How can words instruct machines?
When converted to 0s and 1s, they're not words anymore, they are a configuration for the machine. In a way, they are words only as a help to our human understanding. As it often happens, we end up confusing our own conceptions with reality.

Computer networks, distributed systems and interactive computing add other layers of complexity to this picture. Since you cannot consider standalone computer as closed systems of hardware and software, it becomes even more tempting to see programs as transcendent writings, whose meaning commands the machines were they run. 

It is definitely not the case. Words are aids, nothing more.

To put it differently: a program, or any kind of source code, is already given to the compiler as a sequence of 0s and 1s. Even if not directly composed of machine instructions, this sequence of bits can be deterministically converted to machine code. That's what a program translator (compiler, interpreter, emulator, etc.) does.