Comment Re:cis and mi regulation is not "bad" code (Score 2) 14
For small genomes, yes, but for large genomes, there is a lot of "unused" material.
Only about 6-10% of the human genome is transcribed into RNA, either protein the coding kind or non-coding types used in regulation. (small genomes are almost always entirely coding and even include overlapping coding regions, large genomes are the ones that have "junk" DNA in them)
Transcription is most closely related to a processor reading machine code and doing something with it. In a computer program, we know that we can safely remove dead code paths and the code will still function. This is not true for DNA. Remove a portion of someone's genome and they usually die.
It's much more likely that the "junk"/"noise" regions of the genome are structural and help the DNA coform so the chromosomes can specialize for different functions. DNA folds differently depending on the cell type in multicellular organisms. Because the nucleus of a cell is a fairly crowded place, the way the DNA folds determines which sites on it are even accessible for transcription. Muscle cells expose one set of gene coding regions, fat cells expose another.
Taken from this perspective, large genomes are more akin to an origami fortune teller than machine code. Depending on the series of folding/unfolding events, a specific fortune is revealed. The fortunes are encoded directly onto the paper, but the paper also forms the structure used to access the fortunes. Another actor reads the instructions and acts on them (a person in the origami case or polymerase for DNA).