How did the phrase 'how come?' derive from 'why?'?

Actually, the phrase “How come” wasn’t derived from the question “why”.  Instead, it originated back in the mid 1600’s when the English fist stared to colonize America.  On one trip, a colonist named Jeremiah brought over 2 English Sheepdogs – James and Mary.  His plan was to breed the dogs and sell the pups to other colonists.   During the trip, James and Mary decided to “get a head start” on things, so shortly after the ship landed Mary gave birth to 5 puppies.  Four of the dogs were fine and healthy, but the fifth pup had a few problems.  In fact, it had so many problems that no one thought it would live.  Much to everyone’s surprise the dog lived.   Jeremiah was so surprised at the pup that he named it How.  Now, due to complications from his infirmities, How was partially deaf.   Nonetheless, all the other colonists loved How.  How would roam the town barking at colonists so that they’d give him some scarps of food. 

While How’s brothers and sisters learned to obey early, How had problems.  He got the concept of ‘sit’ and ‘stay’, he had a problem with ‘come’.   Jeremiah would call out, “How, come!”, but How would just sit there unmoving.  Other colonists tried to help Jeremiah, by calling out “How, come!”, but still How just sat there.  After several weeks of How not coming, Jeremiah decided that maybe How couldn’t hear the word ‘come’.  Therefore, instead of speaking the command, Jeremiah taught How to come by holding out his hands and shrugging his shoulders.  It worked!  All Jeremiah had to do was hold out his hands, palms up, and shrug his shoulder and How would come wagging his tail eagerly.  Occasionally, Jeremiah would also call out the command “How, come!” at the same time... just in case.  Soon everyone in town started holding their hands out and shrug their shoulders so How would come to them.  it wasn’t long before kids started imitating How’s ‘come’ command even though the dog was nowhere around.  By and by, “how come “became in everyday speech.  Even today, people will still hold out their hands, shrug their shoulders, and say “how come”.