Obviously the true reason is that I'd like to get MSTP training, but to answer their questions should I point out PIs that I want to work with or departments that are strong? I think all the schools I listed have departments that fit these two criteria.
Yes, PIs + Departments is a good idea.
Furthermore, if the school has institutions you like, point it out. Lastly, know about the school's culture and curriculum. If you are interviewing at a school that has no grades and you think that is awesome, mention it. Most schools are interviewing you partly to see if you'll "fit in" (if you're interviewing you probably met all their standards, so they want to get a feel for your personality / communication skills / etc).
Which ones would you suggest? I'd rather not say where I am from but I am okay being on either coast.
I'm hesitant to list specific schools I wouldn't apply to, because the entire list you put there is good and I would feel arrogant saying "school X is bad, don't go there." Furthermore, it's very hard to actually know which schools are a bad fit for you, due to my lack of experience.
Lastly, it'll be hard for YOU to know which place you want to go to school until you actually go there.
You're going to spend almost a a decade (or more, if you do a residency there!). That is such a long time that it'll actually have a huge influence on your life-long friends, and possibly who you start a family with.
Unless you've lived in both city / suburban environment or on both coasts / the midwest, etc, you might not realize how much you might enjoy or dislike a bunch of locations. For example, Einstein / UCI / UCLA / UCSD / Chicago all have very different environments...some of which some people hate during the winter, some people hate culturally, etc, etc. Until you go there you won't know for sure.
That being said, your app is so strong that you can cut a few schools and still sleep well at night.
A couple rookie questions here--do MSTP programs always specify the letters they want? Would letters from volunteer ECs where I had leadership experience be helpful? Would it look bad if I had only 1 letter from professor who taught me, and I don't submit a humanities letter? And unfortunately my PI doesn't teach classes that I could take.
No problem, we all start off not knowing this answer!
I believe they all should specify in their website who the want letters from.
They typically only want three letters. Most schools specify a minimum of one letter from a researcher you worked under.
Some specify at minimum two research letters.
I believe there are extra requirements from schools like Chicago / Columbia / Boston University. I recall that a few schools wanted at least one letter from a someone who taught one of my science courses, and I think one school asked for two letters from someone who taught my science courses.
I personally got 3 letters when I started my secondaries. Two were from MDs I researched with, one was an MD-PhD. One letter was from someone who also taught me three times (used this as science). Last minute, I got a 4th LoR from one my science professors from undergrad, but I don't remember where / if I actually used it.
Don't worry - it won't look bad if you only have 1 LoR from one of your professors (with the exception of schools that require 2).
Your GPA / MCAT is so good that no one will have any doubt you can handle the medical school coursework.
If your GPA was considerably lower, I might have given slightly different advice, but for MD/PhD, your letters are supposed to convey
1) You think like a scientist and turn out good research / will be a superb researcher in the future.
2) You understand what you're getting into.
3) You have good motivations for what you're doing. If they have a sentence about your ECs, it can help during interviews.
4) You have good character. (e.g., people like you).
A note on Letters
You may have read a bunch of advice on getting your letters early. The reason for this is it can randomly delay your application, and it's quite stressful to be in a position of having to remind your letter writer to finish the letter (it feels rude to effectively be saying "hurry up!").
Humanities Letter
Almost never matters unless they school specifically asked for it, and even then it might not matter because you're doing MD-PhD. I asked one of my mentors if this would help and she said it had no influence at UCLA (maybe she's wrong?).
Leadership Letters
Matters less than you think for MD-PhD. This won't hurt you, and you should get them. (use a LoR service).
Here is what I recommend you consider:
Your interviewers will often glance through your letters of recommendation, and will probably pay close attention to your LoR from your PI(s).
During the interview, they will raise specific points brought up in those LoRs. If you had a million LoRs about stuff you're not passionate about, this isn't as helpful compared to having 3x letters from researchers, one who specifically mentioned "X taught 6 high school students who loved him! They especially liked blah blah blah."
This actually happened to me during an interview, and it took me off guard (in a good way!)
I was explaining my research (which was a highly technical physics simulation) and my interviewer said "wow, I learned so much just from talking to you. I can see why the students you mentored raved about you in their reviews!"
A Note on Leadership + Education
The fact that you're doing MD-PhD raises the value of education-related ECs. Proving you have an interest in teaching is valuable, because your dream job should be Professor or Clinical Professor. This means in your dream job, you're either teaching residents or students of some kind.
Lastly, if you actually love teaching and it shows, you'll likely share this in common with your interviewer and the two of you can talk about it.
This is a really good point and something I was considering as I started to write my PS draft. I plan to talk about CS more as an addition to a toolbox that I can use both as a physician and a scientist. Do you think it would be a good idea to scale down how much I talk about personalized medicine and big data?
Well, I'm very happy to hear you're thinking about this! I personally feel that medicine needs more people like you.
Sadly, I am not on the admissions committee of every medical school.
I don't know if anyone has a good answer to this.
A lot of people told me to dumb down my essays. This
is likely the correct for the PS, but I don't think know if it's correct for the MD-PhD essay or for secondaries.
Your PS
The fact that you have a CS degree is going to telegraph that you don't have social skills / care about people.
Your research probably doesn't dramatically help this.
Use your PS to explain why you want the MD. (implicitly, this answers "why not get a PhD?")
If you'd be happy doing a PhD, no problem, just do a PhD! However, if you want the MD, there should be a calling you feel that is
not related to the good you can do as a person. You can do plenty of good as a PhD, especially considering your computing skills.
Your PS should explain why you want to see patients, and this goes beyond your philosophy of a scientist.