regulation of gene transcription by either blocking or making accessible the promotor regions of various genes.

Just how important this context is can be appreciated by considering how sensitive the process of embryonic development is to certain chemical toxins. Far from being "independent of its environment", the path of cell differentiation can be sent tragically astray by exposure to even small amounts of certain chemical compounds at certain stages of development. This is why expectant mothers are so strongly cautioned against smoking, drug use, etc.

Hope that helps.

#24 Guest_92g_*

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Posted 16 April 2005 - 03:06 AM

It is the cell itself, and not the DNA, that directly performs the critical regulation of gene transcription by either blocking or making accessible the promotor regions of various genes.


This goes back to the place where say a computer is a "dumb and blind" process, the same as a cell. In essence, the problem with this argument can be seen right there. You know that one of these systems has encoded information in it, and that information has a mental origin. Hypothetically, the other system is unknown, but both have the very similiar operational mechanistic characteristics. Consequently, expounding on the operational mechanistic viewpoint has nothing to do with the informational viewpoint, since Information and Matter are different things.

Sure, a binary executable file has little to no use outside of the context it can be processed in, i.e. the given microcontroller that it was compiled for. That's all your argument boils down to, and has no bearing on its information content, the source of that information, and the characteristics of the code that is used to store the information.

None of this does anything to dispute the fact that DNA stores coded information, that is used by the cell.

Terry

#25 Guest_92g_*

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Posted 16 April 2005 - 03:27 AM

So it has been asserted.


So it has been observed. If drawing conclusions from observed reality is circular logic, then drawing dogmatic conclusions from materialistic biased inferential scientific claims can hardly be considered rational thinking.

The funny thing about this is that your side acts as if the concept of DNA having a code, and containing information is somekind of creationist ploy. As Fred pointed out, this concept is widley held in the scientific comunity.

Even if we agreed to use Plato's "necessary and sufficient conditions", who gets to decide what those are? And who gets to determine when they have been met? How can they possibly hope to be met if critical terms remain undefined?


Well, write a book like Dr. Gitt, and lets see how far you get. This is always an issue in science. At some point it boils down to philosophical viewpoints. Part of this argument is that materialistic bias seeks to limit discussion to materialistic philosophy. Materialistic philosophy is altogether at add odds with observed reality concerning information.

It has been proposed that among the N&S conditions for 'code' is that: "A uniquely defined set of symbols is used". In an earlier response to that, I pointed out that the challenge of showing how biological systems utilize symbols (or even defining that term in a non-circular way) has yet to be met. I don't think defining 'code' as: "something which uses symbols", and 'symbols' as: "something used in a code" is going to get it.


Nowhere has anyone said that all symbols can constitute a code, only that a code system requires symbols, is necessary to store information, and that all codes for storing information require a mental origin.

Terry

#26 Modulous

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Posted 16 April 2005 - 04:55 AM

[list=1]
[*]Easily the most common tactic used by evolutionists is to equivocate on what a code is.

Hardly surprising, since so many creationists use strawman and equivocation to develop proofs. The infamous thermodynamics debate is an example of this. So, before going into a discussion about anything, one must be careful that the definitions used are agreed upon. A code could be defined as something that carries information, then we have to define information. Since there are many different implications in the term information, this gets tricky.

[*]Another fairly common claim is that information science doesn’t apply to genetics. This is somewhat related to #1 but approached from a different angle. This one seems to be fading as I hear it less often, probably because it is become more widely known that there are some prominent evolutionist scientists who apply information science to their study of the genetic code!

Actually I agree that information can apply to genetics. That is how evolution can work. However, a common claim by creationists is to say that if this information is changed somehow, it has lost its meaning, and after enough time its original meaning is completely screwed up. Funnily enough this is what evolutionists have been trying to say all along, but creationists slip in the proviso that information cannot be gained in this manner. And once again, we have to define what information is, to see whether or not it can be gained.


[*]On occasion, deny that information has no mass. If information does not have mass or energy (supposedly the only two fundamental entities in the material universe), where does it come from? Some evolutionists understand the implications of this, and will fight tooth and nail trying to explain how information has mass!!!

