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Well, stipends are high because they're heavily subsidized by NIH -- NIH pays $20,976 per year for each biology PhD student on a training grant (which basically everybody is), so a program in Boston like Harvard or MIT is only coughing up about $8000 for each student's stipend.
I can't answer why starting salaries are so low, other than that perhaps it's to make it more attractive to go back to grad school, further education being necessary for advancement in biology, but not so much in engineering.
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