For clarity DARPA isn't part of the DoD it's a civilian run federal research organization.
https://en.wikipedia.org/wiki/List_of_U.S._Department_of_Def...
If you doubt Wikipedia, here's a DOD org chart from inside government: http://dcmo.defense.gov/Portals/47/Documents/PDSD/201509_DoD...
I'm also not sure what point you're trying to make, because of course the DoD is also civilian run. That's been fundamental to the Department of Defense since its founding.