Dr. Anirban Bandyopadhyah, of the National Institute of Materials Science in Tsukuba, Japan, has developed a chemical "brain" capable of controlling nanobots. This "brain", soon to be known by the few remaining humans not killed in the machine uprising as "Mother Brain" will control the bots responsible for the demise of humanity. The cave dwelling survivors of the apocalypse will regularly pray to Samus Aran that she return in all her hotness and destroy said brain to make the planet safe for humans once more.
Anyway, the two nanometer "brain" is made of 17 molecules of duroquinone, each considered a "logic device" and controlled by a center "control" molecule. By switching the control molecule in the center with a scanning tunneling microscope, the other 16 are switched based on the logical instructions received. There are over four billion combinations of outcome. At least three billion being "We're all going to die", and the other billion being "We're all going to die slowly."
Chemical brain controls nanobots [bbcnews]
Thanks to Justin, who may have to step in for Samus if things get out of hand, for the tip