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DNA/RNA is a digital code. just like joe said

Mhykiel
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2/27/2015 11:55:43 AM
Posted: 1 year ago
All digital information possesses common properties that distinguish it from analog communications methods:

Synchronization: Since digital information is conveyed by the sequence in which symbols are ordered, all digital schemes have some method for determining the beginning of a sequence. In written or spoken human languages synchronization is typically provided by pauses (spaces), capitalization, and punctuation. Machine communications typically use special synchronization sequences.

http://www.chemguide.co.uk...

The transport RNA is assigned to ONE 1 specific peptide. The 3 chemical arrangement of tRNA will only grab the one peptide. The differences between the tRNA do NOT exclude it from chemically attaching to other peptides. The peptides when made are only crafted with the right tRNA. it is an assignment of a handle. And hence synchronization between the peptide and an abstract representation of it by the tRNA "HANDLE" and I am using handle in the sense of computer language.

Language: All digital communications require a language[disambiguation needed], which in this context consists of all the information that the sender and receiver of the digital communication must both possess, in advance, in order for the communication to be successful. Languages are generally arbitrary and specify the meaning to be assigned to particular symbol sequences, the allowed range of values, methods to be used for synchronization, etc.

Same as above the establishment of representing real peptides by tRNA that is an abstract representation because the tRNA has no physical necessity to be the handle for the peptide. The only necessity comes from the cells established language.

Errors: Disturbances (noise) in analog communications invariably introduce some, generally small deviation or error between the intended and actual communication. Disturbances in a digital communication do not result in errors unless the disturbance is so large as to result in a symbol being misinterpreted as another symbol or disturb the sequence of symbols. It is therefore generally possible to have an entirely error-free digital communication. Further, techniques such as check codes may be used to detect errors and guarantee error-free communications through redundancy or retransmission. Errors in digital communications can take the form of substitution errors in which a symbol is replaced by another symbol, or insertion/deletion errors in which an extra incorrect symbol is inserted into or deleted from a digital message. Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication.

Now you are just copy pasting because it should be obvious how this description of errors in digital information is a perfect match for mutations in genetic code. "Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication."

Copying: Because of the inevitable presence of noise, making many successive copies of an analog communication is infeasible because each generation increases the noise. Because digital communications are generally error-free, copies of copies can be made indefinitely.

Granularity: The digital representation of a continuously variable analog value typically involves a selection of the number of symbols to be assigned to that value. The number of symbols determines the precision or resolution of the resulting datum. The difference between the actual analog value and the digital representation is known as quantization error. For example, if the actual temperature is 23.234456544453 degrees, but if only two digits (23) are assigned to this parameter in a particular digital representation, the quantizing error is: 0.234456544453. This property of digital communication is known as granularity.

tRNA http://www.chemguide.co.uk...

Dead on exact description of tRNA again. The description of Digital Code in information theory for computer systems, cryptography and other systems is a perfect description of the "Genetic CODE"

"involves a selection of the number of symbols to be assigned to that value."

The granularity error can even be calculated of DNA in that each codon is 3 chemicals in length. the Codon is the digital representation of a peptide.

Compressible: According to Miller, "Uncompressed digital data is very large, and in its raw form would actually produce a larger signal (therefore be more difficult to transfer) than analog data. However, digital data can be compressed. Compression reduces the amount of bandwidth space needed to send information.

Why don't you read the description. Feign stupidity you don't know DNA is compressed as a double helical stranded twisted around histone spines.

http://www.biology.emory.edu...

Read the article "...This association is unfavorable to the process of transcription and must be altered in order for the pre-initiation complex to access promoter regions, i.e. in order for transcription to start..."

Compression!!! an exact description for DNA is DIGITAL INFORMATION IN EVERY WAY!

Some say it is not a code and define DNA as the double helix of molecules. This is not a definition that excludes DNA being code. Just like describing a computer program as being a string of 0s and 1s does nothing to dissuade from DNA being a representation of information. Digital an abstract at that. If it was a "mold" or chemically necessary like a crystalline structure the information could be easily concluded to be from a natural process derived purely from physical laws. But that is not what we have.
Burzmali
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2/27/2015 2:28:40 PM
Posted: 1 year ago
At 2/27/2015 11:55:43 AM, Mhykiel wrote:
Granularity: The digital representation of a continuously variable analog value typically involves a selection of the number of symbols to be assigned to that value. The number of symbols determines the precision or resolution of the resulting datum. The difference between the actual analog value and the digital representation is known as quantization error. For example, if the actual temperature is 23.234456544453 degrees, but if only two digits (23) are assigned to this parameter in a particular digital representation, the quantizing error is: 0.234456544453. This property of digital communication is known as granularity.


tRNA http://www.chemguide.co.uk...

Dead on exact description of tRNA again. The description of Digital Code in information theory for computer systems, cryptography and other systems is a perfect description of the "Genetic CODE"

"involves a selection of the number of symbols to be assigned to that value."

The granularity error can even be calculated of DNA in that each codon is 3 chemicals in length. the Codon is the digital representation of a peptide.

How is that quantizing error? You can't just say going from 3 to 1 causes quantizing error because the 3 and 1 aren't data. How is going from AUA to Isoleucine an example of granularity?

Compressible: According to Miller, "Uncompressed digital data is very large, and in its raw form would actually produce a larger signal (therefore be more difficult to transfer) than analog data. However, digital data can be compressed. Compression reduces the amount of bandwidth space needed to send information.

Why don't you read the description. Feign stupidity you don't know DNA is compressed as a double helical stranded twisted around histone spines.

http://www.biology.emory.edu...

Read the article "...This association is unfavorable to the process of transcription and must be altered in order for the pre-initiation complex to access promoter regions, i.e. in order for transcription to start..."

Compression!!! an exact description for DNA is DIGITAL INFORMATION IN EVERY WAY!

That's not digital compression. It's the equivalent of defragging a hard drive or converting between file system schema. Actual compression would involve something like replacing repeating, common segments with shorter substitutes. As you say, this process makes it harder to read, but it also makes it harder to transmit. Compression of digital code makes transmission easier, not harder.
RuvDraba
Posts: 6,033
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2/27/2015 3:17:47 PM
Posted: 1 year ago
In other news:

All spanners are crab claws!
All vices are molars!!
All hammers are goat-horns!
All chisels are woodpecker-bills!
Paper invented by wasps!
Refrigerators invented by termites!
Boats invented by ants!

And yes -- if you squint and tilt your head a bit, all software can be thought of as DNA. In fact, there are people who write software using genetic algorithms, and it turns out it can eventually solve certain problems on its own -- and even evolve beautiful and intricate music (http://game.darwintunes.org...)

You can run such software on your laptop.

But work in genetic computation started as early as 1957. After decades of haughty indifference to science, its processes and products, it seems the religiously aloof are just catching up.

Yet the key insight here is that as with many human inventions, nature did a version of programmatic data replication and transformation first. Even viruses -- proteins on the very edge of life -- can do this.

It's marvelous, but is it miraculous?

Really?

As judged by what standard, beyond that of our own conceit?
Mhykiel
Posts: 5,987
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2/27/2015 7:37:54 PM
Posted: 1 year ago
At 2/27/2015 2:28:40 PM, Burzmali wrote:
At 2/27/2015 11:55:43 AM, Mhykiel wrote:
Granularity: The digital representation of a continuously variable analog value typically involves a selection of the number of symbols to be assigned to that value. The number of symbols determines the precision or resolution of the resulting datum. The difference between the actual analog value and the digital representation is known as quantization error. For example, if the actual temperature is 23.234456544453 degrees, but if only two digits (23) are assigned to this parameter in a particular digital representation, the quantizing error is: 0.234456544453. This property of digital communication is known as granularity.


tRNA http://www.chemguide.co.uk...

Dead on exact description of tRNA again. The description of Digital Code in information theory for computer systems, cryptography and other systems is a perfect description of the "Genetic CODE"

"involves a selection of the number of symbols to be assigned to that value."

The granularity error can even be calculated of DNA in that each codon is 3 chemicals in length. the Codon is the digital representation of a peptide.

How is that quantizing error? You can't just say going from 3 to 1 causes quantizing error because the 3 and 1 aren't data. How is going from AUA to Isoleucine an example of granularity?

Granularity is the extent to which a material or system is composed of distinguishable pieces or grains. It can either refer to the extent to which a larger entity is subdivided, or the extent to which groups of smaller indistinguishable entities have joined together to become larger distinguishable entities. For example, a yard broken into inches has finer granularity than a yard broken into feet. In contrast, molecules of photographic emulsion may clump together to form distinct noticeable granules, reflecting coarser granularity.

