Each school/college/university has a numbering scheme for its courses. From the Harvard University 2013-2014 Guideline for Courses of Instruction
Course Number
Courses may have only one number and be listed in full by only one department or committee. The course number includes the two, three or four
digit number used to identify the course within its course group. They may be numbers only or letters only. Additional letters that signify credit,
duration, etc., may be added to each type. Courses are numbered according to the following scheme:
Explanation of Course Numbers as Numbers
Most courses are numbered with the following general scheme:
1–99 Primarily for Undergraduates
If I recall from my college days, the higher the number, the more advanced the course. I would speculate that 50, in the middle of the range, was chosen, so that "easier" or "harder" courses could be appropriately numbered. Or not :)