Information, the abstract term, has no mass. I think the point here is that information is generally thought of has having some kind of physicality (ie, it must manifest itself somehow, DNA or ink etc)

[*]There are evolutionists who admit that the genetic code indeed meets the criteria for a code, but they simply ignore the implications. Yockey is a good example!

You see, the implications depend on how you make your definitions. It strongly ties in with the definition of information.


[*]There are evolutionists who admit that the genetic code indeed meets the criteria for a code, and also acknowledge the implications that a sender is required. So they invent a sender. The current paradigm is panspermia, promoted by Crick, Holye, and others.

So the implication of a code is that a sender is required? This is once again, where our definitions are important and must be straightened out before discussion can begin. At which point does a code require a sender? And at what point does that sender have to be some kind of intelligent being? Why can the sender not just be a natural occurance? And even if the sender was an intelligent being? Which intelligent being? And why? And how does having an intelligent sender of this code pose a problem for evolutionary theory anyway? In fact - if there is a code, and it was sent by an intelligent being of some kind for some purpose, and the code has become corrupted over time, wouldn't it be a good idea to try and work our way backwards and try and work out what the code was in the first place? Isn't that exactly what evolutionary theory is trying to do? Trace the code back to its roots? Explain possible mechanisms that led to this code getting mangled?

#27 Modulous

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Posted 16 April 2005 - 05:23 AM

OK, if we look up information we can see where this equivocation comes from:

Information is a message, something to be communicated from the sender to the receiver, as opposed to noise, which is something that inhibits the flow of communication or creates misunderstanding.


This is the defintion of information that Information Theory focuses on. So when we look at DNA, we have to decide 'Is this a message'? Creationists say it is, naturalists generally think otherwise (unless they go for xenogenesis).

Information is any represented pattern. This view assumes neither accuracy nor directly communicating parties, but instead assumes a separation between an object and its representation, as well as the involvement of someone capable of understanding this relationship.


This is the definition that naturalists sometimes drive towards...though it isn't really what they mean.

As a more physically scientific definition, information is possibly a property in physics. This is demonstrated by the phenomena in quantum entanglement where information itself cannot travel faster than light, even if the information is transmitted indirectly. This could lead to the fact that all attempts at physically observing a particle with an "entangled" relationship to each other could slow down, even though they are not connected in any other way other than information.


Now, this is where the evolutionists that claim information might be tangible after all are seemingly coming from.

Information is any type of sensory input. When an organism with a nervous system receives an input, it transforms the input into an electrical signal. This is regarded information by some. The idea of representation is still relevant, but in a slightly different manner. That is, while abstract painting does not represent anything concretely, when the viewer sees the painting, it is nevertheless transformed into electrical signals that create a representation of the painting. Defined this way, information does not have to be related to truth, communication, or representation of an object.


Not a definition we need concern ourselves with overly in this debate.

Information is any type of pattern that influences the formation or transformation of other patterns. In this sense, there is no need for a conscious mind to perceive, much less appreciate, the pattern. Consider, for example, DNA. The sequence of nucleotides is a pattern that influences the formation and development of an organism without any need for a conscious mind. Systems theory at times seems to refer to information in this sense, assuming information does not necessarily involve any conscious mind, and patterns circulating (due to feedback) in the system can be called information. In other words, it can be said that information in this sense is something potentially perceived as representation, though not created or presented for that purpose.


And there we have it. This is the ultimate definition of information that naturalists use when talking about DNA. It is a pattern that influences the formation or transformation of other patterns.

So that is why the equivocation exists: there are at least five wildly varying definitions, with wildly varying implications. Creationists choose the first one, and all its implications. Evolutionists choose the fifth one, with its implications. The two parties can never seem to agree on an answer, because if they do, their argument falls down.


Definitions ganked from answers.com

#28 Guest_Paul C. Anagnostopoulos_*

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Posted 16 April 2005 - 07:55 AM

DNA contains information. Whether we call it a code or not depends on our definition of code. But it doesn't matter. Information can arise from random sequences of DNA, as Tom Schneider has shown with Ev.

