DNA as a programming language

[ChetSinger]

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033003/

I'm a programmer and I see some similarities with programming systems.

• The data is binary.
• Error-correction is possible because each kind of "bit" (rung) is made of two distinct parts.
• Genes and their switches remind me of objects and their methods.

Pretty cool, imo.

 

[pat34lee]

Not a very good programming language. Every human generation contains, on average, about 60 mutations.
Over 25% of pregnancies end in miscarriage. Due, in part, to more severe "copying" errors.

How many errors are there in a 'sophisticated' programming language such as Windows 10? How fast does it become corrupt through copy errors and software/hardware glitches?

 

[morse86]

How many errors are there in a 'sophisticated' programming language such as Windows 10? How fast does it become corrupt through copy errors and software/hardware glitches?

Are you really comparing programming with DNA?!?!? With current hardware, software can be copied billion times without any issues (it used to be a problem).

Yes there are unknown errors in any software program.....but that doesn't mean it can be compared with DNA. Software is programmed by man, DNA (if it exists) is by God. I doubt DNA exists, I think that all these "scientists" are looking at is just cell debris (or another form of cell debris). It's a hoax.

 

[[serious]]

I'm a programmer and I see some similarities with programming systems.

• The data is binary.
• Error-correction is possible because each kind of "bit" (rung) is made of two distinct parts.
• Genes and their switches remind me of objects and their methods.

Pretty cool, imo.

in what way is DNA binary? There are 4 letters that code for ~20 amino acids.

 

[ChetSinger]

in what way is DNA binary? There are 4 letters that code for ~20 amino acids.

Each rung in the ladder is always either an adenine/thymine pair or a cytosine/guanine pair. There are no other combinations, so it's binary. The rungs remind me of "bits" in a computer storage system, which always have one of two possible states.

 

[ecco]

I'm a programmer and I see some similarities with programming systems.

• The data is binary.
• Error-correction is possible because each kind of "bit" (rung) is made of two distinct parts.
• Genes and their switches remind me of objects and their methods.

Pretty cool, imo.

DNA is not binary
Error correction is not 100%. There are, on average, 60 mutations per generation.

 

[pshun2404]

in what way is DNA binary? There are 4 letters that code for ~20 amino acids.

Actually 64...the 20 are only referred to regarding those necessary for protein synthesis the others have to do with other aspects of defining form and function...

 

[ChetSinger]

in what way is DNA binary? There are 4 letters that code for ~20 amino acids.

As I understand it, the rungs are interpreted in ways other than just amino acid coding. For example, they're used as switches, regulating the timing and amount of expression.

 

[Loudmouth]

As I understand it, the rungs are interpreted in ways other than just amino acid coding. For example, they're used as switches, regulating the timing and amount of expression.

How are do these switches work? How does it compare to the mechanical switches you are comparing them to?

 

[ecco]

How many errors are there in a 'sophisticated' programming language such as Windows 10?

You are confusing a programming language with applications written in that language.
Windows (any version) is not a programming language. It is an application. A large portion of Windows 10 is written in variations of C++.

If I write:
a=2
b=3
Print a*b

6 Will always be printed once.

a=0
do a loop until a = 100

a=a+1
a=a-1
Print "Hello"​

end of loop

Hello will print until someone pulls the plug, runs out of paper, whatever

How fast does it become corrupt through copy errors and software/hardware glitches?

You can copy a cd/dvd/BluRay millions of times without any errors. Whether the media contain music or code makes no difference.

Good software/hardware catches copy errors by reading the original and the copy and comparing the two.

 

[ChetSinger]

How are do these switches work? How does it compare to the mechanical switches you are comparing them to?

I don't know the details, but apparently they regulate both the timing and amount of gene expression. Other switches are turned on and off specifically during fetal development.

 

[Loudmouth]

I don't know the details, but apparently they regulate both the timing and amount of gene expression. Other switches are turned on and off specifically during fetal development.

Don't you think you should know the details?

 

[sfs]

Each rung in the ladder is always either an adenine/thymine pair or a cytosine/guanine pair. There are no other combinations, so it's binary. The rungs remind me of "bits" in a computer storage system, which always have one of two possible states.

DNA is not binary. Reading along one strand, each position can be occupied by 4 different bases, so it's 2 bits per base. The fact the each of those bases will only pair with one possible other base on the complementary strand is irrelevant for storing information in the strand.

But DNA isn't really digital, in fact. A triplet of bases may be a stop codon, for example, telling the protein translation machinery that the end of the protein has been reached, which seems like a digital coding analogous to a computer instruction. Except that, in some cases, the machinery will sometimes randomly read right through the stop codon, generating a longer protein that is also biologically important. A properly functioning digital computer has no analogous operation.

 

[ChetSinger]

In this peer-reviewed publication they find the "redundancy of the genetic code enables translational pausing". Which alone is fascinating, but in reading about how they found this out was the interesting part:...

Not only that, but the cell containing the DNA reminds me of a computer system.

• Information storage: DNA
• Processors: Enzymes
• Process spawning: Ribosomes
• Message handlers: RNA

 

[ChetSinger]

DNA is not binary. Reading along one strand, each position can be occupied by 4 different bases, so it's 2 bits per base. The fact the each of those bases will only pair with one possible other base on the complementary strand is irrelevant for storing information in the strand.

But isn't any single rung interpreted in only one way or another? For example, does the interpretation of an adenine/thymine rung depend on which side of the ladder the adenine is attached to? If yes, then the data interpretation is indeed base-4 instead of base-2. But that wasn't how I understood it (because I've been speaking of data interpretation).

 

[ChetSinger]

But DNA isn't really digital, in fact. A triplet of bases may be a stop codon, for example, telling the protein translation machinery that the end of the protein has been reached, which seems like a digital coding analogous to a computer instruction. Except that, in some cases, the machinery will sometimes randomly read right through the stop codon, generating a longer protein that is also biologically important. A properly functioning digital computer has no analogous operation.

That's interesting, especially that the result is biologically important.

 

[sfs]

But isn't any single rung interpreted in only one way or another? For example, does the interpretation of an adenine/thymine rung depend on which side of the ladder the adenine is attached to? If yes, then the data interpretation is indeed base-4 instead of base-2. But that wasn't how I understood it (because I've been speaking of data interpretation).

The answer is yes. TTT codes for a different amino acid than AAA (or AAT, etc).

 

[sfs]

That's interesting, especially that the result is biologically important.

Yes -- the system has digital aspects, but it's fundamentally chemistry, not an abstract computational process.

 

[Loudmouth]

As I understand it, the rungs are interpreted in ways other than just amino acid coding. For example, they're used as switches, regulating the timing and amount of expression.

They aren't interpreted at all. There are no interpreters inside of a cell. It is the actual physical and chemical properties of those stretches of DNA that give them their function. They serve as a physical substrate for the binding of proteins, to be more specific.

 

[Loudmouth]

But isn't any single rung interpreted in only one way or another? For example, does the interpretation of an adenine/thymine rung depend on which side of the ladder the adenine is attached to? If yes, then the data interpretation is indeed base-4 instead of base-2. But that wasn't how I understood it (because I've been speaking of data interpretation).

As sfs mentions, it is base-4, if you will. If it was base 2 then you could only have 2^3 different combinations per 3 base codon which would limit you to 8 amino acids, not to mention lacking any start or stop codons. Since there are 4 possible bases at each position, there are 4^3, or 64, possible codons.