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Does Dna Contain A Code?


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#1 Guest_92g_*

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Posted 10 April 2005 - 02:33 PM

I’ll have a read of the link later. But to my way of thinking, a valid code or cipher has ‘hidden’ meaning thus:

If C= p, A = X, T = h, then ‘cat’ would equal pXh if the substitutions relationships were changed on a daily basis, then ‘cat’ could equal ‘dog’.   This way the original language carries information to a receiver, yet the language is still English (garbled English). 
For DNA to qualify as code it would have to do the same, e.g.  DNA string GAT = protein X, will ATG ever produce protein X, ? because if it were a code it should be able to.

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I would like to keep the other thread running along the direction of semantics if possible, but this is still a very important issue.

Here's a link that describes the characteristics of the genetic code. There are a number on the web.

Control processes cannot be understood in detail, if the meaning of information is not completely clear. The exchange of information between individuals (or functional elements) is called communication. Communication is based on the transmission of information that consists of signs. Each sign stands for or speaks of something. An information can therefore be regarded as a sum of signs. Information as such can neither be captured physically nor energetically.

The assignment of an information to a certain physical state is called coding. Each sign carries a meaning and is thus part of a signal. The letters of an alphabet are signs.

Code: The information theory distinguishes between languages that have evolved during historical periods of time and codes that have been developed for special purposes. But in a strictly formal sense, a language is a code, too. Probably the most famous natural code (according to the information theory a language) is the genetic code. The genetic information that is stored in the DNA with a content of four nucleotide signs is used for the production of proteins with a content of 20 amino acids signs.


http://www.biologie..../15b.htm#redund

This is just a web page that I stumbled across.

Terry

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Posted 11 April 2005 - 06:57 AM

This question requires a rigorous definition of the term code. Let's start here:

Define code so that DNA contains a code, whereas the information in a crystal that allows it to replicate more-or-less accurately does not.

Or, agree that both DNA and crystals contain a code.

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#3 Guest_92g_*

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Posted 12 April 2005 - 06:52 PM

This question requires a rigorous definition of the term code. Let's start here:

Define code so that DNA contains a code,


Fair Enough,

From In the Beginning was Information:

Necessary Conditions:
1) A uniquely defined set of symbols is used
2) The sequence of the individual symbols must be irregular
3) The symbols appear in regular structures
4) At least some symbols must occure repeatedly

Sufficient Condition:
It can be decoded succesfully and meaningfully

whereas the information in a crystal that allows it to replicate more-or-less accurately does not.


I don't think crystals meet that criteria.

Terry

#4 OC1

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Posted 12 April 2005 - 09:38 PM

Necessary Conditions:
1) A uniquely defined set of symbols is used


What are the symbols in DNA? Isn't DNA just a bunch of proteins?

If molecules with different shapes in DNA are considered symbols, why aren't the molecular shapes that govern crystal growth not symbols?

#5 Guest_Calipithecus_*

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Posted 13 April 2005 - 12:55 AM

What are the symbols in DNA? Isn't DNA just a bunch of proteins?


No. The protein is the end product. It goes:
DNA=> RNA=> amino acid=> protein. The nucleotide bases (of which there are four) are transcribed into amino acids (of which there are twenty) which are chained together to form proteins (of which there are an apparently unlimited number).

Biologists refer to the four nucleotide bases by symbols. The symbols they use are the first letters of the chemical names. The names are themselves symbols; "cytosine", for example, isn't a nucleotide; it's just the name of a nucleotide (that's why they call that nucleotide "cytosine").

What is at issue here is whether it is accurate to consider an actual nucleotide to be a 'symbol'. Or perhaps the symbol level is the nucleotide triplet instead. For that matter, we might even consider the amino acid to be the symbol level. The mere fact that biologists utilize symbols to refer to elements in biological systems doesn't automatically justify considering them to be symbols in the biological systems themselves.

So what we would need to determine is: at what point should we consider the 'message' to have been 'recieved', and what component of the system deserves to be considered to be acting as the 'agent' which performs the actual decoding?

'The other thread' contains this quoted suggestion:

"The amount of meaningful information in a string of symbols depends on the amount of matches it has with strings in an established dictionary."

