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I really want to pursue a science PhD, but I'm concerned about a red flag in my application.

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I will try to make this as short and sweet as possible. I'm including my "story" at the end. Look within the --- for a simpler stats/summary.


Double major in Chemistry (biochem conc.) and Biology, minors in mathematics & statistics at a large public R1 university

4.0 GPA (~3.9 if you factor in a B&C from over 5 years ago when I attended community college). I attended community college on and off from 2013-2016 while working with no real direction. Attended my university from 2017-2020 full-time, graduated May 2020. 

Haven't taken the GRE and not sure if I will considering it seems to be getting phased out. We'll see how may schools ask for it in the future.

1 year of research experience in a pharmacology lab, spanned summer 2018-summer 2019, did a senior thesis, poster presentation, and oral presentation.

sub-1 year experience in a chemical biology lab, cut short by covid. Aside from the lab experiences, did not produce anything tangible.

Worked as a TA for two years for organic, 1 semester for cell biology, 2.5 years as a tutor for chem/bio/math. I doubt grad schools care too much about teaching experience but it was something I really loved doing and definitely played a part in solidifying my passion for science.

Post-grad, I've been working as a metrologist (analytical equipment maintenance, troubleshooting etc.) at a pharma company. COVID put me in the "I just need a job" position and I ended up here.

LoRs would be:

Pharmacology lab PI. As far as research, worked closely with him for the longest.

Organic chemistry professor. Took her class for 2 semesters and then was her TA for the next 2 years. Did exceptionally well (I know that grades aren't all that important for phd applications, but got the highest grade in her class both semesters out of 150-250 people) and knows how much of a passion I have for chemistry. Have known and worked with her for the longest.

??? This is the red flag. I do not feel comfortable asking my second year of research PI for a LoR. There are a few reasons for this, but I won't bore you with them.


My goal right now is to get a year+ of fulltime research experience down at the NIH postbacc program, which would provide me with plenty to talk about in my SOP and hopefully a third letter. I intend on applying to chemistry/chembio/somewhere in between chemistry and biology PhD programs. I'm thinking 1-2 years of fulltime research at a reputed organization like the NIH and a letter from a PI there would be more than enough to counteract that, but I'm not sure. I have a narrative that might impact things but this post is already too long. My big concern is not having a letter from one of my research experiences. Note that I am aiming for top programs - not necessarily Berkeley/Harvard/MIT etc. but at least top 20-30. 

I've been beating myself up about how my last undergrad research experience ended (the fact that I won't get a letter from it) and I'm wondering if it's actually the nail in the coffin for me or if there's hope. 

My story is: First-gen low-income student. Went to community college while working retail, didn't really know what I was doing, went part time some semesters, skipped some semesters, did okay from 2013-2016. Was bored with life, went back to school Fall 2017. Fell in love with organic chemistry, did incredibly well grade-wise all 3 years. Decided to work in a pharmacology lab starting that summer as a attempt to follow my passion for chemistry despite being a biology major. Enjoyed it but the chemistry side of things was my passion. Decided to switch majors to chemistry starting Spring 2019 but ended up just double majoring since I had so many biology credits. This added another year to college, which was probably stupid, but whatever. I also had to cram chemistry major classes into just 3 semesters. I was basically like wow, I really love chemistry and I need to major in it if I want to pursue it! So I did that. I ended up taking calc I/II back to back 4 weeks each that summer - 5 years after taking precalc - just so that I could take PChem. I also took orgo my first semester back in college 3-4 years after taking gen chem, same with analytical etc. Aced everything.

