Biological Information in 3 Dimensions- Evidence for Life's Software, Again

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Up to now biological information has always been related to the DNA sequence (sequence related). IOW the information depended on the sequence.

I do not believe this is a tenable position. I say that because in biology we observe that DNA just doesn't replicate itself, it does so with the help of other molecules in the cell. Those molecules are constructed by the information stored in the DNA. That's right- stored in- as in the data that is stored in a computer's hard drive, ROM and RAM.

And this is my point- that DNA, RNA and other cellular components are actually data carriers just like the computer components I just mentioned.

IOW the sequence is not the information. The sequence is important to carry out the instructions, that is the information embedded in the DNA (and perhaps other cellular components).

As I said in an earlier entry- Just for a eukaryotic cell to make an amino acid (polypeptide) chain-

Transcription and Translation:

You start with a tightly wound piece of DNA. Enzymes called RNA polymerases, along with transcrition factors, begin the process by unwinding a portion of DNA near the start of a gene, which is specified by sequences called promoters. Now there are two strands exposed. One strand is the coding strand- it has the correct sequence information for the product- and the other strand is the non-coding strand. That strand contains the complimentary layout.

At this point decisions have to be made. Where to start, where to stop and although it may seem counterintuitive the mRNA goes to the non-coding strand in order to reconstruct the proper codon sequence (nucleotide triplets which code for an amino acid) for the protein to be formed. Both sides of the parent DNA are exposed yet the mRNA "knows" to only form on one.

This process is unidirectional (5’-3’). There is only one start codon which also codes for an amino acid (met) and therefore all amino acid sequences start with methionine. The stop codons don’t code for an amino acid. Transcription actually starts before the “start” codon and continues past the stop codon. Before the mRNA leaves the nucleus any/ all introns are cut out and the remaining exons spliced together. A chemical cap is added to the 5’ end, the non-coding stuff at the end is cut off by a special enzyme (endonuclease) and a string of A’s is added in its place. You now have a processed mRNA.

So now we have this piece of processed mRNA which leaves the nucleus and has to rendezvous with a ribosome-the protein factory within the cell.

A ribosome consists of over 50 proteins and 3-4 different kinds of rRNA (ribosomal), plus free-floating tRNA (transfer). Each tRNA has a 3 nucleotide sequence- the anti-codon to the mRNA’s codon plus it carries the appropriate amino acid molecule for its anti-codon. To attach the appropriate amino acid to the correct anti-codon an enzyme called amino-acid synthase is used.

There, large workbenches made of both protein and nucleic acid grab the mRNA so the correct amino acids can be brought up to the mRNA. Each amino acid is escorted by a module called tRNA or transfer RNA. It is important to note that the escort molecules have three bases prominently exposed on their backsides and that these molecules also use the base U instead of T. The kind of amino acid is determined precisely by the tRNA escort’s anticodon, or triplet set of bases on the escort’s backside.-pg 23

And then the chain starts forming until the stop codon terminates the process.

Next is the folding process. That is what allows the protein to be useful- its spatial configuration.

That is just the basics of what one is introduced to when reading biology textbooks. And it doesn't include the proof-reading and error correction that accompanies the process.

So this is how I envision DNA- both sides of the ladder carry redundant information. One side does the work, that is transfers programming data to other molecules it contacts (mRNA for example) and the other side is a template for DNA replication.

Once DNA replication is complete the program is transferred to the newly constructed side via the hydrogen bonds that connect the two sides.

When other molecules are made- mRNA for example- they are given their instructions via the same hydrogen bonds. That information consists of editing instructions, as well as configuration/ assembly instructions and destination instructions.

These instructions are not the sequence, rather they are embedded on the sequence, just as computer data is embedded on the disk.


The ribosome is a genetic compiler!

The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.

Think about it-

What happens to a newly written or modified computer code that has an error? All new and modified codes have to go through a compiler.

A compiler is nothing if not an editorial perfectionist!

I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free.

Biologists need to be introduced to and experience computer science.

Then this sort of discovery wouldn’t be so “shocking”.

Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids).

So where is the software? In the cell, meaning it is all throughout the cell- it isn't just in one place in the cell.