Perhaps one or more of the recommendations written on your behalf were just neutral, which would not help a graduate school applicant, especially in the sciences. Also in your CV, have you described how you have contributed to and emphasized what you understand about the projects you worked on? For example, “I used techniques X1 and X2 to investigate if Y binds with Z to form a complex, which is required for other processes downstream”, instead of, “I know techniques X1, X2…”. In some of the selective science programs at the graduate level, a masters degree is a consolation prize for those who have not passed their Ph.D. qualifying exams; however, master degrees are useful for employment in the industries.
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