To qualify as a 'code' (in the strong sense insisted on by ID proponents), we would need to find the point in the system where something like this takes place. The closest thing to an 'agent' performing such a decoding is the action of the aminoacly-tRNA synthetase. But close examination reveals that this enzyme does not perform its action by anything remotely resembling the requisite 'dictionary lookup'; it matches a tRNA molecule with an amino acid by 'sniffing' its DHU (dihydrouracil) loop. Details here

The whole thing is an utterly blind, utterly dumb sequence of chemical events. Nowhere is there any 'agent'; there isn't any 'decoding' -- why bother, since no part of the system 'knows' (or needs to know) what the DNA 'means' anyway?

#6 Method

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Posted 13 April 2005 - 09:51 AM

The whole thing is an utterly blind, utterly dumb sequence of chemical events. Nowhere is there any 'agent'; there isn't any 'decoding' -- why bother, since no part of the system 'knows' (or needs to know) what the DNA 'means' anyway?

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Precisely. The process of transcribing RNA and translation into protein is utterly mechanistic. This is completely different than reading a blueprint, where the blueprint must be abstractly translated into ideas that are then transformed into reality. If DNA were equivalent to a building blueprint, then we should be able to throw lumber at the blueprint and watch a building form on it's own.

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Posted 13 April 2005 - 06:38 PM

The nucleotide bases (of which there are four) are transcribed into amino acids (of which there are twenty) which are chained together to form proteins (of which there are an apparently unlimited number).


Its also important to note that the bases use triplets to form the code.

Biologists refer to the four nucleotide bases by symbols. The symbols they use are the first letters of the chemical names. The names are themselves symbols; "cytosine", for example, isn't a nucleotide; it's just the name of a nucleotide (that's why they call that nucleotide "cytosine").


Ok, the letter "A" isn't sound, its just the name of a sound.

What is at issue here is whether it is accurate to consider an actual nucleotide to be a 'symbol'. Or perhaps the symbol level is the nucleotide triplet instead. 


Its true at both of those levels, statistical(the bases, A,G,C,T), the synatical(61 amino acid codons, plus 3 stop codons).

For that matter, we might even consider the amino acid to be the symbol level.


The amino acids are coded for by the information stored in DNA, they are not part of the coding system, but a result of the information stored to use them in creating proteins.

The mere fact that biologists utilize symbols to refer to elements in biological systems doesn't automatically justify considering them to be symbols in the biological systems themselves.


Mere fact... Hubert Yockey, an evolutionist, made some insightful observations about the genetic code:

Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.

The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter or energy. We could, in principle, send the genome of a mosquito to our little green friends on an Earth-like planet somewhere in the Milky Way Galaxy.


Hubert Yockey:Information Theory, Evolution and the Origin of Life
http://www.cambridge...21802938&ss=exc

The whole thing is an utterly blind, utterly dumb sequence of chemical events. Nowhere is there any 'agent'; there isn't any 'decoding' -- why bother, since no part of the system 'knows' (or needs to know) what the DNA 'means' anyway?


The operation of your computer is just a dumb sequence of electrical events. It, like the the living cell, requires information to function. Information has to be stored in a code. There is no doubt that the cell decodes the information stored in DNA. Start codons, stop codons, triplets that abstractly substitute for amino acids, hardly constitute a blind process.

Yockey again:

The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is much larger than the information content of these laws.....

The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.


Terry

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Posted 13 April 2005 - 10:19 PM

"The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment."

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.

The operation of your computer is just a dumb sequence of electrical events.

I wholeheartedly agree.

It, like the the living cell, requires information to function.

But I don't agree with that. Furthermore, I suggest that those two propositions are mutually exclusive under the ID definition of 'information'. I expanded at some length
here.

And this, from the last Yockey quote:

"If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences."

makes absolutely no sense to me. Was he quoting Mayr there? I couldn't quite tell. Maybe you can explain to me what that means.

