This video comprehensively explains how a hypothetical attack could be carried out by an attacker using the Stuxnet worm. This has very serious implications because it means that low-level industrial embedded systems are also now targets for attack. These SCADA systems are used everywhere and lack the necessary resources to defend themselves from attack.
The technique used is a fairly straight-forward one. The attacker can download and modify a programming library and use that to intercept the actual programme being downloaded onto the SCADA system.
This technique has been used for ages, in a non-malicious way. For example, my Xilinx board does not properly support my OS for programming. Thankfully, someone out there has written an open source driver to intercept all the Xilinx calls. Install this driver and the Xilinx ISE will think that it is talking to its own driver while all its calls are actually being intercepted by the wrapper.
Interesting, and cool.
This makes me think that I will probably need to build in some protection to my future cores to at least enable a limited amount of security checking of downloaded code.