Applied for a scholarship that summer and didn't get it. Was way more bummed out about this than I should have been. Led me to switch to another lab more chemistry-focused - I lost the scholarship, in my mind, because everything pointed to my passion in chemistry whereas my research (it was a prestigious undergrad research scholarship) was not really chemistry. Interview was also pretty bad, partially because of that. So, I was able to switch labs. Contacted an old professor, his lab was full but there was a new PI setting up a lab who he was working with. This was supposed to be my grand entry into chemistry research. Ended up working with both of them on a single project. Long story short, my time was spent between two labs, never really was able to fully get my footing in each because I started at the beginning of the fall semester, I was working 20 hours a week TA/tutoring because research wasn't going to pay the bills, and taking the hardest classes of my college career. I basically proved the concern every PI has about undergrads - they won't have enough time or aren't committed enough. I had finally started getting my footing at the beginning of 2020, and then COVID hit and I couldn't work in the lab.

All in all, my time in undergrad involved me getting straight A's and trying to do research while having hard class schedules every semester (summers included) and working as a tutor/TA ~20 hours a week because I'm poor. My first year of research was more productive because I had a month in the summer to get started, and when I had the chance to do the research I wanted to I messed it up. Once COVID hit I couldn't really fix that, and then I got on unemployment and just needed a job and here I am now. Happy to be employed, but bored with the 9 to 5 life and looking into my career once more. I've been beating myself up about my last year of college, but I'm trying to move forward. The goal is a year or two of postbacc research fulltime - without classes or work to worry about. Ideally when I apply in a year or two the narrative will make some sense - basically "guy who had to work his way through school while taking hard classes couldn't fully invest in research in undergrad, COVID made survival a priority immediately afterwards, decided to get some fulltime research experience under his belt after school to make sure it was for him and prove he had what it takes, and here he is." I basically spread myself thin trying to do my best at everything - I got the best grades, was known as the best orgo TA/tutor, and research... did not get the attention it should have. I also wasn't decided on if I wanted to do med school, grad school, md-phd, etc. I basically wanted to do everything and this led to everything suffering a little, especially in my final year. This isn't something that'll go into my PS when the time comes, but socially my entire self esteem was also tied to my grades and being everyone's favorite organic chemistry tutor/TA. Not healthy at all and led me to invest more time into those things than I should have.

Edited by orgopapi
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You post a lot of info here, so I might be able to touch on it all.  

Off the bat, you already have a solid background so no need for the NIH postbacc unless you specifically want to do biomedical or chem-med.  Doing it simply for the LOR is a waste of your time, the potential PIs time, and you may take a spot from someone who legitimately needs the postbacc.  You already have 'plenty to talk about in your SOP' and it is perfectly acceptable for a third letter to be from a professor. 

Ph.D. programs are internships.  They are on-the-job training with the goal of training you to do things the way that they do them; one reason why fit is so important.  "Perfect' applicants say nothing about their ability to be trained, only that they test well.  Not all applicants have published papers (to be frank, this pretty rare for those applying straight from undergrad), and the average amount of research ranges from one summer to one year.   Ph.D. students drop out all the time and for a variety of reasons, one of which is the realization that they ultimately do not like doing research (because it is different than from what they thought it would be).  That is the whole point for having research experience prior to applying to grad school, so that you know the ins and outs and can see yourself doing nothing else for a career. You don't have to produce anything, it is all about the experience, and I know this may sound odd but that second research experience of yours was not a failure.  It's likely to not only be a strength to your application, but a very strong one at that.  Screwing up in research and other setbacks are common and good lessons to learn before you embark on a Ph.D.  Instead of looking at this as a failure, reframe it as a lesson learned. 

You took Calc I and II just so you could take PChem, after deciding to double-major knowing it would add a year to your program!  How many other applicants do you think did that?  Or would do something like?  Close to zero.  This alone puts you a head of the rest as it shows drive and passion.  

Your typical applicant, even those accepted into top programs, have pretty much average undergraduate careers.  That is to say they took (and only took) the required courses for their programs with an elective or two out of interests (but still within their field), did perhaps one (or two) summer REUs, and got good grades and GRE scores.  Obviously, they wrote a good SOP and had good LORs (with one or two of them likely being from professors, not research PIs).  

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