Is a codon distinguishable from other codons? The 4 chemicals that can possibly make a codon don't relate to the peptide until the proper sequence is established.

There is error in DNA coding. We know this is different for different taxa. We call this mutation rates of different taxa. It stems directly from the quantization of DNA sequences.

http://www.nature.com...

And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...

http://www.ncbi.nlm.nih.gov...
RNA polymerases make about one mistake for every 104 nucleotides copied into RNA (compared with an error rate for direct copying by DNA polymerase of about one in 107 nucleotides), and the consequences of an error in RNA transcription are much less significant than that in DNA replication.

Although RNA polymerases are not nearly as accurate as the DNA polymerases that replicate DNA, they nonetheless have a modest proofreading mechanism. If the incorrect ribonucleotide is added to the growing RNA chain, the polymerase can back up, and the active site of the enzyme can perform an excision reaction that mimics the reverse of the polymerization reaction, except that water instead of pyrophosphate is used (see Figure 5-4). RNA polymerase hovers around a misincorporated ribonucleotide longer than it does for a correct addition, causing excision to be favored for incorrect nucleotides. However, RNA polymerase also excises many correct bases as part of the cost for improved accuracy.


Compressible: According to Miller, "Uncompressed digital data is very large, and in its raw form would actually produce a larger signal (therefore be more difficult to transfer) than analog data. However, digital data can be compressed. Compression reduces the amount of bandwidth space needed to send information.

Why don't you read the description. Feign stupidity you don't know DNA is compressed as a double helical stranded twisted around histone spines.

http://www.biology.emory.edu...

Read the article "...This association is unfavorable to the process of transcription and must be altered in order for the pre-initiation complex to access promoter regions, i.e. in order for transcription to start..."

Compression!!! an exact description for DNA is DIGITAL INFORMATION IN EVERY WAY!

That's not digital compression. It's the equivalent of defragging a hard drive or converting between file system schema. Actual compression would involve something like replacing repeating, common segments with shorter substitutes. As you say, this process makes it harder to read, but it also makes it harder to transmit. Compression of digital code makes transmission easier, not harder.

Compression of genetic code into a tightly twisted helical strings is easier to transport than if the genes were uncompressed. This is just obvious in that something squeezed down 100 times smaller it would than be easier to transport around.

But if you want to talk about the compression of information at the signal level than that is the difference between DNA and the RNA it transcribes.
Mhykiel
Posts: 5,987
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2/27/2015 7:53:19 PM
Posted: 1 year ago
At 2/27/2015 3:17:47 PM, RuvDraba wrote:
In other news:

All spanners are crab claws!
All vices are molars!!
All hammers are goat-horns!
All chisels are woodpecker-bills!
Paper invented by wasps!
Refrigerators invented by termites!
Boats invented by ants!

And yes -- if you squint and tilt your head a bit, all software can be thought of as DNA. In fact, there are people who write software using genetic algorithms, and it turns out it can eventually solve certain problems on its own -- and even evolve beautiful and intricate music (http://game.darwintunes.org...)

You can run such software on your laptop.

But work in genetic computation started as early as 1957. After decades of haughty indifference to science, its processes and products, it seems the religiously aloof are just catching up.

Yet the key insight here is that as with many human inventions, nature did a version of programmatic data replication and transformation first. Even viruses -- proteins on the very edge of life -- can do this.

It's marvelous, but is it miraculous?

Really?

As judged by what standard, beyond that of our own conceit?

Your sarcasm isn't lost on me.

It's rather simple. When I say something is a pyramid in structure what am I saying? I am saying it has a square base that comes to a point at the top.

How amazing the human language is! I express an idea by using words that having meaning. And you hear the words and no what meaning I am expressing. And this is because we agree on the definition of those words.

So to describe something as digital information means it must exhibit the qualities encompassed in the word "digital information".

Is the description accurate when applied to genetic processes? absolutely.

Of course you and others respond with derision because DNA being a digital code infers a designer, which is what you really have contention with.

So do you want to explain why DNA is NOT digital information? Because that would be a logical rebuttal.
UndeniableReality
Posts: 1,897
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2/28/2015 3:54:28 AM
Posted: 1 year ago
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.
Mhykiel
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2/28/2015 12:04:09 PM
Posted: 1 year ago
At 2/28/2015 3:54:28 AM, UndeniableReality wrote:
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.

So ID would be more viable if more people with higher degrees did papers on it.

The fact is DNA/RNA is digital information and is information encoded.

So many trying to say it is not still haven't offered any rebuttal to why it appears to be code but is infact not.
Mhykiel
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2/28/2015 12:07:01 PM
Posted: 1 year ago
At 2/28/2015 12:04:09 PM, Mhykiel wrote:
At 2/28/2015 3:54:28 AM, UndeniableReality wrote:
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.

So ID would be more viable if more people with higher degrees did papers on it.

That is not thinking for yourself and is a fallacy.


The fact is DNA/RNA is digital information and is information encoded.

So many trying to say it is not still haven't offered any rebuttal to why it appears to be code but is infact not.
Burzmali
Posts: 1,310
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2/28/2015 11:37:01 PM
Posted: 1 year ago
At 2/27/2015 7:37:54 PM, Mhykiel wrote:
Granularity is the extent to which a material or system is composed of distinguishable pieces or grains. It can either refer to the extent to which a larger entity is subdivided, or the extent to which groups of smaller indistinguishable entities have joined together to become larger distinguishable entities. For example, a yard broken into inches has finer granularity than a yard broken into feet. In contrast, molecules of photographic emulsion may clump together to form distinct noticeable granules, reflecting coarser granularity.

Is a codon distinguishable from other codons? The 4 chemicals that can possibly make a codon don't relate to the peptide until the proper sequence is established.

There is error in DNA coding. We know this is different for different taxa. We call this mutation rates of different taxa. It stems directly from the quantization of DNA sequences.

http://www.nature.com...

And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...

http://www.ncbi.nlm.nih.gov...
RNA polymerases make about one mistake for every 104 nucleotides copied into RNA (compared with an error rate for direct copying by DNA polymerase of about one in 107 nucleotides), and the consequences of an error in RNA transcription are much less significant than that in DNA replication.

Although RNA polymerases are not nearly as accurate as the DNA polymerases that replicate DNA, they nonetheless have a modest proofreading mechanism. If the incorrect ribonucleotide is added to the growing RNA chain, the polymerase can back up, and the active site of the enzyme can perform an excision reaction that mimics the reverse of the polymerization reaction, except that water instead of pyrophosphate is used (see Figure 5-4). RNA polymerase hovers around a misincorporated ribonucleotide longer than it does for a correct addition, causing excision to be favored for incorrect nucleotides. However, RNA polymerase also excises many correct bases as part of the cost for improved accuracy.

None of that matches the type of granularity and error you references before as involved with digital code. Quantizing error was shown with the example of going from an analog value (float) to an int: 23.234456544453 to 23. There's loss of granularity and therefore an error. The errors that occur in transcription and replication are things like substitutions and duplications. They're like overflow and paging errors. In contrast to the quantizing error that occurs with granularity, DNA errors would be like going from 23.234456544453 to 33.234456544453 or 1050.

If you really want to answer this, just tell me what analog value is being represented digitally in DNA and give an example of an error that occurs as a result. That would actually prove the granular property you're trying to claim exists.

Compression of genetic code into a tightly twisted helical strings is easier to transport than if the genes were uncompressed. This is just obvious in that something squeezed down 100 times smaller it would than be easier to transport around.

But if you want to talk about the compression of information at the signal level than that is the difference between DNA and the RNA it transcribes.

Now you seem to be confusing transport and transmission, and you're talking about increasing physical density rather than informational density. What you're talking about is like going from a 32 GB IDE hard drive to a 32 GB flash drive. That isn't compression of information. And DNA to RNA isn't information compression, either. There's a loss of information from one to the other when introns are removed. Again, that isn't compression of information.
Mhykiel
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3/1/2015 12:40:39 AM
Posted: 1 year ago
At 2/28/2015 11:37:01 PM, Burzmali wrote:
At 2/27/2015 7:37:54 PM, Mhykiel wrote:
Granularity is the extent to which a material or system is composed of distinguishable pieces or grains. It can either refer to the extent to which a larger entity is subdivided, or the extent to which groups of smaller indistinguishable entities have joined together to become larger distinguishable entities. For example, a yard broken into inches has finer granularity than a yard broken into feet. In contrast, molecules of photographic emulsion may clump together to form distinct noticeable granules, reflecting coarser granularity.