#9 Modulous

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Posted 14 April 2005 - 03:39 AM

Does this mean, that a single Oxygen atom has a code, since it contains instructions to generate an Oxygen Molecule? Indeed, given the correct circumstance 02 will bond to form other oxides including water. Does that mean, that a single Oxygen atom, which has the instructions inbuilt to create water, has a code within it?

We can look at it, and we can see free electrons, energy states and so on. All of these imply a code, since it uses these to create more complex molecules.

So is DNA a code? In a way yes of course it is. We can certainly think of it that way, but what is the primer? What translates this code? The laws of chemistry/physics. They are just chemical interactions. No single of interaction of chemistry says "OK, this is a stop cordon as laid down by the laws of genetics" rather what happens is an interaction is stopped by a stop cordon. OK, so that is a gross simplification, and is slightly misrepresentative I'm sure - but that's what happens when you use metaphors to describe something.

We can say that the sun will one day expand and shrink. This certainly does imply that there is a 'stellar code' that the sun is following. Actually each molecule is just going about interacting away. One day, the laws of physics just dictate they will react in a certain way.

The laws of physics/chemistry simply dictate that molecules will react a certain way during cell replication, the presence of the DNA simply guarantees us of this. If the DNA was taken out, the molecules would react in a different way, and if the DNA sequence was reordered, they would act another way still.

#10 Method

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Posted 14 April 2005 - 12:10 PM

Does this mean, that a single Oxygen atom has a code, since it contains instructions to generate an Oxygen Molecule? Indeed, given the correct circumstance 02 will bond to form other oxides including water. Does that mean, that a single Oxygen atom, which has the instructions inbuilt to create water, has a code within it?



This has been my long standing argument in these types of discussions. No one has yet shown me the difference between the information contained in the valence electrons of an oxygen atom and the information found in DNA. If they are one in the same it makes this type of information all but meaningless.

On another note, does DNA make protein or do proteins make DNA? It is a common misconception that DNA drives the whole thing, but it can easily be argued that proteins are in charge. After all, it is proteins that replicate DNA.

There is also a distinct difference between computer programs and DNA. It relates heavily to Paley's Blind Watchmaker. Computer programs and code are meant for the sole benefit of the computer user. The purpose of DNA is to copy itself. That is it. Proteins that help DNA survive and promote copying are kept. DNA serves no other purpose besides it's own survival, which is quite different than the purpose of a computer program.

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Posted 14 April 2005 - 01:39 PM

Does this mean, that a single Oxygen atom has a code, since it contains instructions to generate an Oxygen Molecule?


Oxygen atoms do not contrain instructions to create an oygen molecule. Each atom is a physical arrangement of atomic particles that form due to the laws of physics. The arrangemt of the sequence of base pairs in DNA is not subject to physcial law. Its completly arbitrary.

Hubert Yockey sad this to say:

Those readers of this book who are computer-oriented will easily understand that the chemistry of life is controlled by digital sequences recorded in DNA, as Gamow (1954a) was the first to realize. Life is guided by information and inorganic processes are not.


Francis Crick put it this way:

The phosphate-sugar backbone of our model is completely regular, but any sequence of the pairs of bases can fit into the structure. It follows that in a long molecule many different permutations are, possible, and it therefore seems likely that the precise sequence of the bases is the code which carries
the genetical information.
(Watson and Crick, 1953b).


http://www.cambridge...21802938&ss=exc

The sequence of the bases is not in anyway shape fashion or form governed by physical law. The arrangement of inorganic molecules are.

These are necessary and sufficient conditions to establish if a code system for storing information is present.

Necessary Conditions:
1) A uniquely defined set of symbols is used
2) The sequence of the individual symbols must be irregular
3) The symbols appear in regular structures
4) At least some symbols must occure repeatedly

Sufficient Condition:
It can be decoded succesfully and meaningfully.

The genetic code meets these conditions, from what I can tell, inorganic process do not.

Terry

#12 Modulous

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Posted 14 April 2005 - 04:26 PM

An oxygen molecule, of course, does not self-replicate...that would be scary. If we look at how DNA replicates first we see no code being decoded.

C----G
A----T
G----C



It splits itself appart so that we now have

C
A
G

and

G
T
C

And then the relevant counterparts naturally bind with one another. Adenine with thymine or cytosine with guanine. And voila! Something that has the ability to replicate itself without any 'code' needed.

