I see two major problems with this:
1. The author fails to realize that the typical hierarchy of a program is that a program requires coreutils (operating system more or less) which require a kernel which requires the hardware itself. To increase speed, the author suggests that the entire algorithms be moved to chips similar to the CPU. A better way would be to utilize what we already have; clusters of Xeon servers and GPU processing which are incredibly fast. How do we utilize that in a more efficient manner? Write a new kernel. The fastest method we can achieve right now would be to, in ASM, write exactly what we need, no more, no less. If your algorithms can't be translated to ASM, then a light weight C/C++/Fortran compiler can be written, and by light weight I mean it leaves out that which you don't need. See problem two on why this is better.
2. When you write a program, do you let it run forever, or do you have to make occasional changes? "Oh, something went wrong, let me just go move around some logic gates on the nanoscopic scale."
Looking back, is this a joke article? Did he also write about aluminum-powered cars being released next year just in case it happened?