Another book that takes this "soup to nuts" approach to the pillar of computer abstractions is Zalewski's "Silence on the Wire". It's mostly focused on computer

Another book that takes this "soup to nuts" approach to the pillar of computer abstractions is Zalewski's "Silence on the Wire". It's mostly focused on computer security, but it does an excellent job of peeling back software abstractions and showing how innocent decisions like blinkenlights and link-following web spiders can be utilized to compromise security. My favorite computer security book, easily.