Is a codon distinguishable from other codons? The 4 chemicals that can possibly make a codon don't relate to the peptide until the proper sequence is established.

There is error in DNA coding. We know this is different for different taxa. We call this mutation rates of different taxa. It stems directly from the quantization of DNA sequences.

http://www.nature.com...

And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...

http://www.ncbi.nlm.nih.gov...
RNA polymerases make about one mistake for every 104 nucleotides copied into RNA (compared with an error rate for direct copying by DNA polymerase of about one in 107 nucleotides), and the consequences of an error in RNA transcription are much less significant than that in DNA replication.

Although RNA polymerases are not nearly as accurate as the DNA polymerases that replicate DNA, they nonetheless have a modest proofreading mechanism. If the incorrect ribonucleotide is added to the growing RNA chain, the polymerase can back up, and the active site of the enzyme can perform an excision reaction that mimics the reverse of the polymerization reaction, except that water instead of pyrophosphate is used (see Figure 5-4). RNA polymerase hovers around a misincorporated ribonucleotide longer than it does for a correct addition, causing excision to be favored for incorrect nucleotides. However, RNA polymerase also excises many correct bases as part of the cost for improved accuracy.

None of that matches the type of granularity and error you references before as involved with digital code. Quantizing error was shown with the example of going from an analog value (float) to an int: 23.234456544453 to 23. There's loss of granularity and therefore an error. The errors that occur in transcription and replication are things like substitutions and duplications. They're like overflow and paging errors. In contrast to the quantizing error that occurs with granularity, DNA errors would be like going from 23.234456544453 to 33.234456544453 or 1050.

If you really want to answer this, just tell me what analog value is being represented digitally in DNA and give an example of an error that occurs as a result. That would actually prove the granular property you're trying to claim exists.

The peptides three dimensional structure is analogous. This is encoded digitally into a 3-letter string.

Errors occur when the 3 letter codon is changed by mutation.


Compression of genetic code into a tightly twisted helical strings is easier to transport than if the genes were uncompressed. This is just obvious in that something squeezed down 100 times smaller it would than be easier to transport around.

But if you want to talk about the compression of information at the signal level than that is the difference between DNA and the RNA it transcribes.

Now you seem to be confusing transport and transmission, and you're talking about increasing physical density rather than informational density. What you're talking about is like going from a 32 GB IDE hard drive to a 32 GB flash drive. That isn't compression of information. And DNA to RNA isn't information compression, either. There's a loss of information from one to the other when introns are removed. Again, that isn't compression of information.

There are 2 kinds of compression. Lossy and Lossless.

Lossless is usually compressing the string by removing redundancy. Going from DNA to RNA is removing 1/2 of the DNA. the half that is redundant of the information in the RNA.
UndeniableReality
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3/1/2015 1:07:10 PM
Posted: 1 year ago
At 2/28/2015 12:04:09 PM, Mhykiel wrote:
At 2/28/2015 3:54:28 AM, UndeniableReality wrote:
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.

So ID would be more viable if more people with higher degrees did papers on it.

Of course not. I think you're referring to my last sentence, which was not intended to argue any point. It was just a remark. It's surprising that you found something like that, and that it was hosted online somewhere.

The point of my question was that I don't see how that paper really has anything to do with this topic, so I was asking what relevance you see in it.


The fact is DNA/RNA is digital information and is information encoded.

So many trying to say it is not still haven't offered any rebuttal to why it appears to be code but is infact not.

I'm fine with it being called a code that contains information given proper definitions. I think the issue is that a lot of people assert that it is a code with information in a narrow sense, and then broaden their definitions in the next sentence to assert implications that do not follow.
UndeniableReality
Posts: 1,897
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3/1/2015 1:08:52 PM
Posted: 1 year ago
At 2/28/2015 12:07:01 PM, Mhykiel wrote:
At 2/28/2015 12:04:09 PM, Mhykiel wrote:
At 2/28/2015 3:54:28 AM, UndeniableReality wrote:
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.

So ID would be more viable if more people with higher degrees did papers on it.

That is not thinking for yourself and is a fallacy.

Since the remark was independent of any argument (in fact, my post didn't even contain an argument), it wasn't a fallacy. Maybe I should label my remarks as such next time.
RuvDraba
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3/1/2015 1:22:16 PM
Posted: 1 year ago
At 2/27/2015 7:53:19 PM, Mhykiel wrote:
So to describe something as digital information means it must exhibit the qualities encompassed in the word "digital information".

Yes. And DNA can be used to create genetic computers. So sure, DNA structures can be used to store digital information, just as deposits of magnetised iron oxide -- rust -- can be used to store digital information on hard disks. Such structures not only can be used by intelligent creatures for information storage and computation they have been: humans have used them.

So... the self-replicating structure of DNA can be used intelligently. But that doesn't make every appearance an intelligent use. Any attempt to conclude that every appearance of DNA is an intelligent use of DNA requires some explanation of intelligence and purpose -- which in another thread, you have disingenuously and evasively have declined to do.
Mhykiel
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3/1/2015 2:39:32 PM
Posted: 1 year ago
At 3/1/2015 1:07:10 PM, UndeniableReality wrote:
At 2/28/2015 12:04:09 PM, Mhykiel wrote:
At 2/28/2015 3:54:28 AM, UndeniableReality wrote:
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.

So ID would be more viable if more people with higher degrees did papers on it.

Of course not. I think you're referring to my last sentence, which was not intended to argue any point. It was just a remark. It's surprising that you found something like that, and that it was hosted online somewhere.

The point of my question was that I don't see how that paper really has anything to do with this topic, so I was asking what relevance you see in it.

The authors apply information theory to DNA. The begin with sections that describe what parts of DNA are equivalent to the terms of information theory. Such codons with data and so forth.

It's relevance is a good scientific explanation of the digital information stored in DNA.

This storage is not information injected by humans. It is the "life" information present in the DNA for the benefit of the cell.



The fact is DNA/RNA is digital information and is information encoded.

So many trying to say it is not still haven't offered any rebuttal to why it appears to be code but is infact not.

I'm fine with it being called a code that contains information given proper definitions. I think the issue is that a lot of people assert that it is a code with information in a narrow sense, and then broaden their definitions in the next sentence to assert implications that do not follow.
Mhykiel
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3/1/2015 2:43:32 PM
Posted: 1 year ago
At 3/1/2015 1:22:16 PM, RuvDraba wrote:
At 2/27/2015 7:53:19 PM, Mhykiel wrote:
So to describe something as digital information means it must exhibit the qualities encompassed in the word "digital information".

Yes. And DNA can be used to create genetic computers. So sure, DNA structures can be used to store digital information, just as deposits of magnetised iron oxide -- rust -- can be used to store digital information on hard disks. Such structures not only can be used by intelligent creatures for information storage and computation they have been: humans have used them.

So... the self-replicating structure of DNA can be used intelligently. But that doesn't make every appearance an intelligent use. Any attempt to conclude that every appearance of DNA is an intelligent use of DNA requires some explanation of intelligence and purpose -- which in another thread, you have disingenuously and evasively have declined to do.

The linguistics of DNA are being used by humans to encode movies and other data.

But in the cell Data is already encoded in DNA. the instructions for the living cell are already stored in digital format in DNA.

The information for the actions, for the peptides, for the functions of the cell are encoded in DNA abstractly. The codons are symbolic of the function or object they represent.

So humans did not put that information into living cells. Either you contend it was encoded and structured by natural process (abiogenesis) or by directed processes (intelligent design).

nature doesn't work with symbols.
RuvDraba
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3/1/2015 2:55:10 PM
Posted: 1 year ago
At 3/1/2015 2:43:32 PM, Mhykiel wrote:
nature doesn't work with symbols.

Please cite the peer-reviewed paper from a respected scientific journal to support this opinion.

Else it looks to me like another ID false duality:

* Planck's constant can't be that convenient -- it must've been created;
* Bananas shouldn't fit the hand -- they must've been created;
* Wings can't sprout from dinosaur backs -- they must've been created;
* Nature can't work with information -- it must've been created

In the benighted and superstitious mind of an ID advocate, nothing can be complex, fortuitous or beneficial -- unless it's created by supernatural agency. :p

If this is science, please cite the paper.
Mhykiel
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3/1/2015 3:07:31 PM
Posted: 1 year ago
At 3/1/2015 2:55:10 PM, RuvDraba wrote:
At 3/1/2015 2:43:32 PM, Mhykiel wrote:
nature doesn't work with symbols.

