Arduino IDE in conflict with pyserial for use of serial port in OSX Yosemite
Ok, I solved it. First I stopped using the IDE serial monitor as Majenko suggested, and focused on getting the Arduino readings within the python code. Besides trying to use the python code and the IDE monitor at the same time (which apparently you can do in Ubuntu but not in OSX), the original problem was that my python code was not clearing the serial buffer in the r/w process. In order to do this, I wrote the following function to be called before and after a serial write:

 ser = serial.Serial('/dev/cu.usbmodem1421', 9600)

 def readarduino(ser):
    did=True
    while ser.inWaiting(): # Check number of characters left in buffer
        if did and ser.inWaiting() &lt; 490: # Select last 500 characters in buffer
            for i in range(6):
                print ser.readline() # Print 6 lines in buffer
            did = False
        ser.readline()  # Clear buffer line by line until ser.inWaiting goes to 0


This ensures that the buffer is clear whenever I am writing to the Arduino.

This solution works for OSX Yosemite and Ubuntu 14.04