Can this be defined as 'information'? For certain definitions, sure. But its only a code in the sense that we can predict what might happen, by 'decoding'. In the same sense if I drop a ball I can work out what will happen given the relevant pieces of data. In a sense we define it as having some kind of information content, when it really is just a sequence of molecules that react with another.

Think of a fractal. Imagine, if you will a triangle. The triangle is actually a bunch of molecules which are shaped like a triangle. Stored within that triangle is a very peculiar sequence of complex molecules, much like DNA, which can self replicate. Also, under certain conditions (with energy), the 'DNA' does replicate, and that 'DNA' then reacts with other molecules that are present, strangely, to form another triangle.

This instruction set doesn't actually 'exist', its just the way the molecules react with one another. Each time our 'DNA' is replicated chemically, and then chemically goes about making another triangle, which passes its 'DNA' on. Very soon we have a very complicated looking shape with a perimeter length that is increasing every time. Its called a Koch snowflake. Look at it here, if you want to see it in action

http://www.shodor.or...ctivities/koch/


Now, does this DNA, with its string of molecules in it construe a code? As said earlier, it does in the way that we can examine the molecules and predict what they will do under certain circumstances.

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Posted 14 April 2005 - 06:06 PM

And then the relevant counterparts naturally bind with one another. Adenine with thymine or cytosine with guanine. And voila! Something that has the ability to replicate itself without any 'code' needed.

Can this be defined as 'information'?


Your talking about copying the data in the cell to make another cell. That has nothing to do with the process of constructing proteins from the information stored in the code.

I suggest this web site for further explanation.

Information on DNA and Gentic Code

Terry

#14 Modulous

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Posted 15 April 2005 - 05:39 AM

Your talking about copying the data in the cell to make another cell.  That has nothing to do with the process of constructing proteins from the information stored in the code.

I suggest this web site for further explanation.

Information on DNA and Gentic Code

Terry

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That's what I started with, yes...but it's not how I ended.

#15 Modulous

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Posted 15 April 2005 - 06:14 AM

So I was looking at the website you posted. Its all very good and all, but it naturally misses out steps for simplicity.

DNA->RNA->mRNA

mRNA goes into a special structure called a ribosome. It attaches to the ribosome and starts creating protiens. The ribosome creates the protiens based on the makeup of the mRNA.

Stop here for a second. How does the ribosome do this? Well, the required amino acids are transferred to the site by t(ransfer)RNA. This tRNA might be AAA for example. Phenylanine will bind to this tRNA, get taken over to the ribosome and will bind with the mRNA with uracil-uracil-uracill


http://cellbio.utmb....io/ribosome.htm (for more details)

So, what we see is no code translation, or instruction reading...just molecules reacting to one according to the rules of chemistry until a protien is built.

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Posted 15 April 2005 - 12:51 PM

DNA->RNA->mRNA

mRNA goes into a special structure called a ribosome. It attaches to the ribosome and starts creating protiens. The ribosome creates the protiens based on the makeup of the mRNA.

So, what we see is no code translation, or instruction reading...just molecules reacting to one according to the rules of chemistry until a protien is built.

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What your describing is how a biological machine works. There is no doubt that the information needed to create specific proteins is encoded in DNA, and is used by the cell in its processing. The sequence in the DNA is what matters, and it cannot be reduced to chemical or phsyical law.

Skipping over that point, and the fact that the genetic code has the characteristics of proper code, does not make your case.

Terry

#17 Modulous

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Posted 15 April 2005 - 01:31 PM

What your describing is how a biological machine works.


Correct, we call it life.

There is no doubt that the information needed to create specific proteins is encoded in DNA, and is used by the cell in its processing. 


Well, yes and no. It depends how you define information really. If information is just a collection of variables, that will produce predictable results, then yes. For example the planets each have a different mass and distance to the sun. Given this piece of information, and the mass of the sun, we can predict what paths they will follow unless some outside agent does something. So the system contains information, right?

The sequence in the DNA is what matters, and it cannot be reduced to chemical or phsyical law.