Please cite the peer-reviewed paper from a respected scientific journal to support this opinion.

Else it looks to me like another ID false duality:

* Planck's constant can't be that convenient -- it must've been created;
* Bananas shouldn't fit the hand -- they must've been created;
* Wings can't sprout from dinosaur backs -- they must've been created;
* Nature can't work with information -- it must've been created

In the benighted and superstitious mind of an ID advocate, nothing can be complex, fortuitous or beneficial -- unless it's created by supernatural agency. :p

If this is science, please cite the paper.

No i think form follows function and natural process can produce prima facie complexity and beneficial things.

And looking at the ending object like wings can look miraculous but small changes over time and selective breeding can account for such things.

And I have explained why nature does not work with symbols. It's called reasoning. Asking for a peer reviewed paper to establish every little thing is petty.

Natural laws are A then B. those are the physical laws. A symbol is A interpreted to then be B.

Nature doesn't work in the abstract because for some consistent result to come from an abstract symbol there would have to be a language of sorts that assigns the result with the source.

If the result has no physical casual contingent necessity to the source then that would be abstract representation. This is obvious, just as obvious as a rock falling due to gravity is the rock doesn't have a choice in the matter.
UndeniableReality
Posts: 1,897
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3/1/2015 3:22:41 PM
Posted: 1 year ago
At 3/1/2015 2:39:32 PM, Mhykiel wrote:
At 3/1/2015 1:07:10 PM, UndeniableReality wrote:
At 2/28/2015 12:04:09 PM, Mhykiel wrote:
At 2/28/2015 3:54:28 AM, UndeniableReality wrote:
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.

So ID would be more viable if more people with higher degrees did papers on it.

Of course not. I think you're referring to my last sentence, which was not intended to argue any point. It was just a remark. It's surprising that you found something like that, and that it was hosted online somewhere.

The point of my question was that I don't see how that paper really has anything to do with this topic, so I was asking what relevance you see in it.

The authors apply information theory to DNA. The begin with sections that describe what parts of DNA are equivalent to the terms of information theory. Such codons with data and so forth.

You can apply information theory to all sorts of things. It doesn't imply that those things are codes, just that we can represent them as codes. I can apply information theory to any sequence of random numbers too, or the spacing between trees in a forest, and all sorts of other things. That is why I don't understand why you think it is meaningful that they are applying information theory to DNA. By the way, I could send you better papers where information theory is applied to DNA, if, for whatever reason, you're actually interested in that topic.


It's relevance is a good scientific explanation of the digital information stored in DNA.

The paper doesn't even attempt to explain the information stored in DNA.


This storage is not information injected by humans. It is the "life" information present in the DNA for the benefit of the cell.


Most information is not injected by humans. So? The definition of information you're using here does not require an intelligence.
RuvDraba
Posts: 6,033
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3/1/2015 3:23:35 PM
Posted: 1 year ago
At 3/1/2015 3:07:31 PM, Mhykiel wrote:
I have explained why nature does not work with symbols. It's called reasoning. Asking for a peer reviewed paper to establish every little thing is petty.

It's not a little thing -- it's central to your thesis, and insisting on you grounding it in science isn't petty, but rigorous.

If you with your casual interest in biology have reasoned this supposedly universal law from scientific observation, then biologists should have too. So, please do the leg-work and cite me a paper.

Else, kindly admit that this is not a scientific inference, but one of religious doctrine meant to support another ID-concocted duality; that your whole thesis hinges on the unsupported assertion that nature can't replicate or process information unaided, and that you were trying to slip this postulate past, unexamined.
Mhykiel
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3/1/2015 3:31:08 PM
Posted: 1 year ago
At 3/1/2015 3:22:41 PM, UndeniableReality wrote:
At 3/1/2015 2:39:32 PM, Mhykiel wrote:
At 3/1/2015 1:07:10 PM, UndeniableReality wrote:
At 2/28/2015 12:04:09 PM, Mhykiel wrote:
At 2/28/2015 3:54:28 AM, UndeniableReality wrote:
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.

So ID would be more viable if more people with higher degrees did papers on it.

Of course not. I think you're referring to my last sentence, which was not intended to argue any point. It was just a remark. It's surprising that you found something like that, and that it was hosted online somewhere.

The point of my question was that I don't see how that paper really has anything to do with this topic, so I was asking what relevance you see in it.

The authors apply information theory to DNA. The begin with sections that describe what parts of DNA are equivalent to the terms of information theory. Such codons with data and so forth.

You can apply information theory to all sorts of things. It doesn't imply that those things are codes, just that we can represent them as codes. I can apply information theory to any sequence of random numbers too, or the spacing between trees in a forest, and all sorts of other things. That is why I don't understand why you think it is meaningful that they are applying information theory to DNA. By the way, I could send you better papers where information theory is applied to DNA, if, for whatever reason, you're actually interested in that topic.

It begins by explaining that information is already in DNA. And it attempts to analyze that information.



It's relevance is a good scientific explanation of the digital information stored in DNA.

The paper doesn't even attempt to explain the information stored in DNA.

Explaining where the information came from would be answered by ID.

As of yet the only abiogenesis explanation for the information is NGE.



This storage is not information injected by humans. It is the "life" information present in the DNA for the benefit of the cell.


Most information is not injected by humans. So? The definition of information you're using here does not require an intelligence.

I don't think all information (I prefer data) requires an intelligence. I think you are create an equivalency error in thinking the only possible intelligence to create symbolic language is humans.

Like a machine that runs on computer code. The machine runs with out real intelligence. But the code had to be programmed in the machine by an intelligence.
UndeniableReality
Posts: 1,897
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3/1/2015 3:42:34 PM
Posted: 1 year ago
At 3/1/2015 3:31:08 PM, Mhykiel wrote:
At 3/1/2015 3:22:41 PM, UndeniableReality wrote:
At 3/1/2015 2:39:32 PM, Mhykiel wrote:
At 3/1/2015 1:07:10 PM, UndeniableReality wrote:
At 2/28/2015 12:04:09 PM, Mhykiel wrote:
At 2/28/2015 3:54:28 AM, UndeniableReality wrote:
And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...


I'm not sure what you think is interesting about this. Of course information theory and statistics are used in analysis, of not just DNA, but all data. All they're doing here is using SOMs to cluster the genes. It looks like someone's school project, possibly from a graduate course.

So ID would be more viable if more people with higher degrees did papers on it.

Of course not. I think you're referring to my last sentence, which was not intended to argue any point. It was just a remark. It's surprising that you found something like that, and that it was hosted online somewhere.

The point of my question was that I don't see how that paper really has anything to do with this topic, so I was asking what relevance you see in it.

The authors apply information theory to DNA. The begin with sections that describe what parts of DNA are equivalent to the terms of information theory. Such codons with data and so forth.

You can apply information theory to all sorts of things. It doesn't imply that those things are codes, just that we can represent them as codes. I can apply information theory to any sequence of random numbers too, or the spacing between trees in a forest, and all sorts of other things. That is why I don't understand why you think it is meaningful that they are applying information theory to DNA. By the way, I could send you better papers where information theory is applied to DNA, if, for whatever reason, you're actually interested in that topic.

It begins by explaining that information is already in DNA. And it attempts to analyze that information.



It's relevance is a good scientific explanation of the digital information stored in DNA.

The paper doesn't even attempt to explain the information stored in DNA.

Explaining where the information came from would be answered by ID.

So yes, this paper doesn't even attempt to explain the information stored in DNA. The simple answer would have been "yes", instead of to bring up ID, which we haven't even gotten to yet.


As of yet the only abiogenesis explanation for the information is NGE.

You haven't even said what NGE is.

This storage is not information injected by humans. It is the "life" information present in the DNA for the benefit of the cell.


Most information is not injected by humans. So? The definition of information you're using here does not require an intelligence.

I don't think all information (I prefer data) requires an intelligence. I think you are create an equivalency error in thinking the only possible intelligence to create symbolic language is humans.

Where did I make this equivocation? I haven't said anything about this.


Like a machine that runs on computer code. The machine runs with out real intelligence. But the code had to be programmed in the machine by an intelligence.