DNA is not a blueprint. It is not a map of the location of the components of the organism. DNA is more like a recipe.

~~ Paul

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Posted 16 April 2005 - 10:03 AM

OK, if we look up information we can see where this equivocation comes from:


This thread is not about information, that's a seperate issue. Its about whether or not a coding system is employed in DNA to store information.

Terry

#30 Modulous

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Posted 16 April 2005 - 10:34 AM

This thread is not about information, that's a seperate issue. Its about whether or not a coding system is employed in DNA to store information.

Terry

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Agreed fully. So before we know whether a DNA contains a code to store information. That is to say, a code implies information. Unfortunately we need to know - does DNA store information? Is that information in the form of a code?

So first, does DNA store information? My answer: Yes, for certain definitions of information.

Is it in the form of a code: No. The pattern we observe (ACGT) is the information...not a coded form of some information.

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Posted 16 April 2005 - 02:15 PM

This goes back to the place where say a computer is a "dumb and blind" process, the same as a cell. In essence, the problem with this argument can be seen right there. You know that one of these systems has encoded information in it, and that information has a mental origin.

As I have pointed out before, the machine does not work with 'encoded information'; only humans do that. The electrical impulses which are the operating of the computer are not encoded.

Sure, a binary executable file has little to no use outside of the context it can be processed in, i.e. the given microcontroller that it was compiled for.

.
I'm glad we agree on that. Would you be willing to go so far as to agree that a binary executable file has little to no meaning outside of the context it can be processed in?

That's all your argument boils down to, and has no bearing on its information content, the source of that information, and the characteristics of the code that is used to store the information.

Before I respond to that, maybe we should review whether or not 'information' is a separate issue to the topic of this thread.

#32 Guest_92g_*

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Posted 17 April 2005 - 04:20 AM

As I have pointed out before, the machine does not work with 'encoded information'; only humans do that. The electrical impulses which are the operating of the computer are not encoded.


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. Likewise, the codons, encoded as A,G,C, & T's, in DNA, direct the chemical processes in the cell.

Terry

#33 Guest_92g_*

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Posted 17 April 2005 - 04:29 AM

I'm glad we agree on that. Would you be willing to go so far as to agree that a binary executable file has little to no meaning outside of the context it can be processed in?


1st its irrelavent if it doesn't have meaning, functional or otherwise, outside of its usable context. It still has meaning, but I don't want to go too fat down that here.

It may, or may not have meaining as far as any other machine is concerned. But, it could be reverse compiled, and if one understands the coding sytem used, the whole original high level language can be recovered. Why? Because it had a mental origin to begin with, and was implemented based on a coding system as set forth by Dr. Gitt:

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.


Code Properties

IMO, if it were not for these propeties, we would not be able to decode DNA, and understand how it works.

That's the stage at which we are in with DNA. We are essentially reverse engineering the software of life. The only reason this is possible is because it had a mental origin to begin with.

Terry

#34 Guest_92g_*

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Posted 17 April 2005 - 04:41 AM

Is it in the form of a code: No. The pattern we observe (ACGT) is the information...not a coded form of some information.


That's like saying that the alphabet is information, and not a coding system for storing information.

If you want to understand this, I suggest you 1st read this article, How information works and then buy the book "In the Beginnin was Information". Otherwise there is not much point in discussing this further.

Terry

#35 Guest_Paul C. Anagnostopoulos_*

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Posted 17 April 2005 - 06:24 AM

IMO, if it were not for these propeties, we would not be able to decode DNA, and understand how it works.

That's the stage at which we are in with DNA. We are essentially reverse engineering the software of life. The only reason this is possible is because it had a mental origin to begin with.

We are figuring out how everything else in nature works, too. Is that only possible because it is all encoded?

We cannot really "decode DNA" and understand how it works. We can sequence some DNA and then derive the corresponding amino acid sequence from it, but that would not tell us what the resulting protein does, because:

(a) Lots of work is done to the mRNA transcribed from the DNA, before it is used to translate.

(b ) The sequence of amino acids in the final protein doesn't tell us much until we figure out how it folds and where it binds.

Both (a) and (b ) are a matter of chemistry, not coding.