I agree that DNA sequence matters any other sequence and different protiens are made in different order, resulting in different things happening.

Skipping over that point, and the fact that the genetic code has the characteristics of proper code, does not make your case.


OK, so lets assume it is a code. Can I confer information to you by sending you a string of DNA? Am I not just telling you which order you should create some protiens in? Is there any meaning to those protiens?

OK, now we have what you might be able to define as possibly being a code of sorts. If we accept that definition, what then?

#18 Modulous

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Posted 15 April 2005 - 03:18 PM

1) A uniquely defined set of symbols is used
2) The sequence of the individual symbols must be irregular
3) The symbols appear in regular structures
4) At least some symbols must occure repeatedly


Now according to this, we might imply that ACG is a code for an amino acid and that ACG TAA AAG could be a code for a protien.

I can use this code to communicate a protien, or even a collection of protiens to someone simply by writing the symbols down on a piece of paper. Can I demonstrate any other naturally occuring code?

1) Set of symbols
1,2,3,4,5,6,7,8,9,0,.

2) An example of irregular sequence:
1.88

3)Regular structures
1.88
39.44


4)Repeated symbol: all of them can be repeated, in this case '.' is repeated.



OK. Now we have a code as defined by the above. Instead of three letters ACG to represent an amino acid I have numbers that represent orbital distances from the sun. I could send this to someone on paper and they could begin to generate a solar system for themselves.


I think we can both agree that our solar system does not contain 'information' can't we? So where does DNA differ?

#19 Fred Williams

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Posted 15 April 2005 - 04:16 PM

I’ve seen evolutionists stumble over the information problem for quite a few years now, employing various methods in an attempt to lessen or remove the problem. Following are the most common evolutionist tactics I’ve observed:
  • Easily the most common tactic used by evolutionists is to equivocate on what a code is. We see it in this thread. A code is extremely easy to define, yet evolutionists will try to get you to spend hours debating it. Essentially it becomes a stall tactic. Once you get them to agree what a code is, they’ll deny the genetic code meets the criteria. This whole equivocation process is extremely prevalent among laymen internet evolutionists. But to be fair, plenty of evolutionist scientists I’ve discussed this with do not resort to this tactic, because frankly it is utterly absurd to deny that the genetic code is not a code! Even Richard Dawkins (at one time at least), who is not an expert in info science, did not employ this tactic. In fact I have never seen evolutionists quote a big name evo scientist who will step to the plate and support their utterly unsupportable view. It is always just their opinion they are sharing with us, with statements that typically make no sense, as is occurring in this thread (examples provided in follow-up post).
  • 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!
  • 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!!!
  • 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!
  • 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.
I submit that all the positions above are not reasonable, some are absolutely absurd (1-3). Number 4 is put your fingers in your ears and go la la la la; number 5 is to take the fingers out and speculate of alien ant farms and other such nonsense. :)

Fred

#20 Fred Williams

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Posted 15 April 2005 - 04:18 PM

Some examples of equivocation in this thread:

Yockey: "The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment."

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! It offers no coherent explanation why Yockey (a very prominent evolutionist physicist) is wrong to conclude the genetic code is a code! The rebuttal tries to lure it’s reader with powerful words “This is marvelously, stupendously wrong”, but only those who want to believe such an empty rebuttal will believe it.

Here’s another funny one:

So, what we see is no code translation, or instruction reading...just molecules reacting to one according to the rules of chemistry until a protien is built.


LOL! Amazing! Everyone, just do a search ‘DNA code translation’ or ‘DNA code synthesis’ and see how many hits you get from evolutionist sites!

It is because of arguments like these that makes it very difficult for me to get involved in information debates on the internet.

OK, one more funny one:

This is completely different than reading a blueprint, where the blueprint must be abstractly translated into ideas that are then transformed into reality. If DNA were equivalent to a building blueprint, then we should be able to throw lumber at the blueprint and watch a building form on it's own.


This is both goofy and a strawman. Not sure which!

Sorry everyone, I realize this is an offensive and flame-inducing post that probably gave some of my moderators heartburn, but this is one of those times I could not resist and realize it is good to be king! :)

Fred




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