DNA from the Perspective of a Coder Excerpts

Of the 20,000 to 30,000 genes now thought to be in the human genome, most cells express only a very small part - which makes sense, a liver cell has little need for the DNA code that makes neurons. But as almost all cells carry around a full copy ('distribution') of the genome, a system is needed to #ifdef out stuff not needed. And that is just how it works. The genetic code is full of #if/#endif statements.

This is why 'stem cells' are so hot right now - these cells have the ability to differentiate into everything. The code hasn't been #ifdeffed out yet, so to speak.

Stated more exactly, stem cells do not have everything turned on - they are not at once liver cells and neurons. Cells can be likened to state machines, starting out as a stem cell. Over the lifetime of the cell, during which time it may clone ('fork()') many times, it specializes. Each specialization can be regarded as choosing a branch in a tree.

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The genome is littered with old copies of genes and experiments that went wrong somewhere in the recent past - say, the last half a million years. This code is there but inactive. These are called the 'pseudo genes'.

Furthermore, 97% of your DNA is commented out. DNA is linear and read from start to end. The parts that should not be decoded are marked very clearly, much like C comments. The 3% that is used directly form the so called 'exons'. The comments, that come 'inbetween' are called 'introns'.

These comments are fascinating in their own right. Like C comments they have a start marker, like /*, and a stop marker, like */. But they have some more structure. Remember that DNA is like a tape - the comments need to be snipped out physically! The start of a comment is almost always indicated by the letters 'GT', which thus corresponds to /*, the end is signalled by 'AG', which is then like */.

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Now, DNA is not like a computer programming language. It really isn't. But there are some whopping analogies. We can view each cell as a CPU, running its own kernel. Each cell has a copy of the entire kernel, but choses to activate only the relevant parts. Which modules or drivers it loads, so to speak.

If a cell needs to do something ('call a function'), it whips up the right piece of the genome and transcribes it into RNA. The RNA is then translated into a sequence of amino acids, which together make up a protein the DNA coded for. Now for the really cool bit :-)

This protein is tagged with a shipping address. This is a marker consisting of several amino acids which tell the rest of the cell where this protein needs to go. There is machinery which acts on these instructions, and delivers the protein, which is potentially on the outside of the cell.

The delivery instruction is then stripped off and several post processing steps may be performed, possibly activating the protein - which is good, because you may not want to transport an active protein through places where it should not do work.