This example doesn't relate here. This is an example where the information has been injected by an intelligence, which is explicitly what we are not talking about here.
Otokage
Posts: 2,347
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3/1/2015 5:56:54 PM
Posted: 1 year ago
At 2/27/2015 11:55:43 AM, Mhykiel wrote:
All digital information possesses common properties that distinguish it from analog communications methods:

Synchronization: Since digital information is conveyed by the sequence in which symbols are ordered, all digital schemes have some method for determining the beginning of a sequence. In written or spoken human languages synchronization is typically provided by pauses (spaces), capitalization, and punctuation. Machine communications typically use special synchronization sequences.

http://www.chemguide.co.uk...

The transport RNA is assigned to ONE 1 specific peptide. The 3 chemical arrangement of tRNA will only grab the one peptide. The differences between the tRNA do NOT exclude it from chemically attaching to other peptides. The peptides when made are only crafted with the right tRNA. it is an assignment of a handle. And hence synchronization between the peptide and an abstract representation of it by the tRNA "HANDLE" and I am using handle in the sense of computer language.

Language: All digital communications require a language[disambiguation needed], which in this context consists of all the information that the sender and receiver of the digital communication must both possess, in advance, in order for the communication to be successful. Languages are generally arbitrary and specify the meaning to be assigned to particular symbol sequences, the allowed range of values, methods to be used for synchronization, etc.

Same as above the establishment of representing real peptides by tRNA that is an abstract representation because the tRNA has no physical necessity to be the handle for the peptide. The only necessity comes from the cells established language.

Errors: Disturbances (noise) in analog communications invariably introduce some, generally small deviation or error between the intended and actual communication. Disturbances in a digital communication do not result in errors unless the disturbance is so large as to result in a symbol being misinterpreted as another symbol or disturb the sequence of symbols. It is therefore generally possible to have an entirely error-free digital communication. Further, techniques such as check codes may be used to detect errors and guarantee error-free communications through redundancy or retransmission. Errors in digital communications can take the form of substitution errors in which a symbol is replaced by another symbol, or insertion/deletion errors in which an extra incorrect symbol is inserted into or deleted from a digital message. Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication.

Now you are just copy pasting because it should be obvious how this description of errors in digital information is a perfect match for mutations in genetic code. "Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication."

Copying: Because of the inevitable presence of noise, making many successive copies of an analog communication is infeasible because each generation increases the noise. Because digital communications are generally error-free, copies of copies can be made indefinitely.

Granularity: The digital representation of a continuously variable analog value typically involves a selection of the number of symbols to be assigned to that value. The number of symbols determines the precision or resolution of the resulting datum. The difference between the actual analog value and the digital representation is known as quantization error. For example, if the actual temperature is 23.234456544453 degrees, but if only two digits (23) are assigned to this parameter in a particular digital representation, the quantizing error is: 0.234456544453. This property of digital communication is known as granularity.


tRNA http://www.chemguide.co.uk...

Dead on exact description of tRNA again. The description of Digital Code in information theory for computer systems, cryptography and other systems is a perfect description of the "Genetic CODE"

"involves a selection of the number of symbols to be assigned to that value."

The granularity error can even be calculated of DNA in that each codon is 3 chemicals in length. the Codon is the digital representation of a peptide.

Compressible: According to Miller, "Uncompressed digital data is very large, and in its raw form would actually produce a larger signal (therefore be more difficult to transfer) than analog data. However, digital data can be compressed. Compression reduces the amount of bandwidth space needed to send information.

Why don't you read the description. Feign stupidity you don't know DNA is compressed as a double helical stranded twisted around histone spines.

http://www.biology.emory.edu...

Read the article "...This association is unfavorable to the process of transcription and must be altered in order for the pre-initiation complex to access promoter regions, i.e. in order for transcription to start..."

Compression!!! an exact description for DNA is DIGITAL INFORMATION IN EVERY WAY!

Some say it is not a code and define DNA as the double helix of molecules. This is not a definition that excludes DNA being code. Just like describing a computer program as being a string of 0s and 1s does nothing to dissuade from DNA being a representation of information. Digital an abstract at that. If it was a "mold" or chemically necessary like a crystalline structure the information could be easily concluded to be from a natural process derived purely from physical laws. But that is not what we have.

Except that DNA was not made by an intelligent designer. Abiogenesis + evolution can explain without any gap the spontaneous generation of nucleic acids and their evolution into more complex nucleic acids. According to your own assumptions, codes are always created by designers and not nature, and therefore by your logic DNA will never be a code.
Burzmali
Posts: 1,310
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3/1/2015 6:55:30 PM
Posted: 1 year ago
At 3/1/2015 12:40:39 AM, Mhykiel wrote:
At 2/28/2015 11:37:01 PM, Burzmali wrote:
At 2/27/2015 7:37:54 PM, Mhykiel wrote:
Granularity is the extent to which a material or system is composed of distinguishable pieces or grains. It can either refer to the extent to which a larger entity is subdivided, or the extent to which groups of smaller indistinguishable entities have joined together to become larger distinguishable entities. For example, a yard broken into inches has finer granularity than a yard broken into feet. In contrast, molecules of photographic emulsion may clump together to form distinct noticeable granules, reflecting coarser granularity.

Is a codon distinguishable from other codons? The 4 chemicals that can possibly make a codon don't relate to the peptide until the proper sequence is established.

There is error in DNA coding. We know this is different for different taxa. We call this mutation rates of different taxa. It stems directly from the quantization of DNA sequences.

http://www.nature.com...

And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...

http://www.ncbi.nlm.nih.gov...
RNA polymerases make about one mistake for every 104 nucleotides copied into RNA (compared with an error rate for direct copying by DNA polymerase of about one in 107 nucleotides), and the consequences of an error in RNA transcription are much less significant than that in DNA replication.

Although RNA polymerases are not nearly as accurate as the DNA polymerases that replicate DNA, they nonetheless have a modest proofreading mechanism. If the incorrect ribonucleotide is added to the growing RNA chain, the polymerase can back up, and the active site of the enzyme can perform an excision reaction that mimics the reverse of the polymerization reaction, except that water instead of pyrophosphate is used (see Figure 5-4). RNA polymerase hovers around a misincorporated ribonucleotide longer than it does for a correct addition, causing excision to be favored for incorrect nucleotides. However, RNA polymerase also excises many correct bases as part of the cost for improved accuracy.

None of that matches the type of granularity and error you references before as involved with digital code. Quantizing error was shown with the example of going from an analog value (float) to an int: 23.234456544453 to 23. There's loss of granularity and therefore an error. The errors that occur in transcription and replication are things like substitutions and duplications. They're like overflow and paging errors. In contrast to the quantizing error that occurs with granularity, DNA errors would be like going from 23.234456544453 to 33.234456544453 or 1050.

If you really want to answer this, just tell me what analog value is being represented digitally in DNA and give an example of an error that occurs as a result. That would actually prove the granular property you're trying to claim exists.

The peptides three dimensional structure is analogous. This is encoded digitally into a 3-letter string.

Errors occur when the 3 letter codon is changed by mutation.

The mutation isn't caused by converting from peptides to triplet nucleotides. Furthermore, amino acids don't have any more of a three dimensional structure, individually, than nucleotides do with their phosphate component. If anything, a triplet set of nucleotides on the DNA backbone is more complex than the individual amino acid that they code for. So how can you possibly make this kind of comparison? Where is the loss of granularity going from a peptide chain to a nucleotide chain?

Compression of genetic code into a tightly twisted helical strings is easier to transport than if the genes were uncompressed. This is just obvious in that something squeezed down 100 times smaller it would than be easier to transport around.

But if you want to talk about the compression of information at the signal level than that is the difference between DNA and the RNA it transcribes.

Now you seem to be confusing transport and transmission, and you're talking about increasing physical density rather than informational density. What you're talking about is like going from a 32 GB IDE hard drive to a 32 GB flash drive. That isn't compression of information. And DNA to RNA isn't information compression, either. There's a loss of information from one to the other when introns are removed. Again, that isn't compression of information.

There are 2 kinds of compression. Lossy and Lossless.

Lossless is usually compressing the string by removing redundancy. Going from DNA to RNA is removing 1/2 of the DNA. the half that is redundant of the information in the RNA.

