But beyond a certain scale, complex systems, including complex software, must be grown and not master-planned. This is one of the main advantages of iterative design and development.
Organic life passed this level of complexity long ago. Yes, evolution is dumb enough that it has passed up some obvious improvements. But humans are not (at least not yet) so smart that they could design even a bacterium from scratch, without resorting to iteration, and trial-and-error.
http://www.ted.com/talks/craig_venter_is_on_the_verge_of_cre...
There is, however, a modicum of refactoring.
Software, bad or good, is not like biology and it's not like construction. Software is mathematics.
Seriously though, as messy as organ systems and biochemistry may be, the weird thing is that it all works by itself, using basic chemical properties. I remember how some textbooks can make it sound like proteins and molecules are ordered around in a cell, but in reality everything just floats around, is attracted and repelled to other stuff in the right places, and it works.
I am quite alright with that.
Whatever point he's trying to make in this post - and I'm not going to take the time to try to figure it out - I'm sure there's a simpler way of saying it.