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OP, if you're describing your fantasy scenario (since you're actually a pre-med right now), maybe you shouldn't go to medical school and should just get a PhD. It honestly sounds like your heart is in research, not clinical work. Doing a PhD between receiving your MD and doing residency would be a financially disastrous idea; even if we set accumulating loan interest aside, we're talking about a >$1M opportunity cost (for a future neurosurgeon, more like $3-4M).
 
Hi guys, so I am about to graduate from medical school, and instead of pursuing residency at the moment, I am very interested in applying to PhD programs, in particular, neuroscience and immunology at Harvard/MIT. I have quite a few faculty members that I aspire to work with there.

In medical school, I did neurosurgical research, published 4 papers, won a few grants, and got a MS from Cambridge University in compneuro.

Would finishing up a PhD and then applying for residency programs in neurosurgery hurt me since I am not a direct applicant from medical school, but about 4-5 years away from my medical school training?

Or would you recommend for me to apply for neurosurgical programs, and immediately matriculate into a residency program, and do a postdoc at Harvard/MIT following my residency?