The nucleotides removed during transcription aren't redundant, they're unnecessary. It's an overall loss of (unnecessary) information. That isn't compression, it's excision.
Mhykiel
Posts: 5,987
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3/1/2015 11:33:59 PM
Posted: 1 year ago
At 3/1/2015 5:56:54 PM, Otokage wrote:
At 2/27/2015 11:55:43 AM, Mhykiel wrote:
All digital information possesses common properties that distinguish it from analog communications methods:

Synchronization: Since digital information is conveyed by the sequence in which symbols are ordered, all digital schemes have some method for determining the beginning of a sequence. In written or spoken human languages synchronization is typically provided by pauses (spaces), capitalization, and punctuation. Machine communications typically use special synchronization sequences.

http://www.chemguide.co.uk...

The transport RNA is assigned to ONE 1 specific peptide. The 3 chemical arrangement of tRNA will only grab the one peptide. The differences between the tRNA do NOT exclude it from chemically attaching to other peptides. The peptides when made are only crafted with the right tRNA. it is an assignment of a handle. And hence synchronization between the peptide and an abstract representation of it by the tRNA "HANDLE" and I am using handle in the sense of computer language.

Language: All digital communications require a language[disambiguation needed], which in this context consists of all the information that the sender and receiver of the digital communication must both possess, in advance, in order for the communication to be successful. Languages are generally arbitrary and specify the meaning to be assigned to particular symbol sequences, the allowed range of values, methods to be used for synchronization, etc.

Same as above the establishment of representing real peptides by tRNA that is an abstract representation because the tRNA has no physical necessity to be the handle for the peptide. The only necessity comes from the cells established language.

Errors: Disturbances (noise) in analog communications invariably introduce some, generally small deviation or error between the intended and actual communication. Disturbances in a digital communication do not result in errors unless the disturbance is so large as to result in a symbol being misinterpreted as another symbol or disturb the sequence of symbols. It is therefore generally possible to have an entirely error-free digital communication. Further, techniques such as check codes may be used to detect errors and guarantee error-free communications through redundancy or retransmission. Errors in digital communications can take the form of substitution errors in which a symbol is replaced by another symbol, or insertion/deletion errors in which an extra incorrect symbol is inserted into or deleted from a digital message. Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication.

Now you are just copy pasting because it should be obvious how this description of errors in digital information is a perfect match for mutations in genetic code. "Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication."

Copying: Because of the inevitable presence of noise, making many successive copies of an analog communication is infeasible because each generation increases the noise. Because digital communications are generally error-free, copies of copies can be made indefinitely.

Granularity: The digital representation of a continuously variable analog value typically involves a selection of the number of symbols to be assigned to that value. The number of symbols determines the precision or resolution of the resulting datum. The difference between the actual analog value and the digital representation is known as quantization error. For example, if the actual temperature is 23.234456544453 degrees, but if only two digits (23) are assigned to this parameter in a particular digital representation, the quantizing error is: 0.234456544453. This property of digital communication is known as granularity.


tRNA http://www.chemguide.co.uk...

Dead on exact description of tRNA again. The description of Digital Code in information theory for computer systems, cryptography and other systems is a perfect description of the "Genetic CODE"

"involves a selection of the number of symbols to be assigned to that value."

The granularity error can even be calculated of DNA in that each codon is 3 chemicals in length. the Codon is the digital representation of a peptide.

Compressible: According to Miller, "Uncompressed digital data is very large, and in its raw form would actually produce a larger signal (therefore be more difficult to transfer) than analog data. However, digital data can be compressed. Compression reduces the amount of bandwidth space needed to send information.

Why don't you read the description. Feign stupidity you don't know DNA is compressed as a double helical stranded twisted around histone spines.

http://www.biology.emory.edu...

Read the article "...This association is unfavorable to the process of transcription and must be altered in order for the pre-initiation complex to access promoter regions, i.e. in order for transcription to start..."

Compression!!! an exact description for DNA is DIGITAL INFORMATION IN EVERY WAY!

Some say it is not a code and define DNA as the double helix of molecules. This is not a definition that excludes DNA being code. Just like describing a computer program as being a string of 0s and 1s does nothing to dissuade from DNA being a representation of information. Digital an abstract at that. If it was a "mold" or chemically necessary like a crystalline structure the information could be easily concluded to be from a natural process derived purely from physical laws. But that is not what we have.

Except that DNA was not made by an intelligent designer.

bare assertion. there is no historical record established so the origin of life is not settled.

Abiogenesis + evolution can explain without any gap the spontaneous generation of nucleic acids and their evolution into more complex nucleic acids.

Evolution can only take hold after a self replicating strand of DNA has been created. Abiogenesis is not fact, nor well supported by experiments. It's the only game in town for you.

According to your own assumptions, codes are always created by designers and not nature, and therefore by your logic DNA will never be a code.

Since what preceded this is unfounded bare assertions then the conclusion is not decided. And saying because you think the conclusion is non-intelligent then the premises is no code is not even logical.
Mhykiel
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3/1/2015 11:47:41 PM
Posted: 1 year ago
At 3/1/2015 6:55:30 PM, Burzmali wrote:
At 3/1/2015 12:40:39 AM, Mhykiel wrote:
At 2/28/2015 11:37:01 PM, Burzmali wrote:
At 2/27/2015 7:37:54 PM, Mhykiel wrote:
Granularity is the extent to which a material or system is composed of distinguishable pieces or grains. It can either refer to the extent to which a larger entity is subdivided, or the extent to which groups of smaller indistinguishable entities have joined together to become larger distinguishable entities. For example, a yard broken into inches has finer granularity than a yard broken into feet. In contrast, molecules of photographic emulsion may clump together to form distinct noticeable granules, reflecting coarser granularity.

Is a codon distinguishable from other codons? The 4 chemicals that can possibly make a codon don't relate to the peptide until the proper sequence is established.

There is error in DNA coding. We know this is different for different taxa. We call this mutation rates of different taxa. It stems directly from the quantization of DNA sequences.

http://www.nature.com...

And an example of scientist using information theory and statistics analyzing DNA of yeast
https://www.ii.uni.wroc.pl...

http://www.ncbi.nlm.nih.gov...
RNA polymerases make about one mistake for every 104 nucleotides copied into RNA (compared with an error rate for direct copying by DNA polymerase of about one in 107 nucleotides), and the consequences of an error in RNA transcription are much less significant than that in DNA replication.

Although RNA polymerases are not nearly as accurate as the DNA polymerases that replicate DNA, they nonetheless have a modest proofreading mechanism. If the incorrect ribonucleotide is added to the growing RNA chain, the polymerase can back up, and the active site of the enzyme can perform an excision reaction that mimics the reverse of the polymerization reaction, except that water instead of pyrophosphate is used (see Figure 5-4). RNA polymerase hovers around a misincorporated ribonucleotide longer than it does for a correct addition, causing excision to be favored for incorrect nucleotides. However, RNA polymerase also excises many correct bases as part of the cost for improved accuracy.

None of that matches the type of granularity and error you references before as involved with digital code. Quantizing error was shown with the example of going from an analog value (float) to an int: 23.234456544453 to 23. There's loss of granularity and therefore an error. The errors that occur in transcription and replication are things like substitutions and duplications. They're like overflow and paging errors. In contrast to the quantizing error that occurs with granularity, DNA errors would be like going from 23.234456544453 to 33.234456544453 or 1050.

If you really want to answer this, just tell me what analog value is being represented digitally in DNA and give an example of an error that occurs as a result. That would actually prove the granular property you're trying to claim exists.

The peptides three dimensional structure is analogous. This is encoded digitally into a 3-letter string.

Errors occur when the 3 letter codon is changed by mutation.

The mutation isn't caused by converting from peptides to triplet nucleotides. Furthermore, amino acids don't have any more of a three dimensional structure, individually, than nucleotides do with their phosphate component. If anything, a triplet set of nucleotides on the DNA backbone is more complex than the individual amino acid that they code for. So how can you possibly make this kind of comparison? Where is the loss of granularity going from a peptide chain to a nucleotide chain?

The analogous information of a three dimensional shape is represented by the 3 nucleotide chain that the tRNA mechanically decrypts.

The shape of the peptide is not stored int he DNA as a flat view of the peptide. Not like a blue print is an isometric view of a house. No the DNA stores the peptide as a 3 unit long string. that is symbolic not relational.


Compression of genetic code into a tightly twisted helical strings is easier to transport than if the genes were uncompressed. This is just obvious in that something squeezed down 100 times smaller it would than be easier to transport around.

But if you want to talk about the compression of information at the signal level than that is the difference between DNA and the RNA it transcribes.