I agree with you that DNA is encoded. But anything that behaves with regularity is encoded, or else its behavior would be random and not regular. You can defined "code" to rule out those other things and only include DNA, but that is really just a rigging of the definition. In particular, I see no reason to conclude that your rigged definition necessitates a mental process. Where do you get that from?

Theorem 6: Once the code has been freely defined by convention, this definition must be strictly observed thereafter.

It's not strictly observed. There are many exceptions to the DNA <-> amino acid correspondence.

~~ Paul

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Posted 17 April 2005 - 06:36 AM

It's not strictly observed. There are many exceptions to the DNA <-> amino acid correspondence.


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

Terry

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Posted 17 April 2005 - 07:23 AM

Both (a) and (b ) are a matter of chemistry, not coding.


There is no doubt that at some point the information stored in a system is carried out by physical or chemical processes. The choice of how to store information is obviously a matter of the characteristics of the physical system that uses it.

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.

I agree with you that DNA is encoded. But anything that behaves with regularity is encoded, or else its behavior would be random and not regular. You can defined "code" to rule out those other things and only include DNA, but that is really just a rigging of the definition.


The definition of a code comes from what we naturally observe when the storage and retreival of information is involved. That will necessarily rule things out that don't serve that purpose.

Things that behave regularly do not necessarily meet those criteria.

In particular, I see no reason to conclude that your rigged definition necessitates a mental process. Where do you get that from?


You asked for a definition, and I gave you Dr. Gitts. Claiming that its rigged is not much of a counter. If anyone was to try and state what a code was, without the knowledge of DNA, then they could probably not come up with a better definition. 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.

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.

Terry

#38 Modulous

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Posted 17 April 2005 - 07:28 AM

That's like saying that the alphabet is information, and not a coding system for storing information.

If you want to understand this, I suggest you 1st read this article,  How information works and then buy the book "In the Beginnin was Information".  Otherwise there is not much point in discussing this further.

Terry



Actually its not. The Alphabet, is a completely intangible thing. You can never, ever, ever demonstrate a physical letter A to me. However, whilst I am incapable of showing you adenine I'm sure you do not dispute its existance.

So, to continue the analogy for a moment. CAT refers to a feline animal (amongst other things). Now, neither C nor A nor T nor CA nor CT nor AT nor CAT have any physical association with any animal of any kind. A cat is something I can stroke. The word cat, is totally abstract from the thing it is describing.

Now, can you say the same for amino acids? Can you say that the letter 'C' to the animal 'Cat' is the same level of abstraction as the chemical cytosine is to an amino acid?


However, I remind you to look at my previous definition of information
Information is any type of pattern that influences the formation or transformation of other patterns. In this sense, there is no need for a conscious mind to perceive, much less appreciate, the pattern. Consider, for example, DNA. The sequence of nucleotides is a pattern that influences the formation and development of an organism without any need for a conscious mind.

Thus, DNA is information is in own right.

Now about the book. Can you recommend a book on the same theme, that isn't written by someone with an agenda? I don't trust the website you cite, since I know for a fact that they wrong in other aspects.

Now, given that I cannot agree to the Creationist's Second Law of Thermodynamics, why do you think I'm going to agree to the Creationist's Information Theory?

#39 Modulous

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Posted 17 April 2005 - 07:38 AM

Now, I agree, that for some definitions of code, that DNA can be thought of as a code. However - code is very tightly connected to the word 'communication'. If we need to think of DNA as a code for any progress to be made in the debate then that is fine, I will. With one point: until some communication is demonstrated to be taking place I do not define DNA as a communications related code.

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Posted 17 April 2005 - 08:07 AM

Now about the book. Can you recommend a book on the same theme, that isn't written by someone with an agenda? I don't trust the website you cite, since I know for a fact that they wrong in other aspects.


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.

This thread is the outcome of another thread where information as defined by Dr. Gitt is being debated. One of the key aspects of that is whether or not DNA contains a code, and what a code is.

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.

...why do you think I'm going to agree to the Creationist's Information Theory?


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.

I recommended the book, and article so that you would have a frame of reference for the discussion.

Terry




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