I think "by"+noun is only used in certain cases, most notably transport and communication:
I went to Aberdeen by train.
I came home by bus.
We keep in touch by letter.
I contacted her by phone.
Your "phone" example is one of these.
The only other example I can think of is the phrase "by hook or by crook", which has an origin so old it doesn't represent modern English.
You can use "by" + "-ing" more widely:
I surfed the net by using a computer.
I found enlightenment by eating cake.