Biological systems, it turns out, do something similar. For years, people have known about genes being duplicated for absolutely no reason whatsoever in the same species. Such gene duplications result in copies - the two copies are now referred to as paralogs. What relationship could these paralogs possibly have? More disturbingly, why does the genome put up with them? The consensus today contradicts the almost pop-culture notion that our DNA comprises mostly of junk - a notion put forth by Dawkins' The Selfish Gene among others. It all really boils down to this: even if somebody once added an extra piece of wire by mistake, that extra piece of wire now confers an advantage. Good for you: you can now turn off your TV without having to switch off the ceiling fan.
DeLuna et al's March 2010 paper "Need-Based Up-Regulation of Protein Levels in Response to Deletion of Their Duplicate Genes" addresses these aforementioned relationships between paralogs in a fundamental way. The idea was: lets take a gene X1 and its paralog X2, and see the effect on the protein product of X1 after knocking out X2. The effect, simply, was noted by fusing X1 with a gene which produces a shiny green fluorescent protein. And what transpired? Well, only about 15% of the genes that were used showed any kind of responsiveness when their paralog was deleted. Does that mean the redundancy was just that? The analog of an annoying aunt who can't seem to stop repeating the same story at Eid?
Possibly. But let's examine that 15%. DeLuna et al carried out a number of follow-up checks which led them to conclude that even where X1 did respond, it was a response of increased expression. DeLuna et al concluded that the responsiveness was need-based: it only showed up where your X1 and X2 performed an overlapping function. Should X2 be knocked out, X1 seemed to compensate for the lack of X2 by up-regulating itself particularly in cases where the function that X1 and X2 were carrying out was strictly necessary for the growth of the organism (a fungus, in this case). Thus, if Lys20 makes the essential amino acid Lysine and Lys20's paralog is knocked out, Lys20 will be up-regulated. However, if Lysine is now provided in the medium, Lys20 will go back to its basal expression rate as if its paralog were fit as a fiddle.
In contrast, another paper by Gitter et al found more extensive evidence of a backup system in genetic systems. A gene regulated by a transcription factor (TF1) still manages to be expressed if TF1 is deleted. How? Why, because TF1 has a paralog, that's why! Notwithstanding the fact that evidences for the backup hypothesis have still not reached any definite consensus, it is clear that something much more meaningful than 'the end result' is going on. The text message is almost definitely not exactly the same each time your message gets sent too many times. Your English is almost definitely not as bad as everybody keeps telling you it is.
Kamil
deluna_2010.pdf |