A 'normal' course counts as 3 credits per semester. However, certain courses stand out as needing more work than the majority. Often these are courses with significant class projects, or other atypical requirements. These classes are frequently given 4.5 credits to reflect this additional effort, so that ideally students taking such courses can take fewer courses in a given semester to ensure they have time to do all the work adequately.
The problem with this arrangement comes from quantization. If you want to take 12 credits in a semester (the usual full-time load for a graduate student), but one of the classes is 4.5 credits, you will either have to find a second 4.5 credit class, try to arrange for 1.5 credit "individual research" project with a professor, or end up taking a non-integer number of credits like 13.5.
This also aggregates to the degree level, where if you are paying for each credit individually it seems pointless to pay for 31.5 credits when you only need 30 to get your MS.
The faculty is aware of these problems, but no easy solution exists. One possibility is to try to shift all courses back to 3 credits, but this requires the agreement of each individual faculty teaching a 4.5 credit class and revision of the syllabus in each case. Also, some students appreciate 4.5 credit classes as a way to earn their MS with fewer, more intense classes.
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