System.nanoTime() is defined as having an arbitrary start time. However, there is no reason to make it random and it is based on an unspecified system call. On Centos 5.7 and other Linuxes I have tried, this appears to be based on the uptime.
System.out.println("/proc/uptime " + new Scanner(new FileInputStream("/proc/uptime")).next()); System.out.println("System.nanoTime " + System.nanoTime() / 1e9);prints
/proc/uptime 265671.85 System.nanoTime 265671.854834206