Now you seem to be confusing transport and transmission, and you're talking about increasing physical density rather than informational density. What you're talking about is like going from a 32 GB IDE hard drive to a 32 GB flash drive. That isn't compression of information. And DNA to RNA isn't information compression, either. There's a loss of information from one to the other when introns are removed. Again, that isn't compression of information.

There are 2 kinds of compression. Lossy and Lossless.

Lossless is usually compressing the string by removing redundancy. Going from DNA to RNA is removing 1/2 of the DNA. the half that is redundant of the information in the RNA.

The nucleotides removed during transcription aren't redundant, they're unnecessary. It's an overall loss of (unnecessary) information. That isn't compression, it's excision.

RNA can code from either side of the DNA helix. These two sides are distinguished in speech by the word "sense" and "anti-sense". The information is the same but complimentary which aids self correcting errors and in suppressing mRNA expression.

The information is not unnecessary because it is useful. And the information of the anti-sense is redundant because it is complimentary to the endogenous sense side of the DNA used by mRNA.
Otokage
Posts: 2,347
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3/2/2015 5:15:05 AM
Posted: 1 year ago
At 3/1/2015 11:33:59 PM, Mhykiel wrote:
At 3/1/2015 5:56:54 PM, Otokage wrote:
Except that DNA was not made by an intelligent designer.

bare assertion. there is no historical record established so the origin of life is not settled.

I'm not speaking about the origin of life, but about DNA.

Abiogenesis + evolution can explain without any gap the spontaneous generation of nucleic acids and their evolution into more complex nucleic acids.

Evolution can only take hold after a self replicating strand of DNA has been created. Abiogenesis is not fact, nor well supported by experiments. It's the only game in town for you.

No. The abiogenesis of any biomolecule is well understood nowadays. Since God is not required to produce nucleic acids, it's cheap speculation to state he intervened.

According to your own assumptions, codes are always created by designers and not nature, and therefore by your logic DNA will never be a code.

So this stands. And as long as this is true, you need to accept that 1) Nature can produce codes, or 2) DNA is not a code.
Mhykiel
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3/2/2015 4:41:16 PM
Posted: 1 year ago
At 3/2/2015 5:15:05 AM, Otokage wrote:
At 3/1/2015 11:33:59 PM, Mhykiel wrote:
At 3/1/2015 5:56:54 PM, Otokage wrote:
Except that DNA was not made by an intelligent designer.

bare assertion. there is no historical record established so the origin of life is not settled.

I'm not speaking about the origin of life, but about DNA.

Abiogenesis + evolution can explain without any gap the spontaneous generation of nucleic acids and their evolution into more complex nucleic acids.

Evolution can only take hold after a self replicating strand of DNA has been created. Abiogenesis is not fact, nor well supported by experiments. It's the only game in town for you.

No. The abiogenesis of any biomolecule is well understood nowadays. Since God is not required to produce nucleic acids, it's cheap speculation to state he intervened.

False abiogenesis is a farce. Since we are on DNA show me the evidence supporting nucleotides joining with a sugar backbone in an abiogenesis scenario

According to your own assumptions, codes are always created by designers and not nature, and therefore by your logic DNA will never be a code.

So this stands. And as long as this is true, you need to accept that 1) Nature can produce codes, or 2) DNA is not a code.

I've argued and showed DNA is a code. You haven't shown at that natural processes produce code.
debate_power
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3/11/2015 4:17:56 PM
Posted: 1 year ago
At 2/27/2015 11:55:43 AM, Mhykiel wrote:
All digital information possesses common properties that distinguish it from analog communications methods:

Synchronization: Since digital information is conveyed by the sequence in which symbols are ordered, all digital schemes have some method for determining the beginning of a sequence. In written or spoken human languages synchronization is typically provided by pauses (spaces), capitalization, and punctuation. Machine communications typically use special synchronization sequences.

http://www.chemguide.co.uk...

The transport RNA is assigned to ONE 1 specific peptide. The 3 chemical arrangement of tRNA will only grab the one peptide. The differences between the tRNA do NOT exclude it from chemically attaching to other peptides. The peptides when made are only crafted with the right tRNA. it is an assignment of a handle. And hence synchronization between the peptide and an abstract representation of it by the tRNA "HANDLE" and I am using handle in the sense of computer language.

Language: All digital communications require a language[disambiguation needed], which in this context consists of all the information that the sender and receiver of the digital communication must both possess, in advance, in order for the communication to be successful. Languages are generally arbitrary and specify the meaning to be assigned to particular symbol sequences, the allowed range of values, methods to be used for synchronization, etc.

Same as above the establishment of representing real peptides by tRNA that is an abstract representation because the tRNA has no physical necessity to be the handle for the peptide. The only necessity comes from the cells established language.

Errors: Disturbances (noise) in analog communications invariably introduce some, generally small deviation or error between the intended and actual communication. Disturbances in a digital communication do not result in errors unless the disturbance is so large as to result in a symbol being misinterpreted as another symbol or disturb the sequence of symbols. It is therefore generally possible to have an entirely error-free digital communication. Further, techniques such as check codes may be used to detect errors and guarantee error-free communications through redundancy or retransmission. Errors in digital communications can take the form of substitution errors in which a symbol is replaced by another symbol, or insertion/deletion errors in which an extra incorrect symbol is inserted into or deleted from a digital message. Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication.

Now you are just copy pasting because it should be obvious how this description of errors in digital information is a perfect match for mutations in genetic code. "Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication."

Copying: Because of the inevitable presence of noise, making many successive copies of an analog communication is infeasible because each generation increases the noise. Because digital communications are generally error-free, copies of copies can be made indefinitely.

Granularity: The digital representation of a continuously variable analog value typically involves a selection of the number of symbols to be assigned to that value. The number of symbols determines the precision or resolution of the resulting datum. The difference between the actual analog value and the digital representation is known as quantization error. For example, if the actual temperature is 23.234456544453 degrees, but if only two digits (23) are assigned to this parameter in a particular digital representation, the quantizing error is: 0.234456544453. This property of digital communication is known as granularity.


tRNA http://www.chemguide.co.uk...

Dead on exact description of tRNA again. The description of Digital Code in information theory for computer systems, cryptography and other systems is a perfect description of the "Genetic CODE"

"involves a selection of the number of symbols to be assigned to that value."

The granularity error can even be calculated of DNA in that each codon is 3 chemicals in length. the Codon is the digital representation of a peptide.

Compressible: According to Miller, "Uncompressed digital data is very large, and in its raw form would actually produce a larger signal (therefore be more difficult to transfer) than analog data. However, digital data can be compressed. Compression reduces the amount of bandwidth space needed to send information.

Why don't you read the description. Feign stupidity you don't know DNA is compressed as a double helical stranded twisted around histone spines.

http://www.biology.emory.edu...

Read the article "...This association is unfavorable to the process of transcription and must be altered in order for the pre-initiation complex to access promoter regions, i.e. in order for transcription to start..."

Compression!!! an exact description for DNA is DIGITAL INFORMATION IN EVERY WAY!

Some say it is not a code and define DNA as the double helix of molecules. This is not a definition that excludes DNA being code. Just like describing a computer program as being a string of 0s and 1s does nothing to dissuade from DNA being a representation of information. Digital an abstract at that. If it was a "mold" or chemically necessary like a crystalline structure the information could be easily concluded to be from a natural process derived purely from physical laws. But that is not what we have.

You can look at it as a code, or you can look at it as deoxyribonucleic acid. Just because it appears to be a code does not mean that it was "intended" by some higher being as a code. Humans call it a "code" because of its similarities to methods of human encryption.
You can call me Mark if you like.
debate_power
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3/11/2015 4:19:07 PM
Posted: 1 year ago
At 2/27/2015 11:55:43 AM, Mhykiel wrote:
All digital information possesses common properties that distinguish it from analog communications methods:

Synchronization: Since digital information is conveyed by the sequence in which symbols are ordered, all digital schemes have some method for determining the beginning of a sequence. In written or spoken human languages synchronization is typically provided by pauses (spaces), capitalization, and punctuation. Machine communications typically use special synchronization sequences.

http://www.chemguide.co.uk...

The transport RNA is assigned to ONE 1 specific peptide. The 3 chemical arrangement of tRNA will only grab the one peptide. The differences between the tRNA do NOT exclude it from chemically attaching to other peptides. The peptides when made are only crafted with the right tRNA. it is an assignment of a handle. And hence synchronization between the peptide and an abstract representation of it by the tRNA "HANDLE" and I am using handle in the sense of computer language.

