Code as an Analogy of DNA?

[DaleCutler]

@Chris_Falter: I have a short memory, as do others. But a ‘stop code’ sequence in DNA is a fairly robust analogy to code in digital electronics, is it not?

[DaleCutler]

Has anyone watched the Trifonov video yet? I love the GRATIS pun at about time 58:00.

[Mercer (John Mercer)]

@Chris_Falter

Per Shannon information theory, it is in fact a code, as I explained 10 posts ago.

I agree, but the definition we were discussing was the plain English one offered by Perry Marshall.

[Mercer (John Mercer)]

@DaleCutler

I guess I know that some are ‘section markers’, if you will, so might not they be considered ‘stop’ codes instead of templates? That is a question for you, too, John @Mercer.

There are three stop codons. There’s only one start codon that also is for methionine. The contrast between the “design” of the starting and stopping fairly screams that the genetic code was not intelligently designed.

[DMath]

@Rumraket

The fact that the mapping today has a direct physical and chemical basis in the structural interactions between aaRS enzymes, their cognate amino acids, and the tRNA molecule’s anticodon, disproves the claim that the code has any abstraction and thus constitutes a code in that sense of the word .

I don’t know that this helps the argument that DNA does not use a code…it just means the code’s conversion table is implemented by the aminoacyl-tRNA-synthetase enzymes. The fact remains that the sequence of the bases specifies (given the correct “hardware” to decode the sequence) the construction of the protein. As a complicating factor…each of the enzymes in question are around 400-500 codons long…and are used in their own construction.

That may not be code to a biologist…but it is code to a coder.

[Timothy_Horton]

@Chris_Falter

A biological cell stores the instructions for making proteins in DNA. There is a mapping between the information and the structures. Ergo, per Shannon, the mapping between instructions and medium (DNA) is properly referred to as a code. Biologists commonly refer to this as “the genetic code.”

I made this same point over a week ago at the start of the thread. DNA is a code by that definition. It isn’t a code under the more common definition of “a system of arbitrarily chosen symbols used as abstract representations to pass messages”. Only the second definition requires an intelligence to decide the arbitrary symbols used for the abstraction in the mapping.

ID-Creationists love to equivocate between the two definitions. That’s why I asked DaleCutler which definition he was using and why (I suspect) he was so hesitant to answer.

[DMath]

@Mercer

There are three stop codons. There’s only one start codon that also is for methionine. The contrast between the “design” of the starting and stopping fairly screams that the genetic code was not intelligently designed.

The are many human defined codes that have stop symbol but no start symbol. If the start is immediately after the end, then having a special symbol for it is redundant. My understanding is that there is an error control function to the specifics of the stop codons in that many frame shift mutations actually increase the frequency of stop codons that prevent long strings of malformed amino acid strings from gumming up the works.

[Mercer (John Mercer)]

@DMath

I don’t know that this helps the argument that DNA does not use a code…it just means the code’s conversion table is implemented by the aminoacyl-tRNA-synthetase enzymes.

There are no abstractions in that process.

@DMath

The are many human defined codes that have stop symbol but no start symbol.

There are none AFAIK that have an elaborate system for working around the “messages” that require the start character to be removed.

An intelligently designed genetic code would have a beginning that is as intelligently designed as the end, with a start codon that allows the desired N-terminal amino acid residue to follow it.

@DMath

My understanding is that there is an error control function to the specifics of the stop codons in that many frame shift mutations actually increase the frequency of stop codons that prevent long strings of malformed amino acid strings from gumming up the works.

I’m having trouble parsing that sentence, but whatever you mean, you’re missing the point that (at least in bacteria) suppressor mutations in tRNA genes that cause them to recognize stop codons, cause amino acids to be inserted instead of stopping. The run-on proteins are tolerated, which is why stop codons are amenable to change.

[DMath]

@Mercer

I don’t know that this helps the argument that DNA does not use a code…it just means the code’s conversion table is implemented by the aminoacyl-tRNA-synthetase enzymes.

There are no abstractions in that process.

Once it is specified and built into the hardware system there are no abstractions in the ASCII table either. The hardware does not know or care that it is conveying a message or using a code…it just follows the instructions it contains.

[Mercer (John Mercer)]

But we inserted the abstractions, so it is a code. “ASCII” is a label that tells us which abstractions were used.

[DMath]

@Mercer

But we inserted the abstractions, so it is a code. “ASCII” is a label that tells us which abstractions were used.

We can say that with confidence because the advent of ASCII is documented. None of us were around when the aminoacyl-tRNA-synthetase enzyme system was encoded.

[DaleCutler]

@DMath

Once it is specified and built into the hardware system there are no abstractions in the ASCII table either. The hardware does not know or care that it is conveying a message or using a code…it just follows the instructions it contains.

Exactly.

[DaleCutler]

@Mercer

@Mercer

The contrast between the “design” of the starting and stopping fairly screams that the genetic code was not intelligently designed.

Elaborate.

[Mercer (John Mercer)]

@DaleCutler

Elaborate.

I did. See above.

[Mercer (John Mercer)]

@DMath

We can say that with confidence because the advent of ASCII is documented. None of us were around when the aminoacyl-tRNA-synthetase enzyme system was encoded.

What’s your point, D?

Are you implying that because none of us were around, none of us should bother testing (or has bothered to test already) the hypothesis that the genetic code is arbitrary?

[Timothy_Horton]

@DMath

Once it is specified and built into the hardware system there are no abstractions in the ASCII table either. The hardware does not know or care that it is conveying a message or using a code…it just follows the instructions it contains.

If you wish to claim an initial arbitrary abstract mapping all you have to do is show how the entire universe including the laws of chemistry and physics were created with the specific properties we see which allow the version of DNA we find to function the way it does. Good luck especially since all the evidence we have shows DNA based life evolved to fit the universe’s parameters, not the other way around.

[DaleCutler]

@Mercer

See above.

Where. Specify a comment number, please.

[DMath]

@Mercer

Are you implying that because none of us were around, none of us should bother testing the hypothesis that the genetic code is arbitrary?

Certainly not…just that we cannot assume that because there is currently no abstraction in the implementation that the abstraction never existed.

[Mercer (John Mercer)]

@DaleCutler

Specify a comment number, please.

There are none [no human codes] AFAIK that have an elaborate system for working around the “messages” that require the start character to be removed.

An intelligently designed genetic code would have a beginning that is as intelligently designed as the end, with a start codon that allows the desired N-terminal amino acid residue to follow it.

Code as an Analogy of DNA?

There are no abstractions in that process. There are none AFAIK that have an elaborate system for working around the “messages” that require the start character to be removed. An intelligently designed genetic code would have a beginning that is as intelligently designed as the end, with a start codon that allows the desired N-terminal amino acid residue to follow it. I’m having trouble parsing that sentence, but whatever you mean, you’re missing the point that (at least in bacteria) suppressor mutations in tRNA genes that cause them to recognize stop codons, cause amino acids to be inserted instead of stopping. The run-on proteins are tolerated, which is why stop codons are amenable to change.

[DaleCutler]

@Timothy_Horton

…fit the universe’s parameters…

If it didn’t, it wouldn’t be here, would it, designed or evolved.