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How long have you been doing research?
I wouldn't worry about med schools questioning you stopping, but I would be concerned with the impact on the quality of the LOR from your PI. Have you established enough of a relationship to get a strong LOR? Is it possible your PI has picked up on your feeling that the project is a "piece of crap" and will see through your excuses for leaving?
Of course, if you stick around with that attitude, I doubt you'll be getting a good LOR anyway...
 
How long have you been in the lab? If you've been in the lab for a while and you think you're no longer going to get anything positive out of the experience, I don't think it's a big deal if you quit. Your PI probably has had a lot of undergrads in his lab, so he should understand that undergrads come and go.

If you stick with it but you're going to reduce your lab hours, you should definitely talk to your PI about this first. Your PI might interpret that as you're being lazy and undisciplined, which could affect your LOR in the end.
 
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If you think you can leave amicably and get a good LOR, leave. If you think your PI is the type who might refuse to write you a letter/write a crappy one if you leave, unfortunately staying might be a better idea. The main thing for the LOR is to maintain a good relationship with your PI, and if you don't have that/don't see yourself able to maintain that because of how it is in the lab, leaving and considering other options for a LOR is best.
I wouldn't worry about med schools asking too many questions about your research since you're an MD-only applicant, and they certainly don't expect you to do research every single semester. If you just joined this lab and leave now, there may be questions about why you left so quickly, and you might not be able to significantly talk about the research that you've done. But if you've been there for a while and can talk about what you did, there's nothing to worry about with respect to the med schools. Very few med schools asked me about my research at interviews, and focused more on my clinical experiences (as an MD-only applicant), but that's my n=1 experience.
 
How long have you been doing research?
I wouldn't worry about med schools questioning you stopping, but I would be concerned with the impact on the quality of the LOR from your PI. Have you established enough of a relationship to get a strong LOR? Is it possible your PI has picked up on your feeling that the project is a "piece of crap" and will see through your excuses for leaving?
Of course, if you stick around with that attitude, I doubt you'll be getting a good LOR anyway...

I have 3.5 years of experience, and I have been with this lab for 1.5 years.
Yes, I do have a good relationship with my PI, and I have not shown any indication of my true feelings on the project. I have worked really hard to produce results and get things going despite the inherent weakness of the project. So yeah I know it seems like I have a slight attitude problem but I'm pretty sure it doesn't translate into my work or interactions with my PI. I make sure to keep things professional and grumble only in the background... haha.

I doubt he would write me a poor letter, he is pretty supportive of his undergrads. But then again who really knows what goes into those letters, so I do want to be careful and stay on his good side no matter what.
 
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