Language: All digital communications require a language[disambiguation needed], which in this context consists of all the information that the sender and receiver of the digital communication must both possess, in advance, in order for the communication to be successful. Languages are generally arbitrary and specify the meaning to be assigned to particular symbol sequences, the allowed range of values, methods to be used for synchronization, etc.

Same as above the establishment of representing real peptides by tRNA that is an abstract representation because the tRNA has no physical necessity to be the handle for the peptide. The only necessity comes from the cells established language.

Errors: Disturbances (noise) in analog communications invariably introduce some, generally small deviation or error between the intended and actual communication. Disturbances in a digital communication do not result in errors unless the disturbance is so large as to result in a symbol being misinterpreted as another symbol or disturb the sequence of symbols. It is therefore generally possible to have an entirely error-free digital communication. Further, techniques such as check codes may be used to detect errors and guarantee error-free communications through redundancy or retransmission. Errors in digital communications can take the form of substitution errors in which a symbol is replaced by another symbol, or insertion/deletion errors in which an extra incorrect symbol is inserted into or deleted from a digital message. Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication.

Now you are just copy pasting because it should be obvious how this description of errors in digital information is a perfect match for mutations in genetic code. "Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication."

Copying: Because of the inevitable presence of noise, making many successive copies of an analog communication is infeasible because each generation increases the noise. Because digital communications are generally error-free, copies of copies can be made indefinitely.

Granularity: The digital representation of a continuously variable analog value typically involves a selection of the number of symbols to be assigned to that value. The number of symbols determines the precision or resolution of the resulting datum. The difference between the actual analog value and the digital representation is known as quantization error. For example, if the actual temperature is 23.234456544453 degrees, but if only two digits (23) are assigned to this parameter in a particular digital representation, the quantizing error is: 0.234456544453. This property of digital communication is known as granularity.


tRNA http://www.chemguide.co.uk...

Dead on exact description of tRNA again. The description of Digital Code in information theory for computer systems, cryptography and other systems is a perfect description of the "Genetic CODE"

"involves a selection of the number of symbols to be assigned to that value."

The granularity error can even be calculated of DNA in that each codon is 3 chemicals in length. the Codon is the digital representation of a peptide.

Compressible: According to Miller, "Uncompressed digital data is very large, and in its raw form would actually produce a larger signal (therefore be more difficult to transfer) than analog data. However, digital data can be compressed. Compression reduces the amount of bandwidth space needed to send information.

Why don't you read the description. Feign stupidity you don't know DNA is compressed as a double helical stranded twisted around histone spines.

http://www.biology.emory.edu...

Read the article "...This association is unfavorable to the process of transcription and must be altered in order for the pre-initiation complex to access promoter regions, i.e. in order for transcription to start..."

Compression!!! an exact description for DNA is DIGITAL INFORMATION IN EVERY WAY!

Some say it is not a code and define DNA as the double helix of molecules. This is not a definition that excludes DNA being code. Just like describing a computer program as being a string of 0s and 1s does nothing to dissuade from DNA being a representation of information. Digital an abstract at that. If it was a "mold" or chemically necessary like a crystalline structure the information could be easily concluded to be from a natural process derived purely from physical laws. But that is not what we have.

The material reality of the world wasn't created by humans. It was the other way around. That's a very human-conceited view.
You can call me Mark if you like.
Mhykiel
Posts: 5,987
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3/11/2015 8:45:19 PM
Posted: 1 year ago
At 3/11/2015 4:17:56 PM, debate_power wrote:
At 2/27/2015 11:55:43 AM, Mhykiel wrote:
All digital information possesses common properties that distinguish it from analog communications methods:

Synchronization: Since digital information is conveyed by the sequence in which symbols are ordered, all digital schemes have some method for determining the beginning of a sequence. In written or spoken human languages synchronization is typically provided by pauses (spaces), capitalization, and punctuation. Machine communications typically use special synchronization sequences.

http://www.chemguide.co.uk...

The transport RNA is assigned to ONE 1 specific peptide. The 3 chemical arrangement of tRNA will only grab the one peptide. The differences between the tRNA do NOT exclude it from chemically attaching to other peptides. The peptides when made are only crafted with the right tRNA. it is an assignment of a handle. And hence synchronization between the peptide and an abstract representation of it by the tRNA "HANDLE" and I am using handle in the sense of computer language.

Language: All digital communications require a language[disambiguation needed], which in this context consists of all the information that the sender and receiver of the digital communication must both possess, in advance, in order for the communication to be successful. Languages are generally arbitrary and specify the meaning to be assigned to particular symbol sequences, the allowed range of values, methods to be used for synchronization, etc.

Same as above the establishment of representing real peptides by tRNA that is an abstract representation because the tRNA has no physical necessity to be the handle for the peptide. The only necessity comes from the cells established language.

Errors: Disturbances (noise) in analog communications invariably introduce some, generally small deviation or error between the intended and actual communication. Disturbances in a digital communication do not result in errors unless the disturbance is so large as to result in a symbol being misinterpreted as another symbol or disturb the sequence of symbols. It is therefore generally possible to have an entirely error-free digital communication. Further, techniques such as check codes may be used to detect errors and guarantee error-free communications through redundancy or retransmission. Errors in digital communications can take the form of substitution errors in which a symbol is replaced by another symbol, or insertion/deletion errors in which an extra incorrect symbol is inserted into or deleted from a digital message. Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication.

Now you are just copy pasting because it should be obvious how this description of errors in digital information is a perfect match for mutations in genetic code. "Uncorrected errors in digital communications have unpredictable and generally large impact on the information content of the communication."

Copying: Because of the inevitable presence of noise, making many successive copies of an analog communication is infeasible because each generation increases the noise. Because digital communications are generally error-free, copies of copies can be made indefinitely.

Granularity: The digital representation of a continuously variable analog value typically involves a selection of the number of symbols to be assigned to that value. The number of symbols determines the precision or resolution of the resulting datum. The difference between the actual analog value and the digital representation is known as quantization error. For example, if the actual temperature is 23.234456544453 degrees, but if only two digits (23) are assigned to this parameter in a particular digital representation, the quantizing error is: 0.234456544453. This property of digital communication is known as granularity.


tRNA http://www.chemguide.co.uk...

Dead on exact description of tRNA again. The description of Digital Code in information theory for computer systems, cryptography and other systems is a perfect description of the "Genetic CODE"

"involves a selection of the number of symbols to be assigned to that value."

The granularity error can even be calculated of DNA in that each codon is 3 chemicals in length. the Codon is the digital representation of a peptide.

Compressible: According to Miller, "Uncompressed digital data is very large, and in its raw form would actually produce a larger signal (therefore be more difficult to transfer) than analog data. However, digital data can be compressed. Compression reduces the amount of bandwidth space needed to send information.

Why don't you read the description. Feign stupidity you don't know DNA is compressed as a double helical stranded twisted around histone spines.

http://www.biology.emory.edu...

Read the article "...This association is unfavorable to the process of transcription and must be altered in order for the pre-initiation complex to access promoter regions, i.e. in order for transcription to start..."

Compression!!! an exact description for DNA is DIGITAL INFORMATION IN EVERY WAY!

Some say it is not a code and define DNA as the double helix of molecules. This is not a definition that excludes DNA being code. Just like describing a computer program as being a string of 0s and 1s does nothing to dissuade from DNA being a representation of information. Digital an abstract at that. If it was a "mold" or chemically necessary like a crystalline structure the information could be easily concluded to be from a natural process derived purely from physical laws. But that is not what we have.

You can look at it as a code, or you can look at it as deoxyribonucleic acid. Just because it appears to be a code does not mean that it was "intended" by some higher being as a code. Humans call it a "code" because of its similarities to methods of human encryption.

It's called a code becuase it is one. Deoxyribonucleic acid is the medium in which the code is written.

There is a symbic assignment of codon to peptide not dependent on or emergent from the chemical or physical properties of the molecules involved.

This pattern of DNA code is not repetitive nor is it random. Segments for different signaling and regularory functions can be distinguished from one another.

The instructions in the DNA code give rise to complex 3 deminsional structures. There is no mechanism or casual agent other than intelligent agency that can embue information of one object symbolically into the arrangment of a different object. As opposed to analogously which nature does.

This particular DNA coding was present in all Least Universal Common Ancestors. Meaning the encoding should have a fittness to it that exceeds other encodings. Again it is independent of pbysical or chemical properties.

Hence there for intelligently designed