I have not used beaglebone. I have worked with arduino's serial I/O. But this post says you have multiple serial I/O ports on BBB. Find appropriate connectors/convertors for serial to USB.
Then use the pyserial python module. On OSX, you will find your device when connected on a path like /dev/ttyo1 where dev is my system name and ttyo1 or something similar will be your device.
import serial as s
device = "/dev/tty01"
bbb = s.Serial(device, 4800) #the second param is baudrate
while(True):
bbb.readline()
# do what you want with the output.
bbb.write('input')
This will read till the end of line character and give you a string. and then write "input" to the serial io on bbb. You will need a similar program running on BBB to read this input and do what you want to do with it.
So there will be two python programs. One on the OSX and the other on the BBB
That way you can give commands from OSX.py, let your BBB.py process and send a response. Which the OSX.py will read and do what is to be done.
You will have to design the input/output cycle properly.
Also if flash is not really necessary you can check out pyside.