My PhD Journey in the U.S.

DGL70🎉

Sunday, June 22

166.4 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (6/6) | ★★★★

After a refreshing workout (6th session this week🙂), I headed to the public library again. Spending part of the weekend there to reflect really helps me reset. Yesterday I finished listening to the recording of Friday’s meeting; today I polished the notes, emailed a clean summary, and shared the materials via Box. Time is flying!

In the evening, I grabbed noodles at Hai Ky Mi Gia (707 Ellis St, San Francisco, CA 94109) with my friend. The wontons were fantastic, though the roast duck wasn’t really my thing🤨 The area has many homeless people, so getting there isn’t exactly pleasant, but I’ve heard there are lots of great restaurants nearby… San Francisco can be wonderful in some pockets and downright unsettling in others. It seems like too hard for the whole city to improve at once.

Getting back home, I kept thinking about my thesis idea. The more I research, the more I worry it could end up as “science for science’s sake” instead of something practical. I’ll ask about my concerns with some senior lab members on Monday.

Monday, June 23

168.6 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6) | ★★★★

I slept well, arrived at work on time, and asked the opinions of several people about Friday’s meeting. No one seems entirely convinced that this idea is really great, and the more I investigate, the more I see that any biological applications we could achieve from this may already be tackled better by other methodologies. After spending the whole day reading papers and considering alternatives, I began to question whether this is the right path or not. I emailed a post-doc who works in a related area to set up a meeting tomorrow; afterward I’ll summarize our discussion and send the professors an update on my thoughts and next steps. + I upload a photo of today’s onion rings. Apparently, I always end up eating something fried at the hospital cafeteria😅

After work, I went to the gym, had dinner, and jumped on Zoom with the friend I saw Saturday. He also does protein design and needs to nail down a new project topic. His proposed direction is closely related to what I worked on during my rotation, so he wanted my feedback before pitching it to his PI. I’m also wrestling with my own topic, so it’s quite helpful to see how others carve out their projects. Hmm…where do real breakthroughs come from? Whatever I choose, I want my thesis to tackle an unresolved biological problem, something I can truly be proud of.

Tuesday, June 24

168.8 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★★

I had a quick meeting with the post-doc I scheduled yesterday and came away with a lot of useful information. Because he works in a similar area, he has a clear picture of what other labs are doing and pointed me to several relevant papers. In fact, he submitted a manuscript to Science just yesterday; the work looks promising, and I hope it’s accepted. The field is so hot that at least two other groups are racing to publish, so he said he felt the pressure to get it out quickly.

I had lunch with the Korean post-doc (I really should start eating more healthfully😛) and took a refreshing walk afterward. Back in the lab, I summarized the meeting, read a few more related papers, and emailed my professors an update before heading home. Hit the gym, did a bit more literature searching, and went to bed early. Tomorrow I have to be up early to help with an event, DGL70.

Wednesday, June 25

🏃🏻 Rest (2/6) | ★★★★★

Today was DGL70, a celebration of Professor Bill DeGrado’s 70th birthday. His actual birthday is in September, but so many of his former students, post-docs, collaborators, and friends are in town for The Protein Society Annual Symposium that we held the party now. From early morning, the room filled with talks and lively conversations; I learned a lot just chatting with the crowd and felt even more motivated to shape my own research topic.

The highlight for me was a wholesome talk by Bill’s longtime friend Professor Jim Wells. He wove together personal stories (he joked that he’s spent more hours with Bill than without him haha) and scientific collaborations that stretched across decades. Their friendship and mutual respect, both as scientists and as people, were inspiring; I found myself snapping photos of nearly every slide.

The day ended with video messages from people who couldn’t attend and a short closing speech from Bill. Moments like this remind me that technical brilliance isn’t enough; genuine kindness and integrity matter just as much. After all, no one admires a genius who treats others poorly. Being consistently considerate requires real effort and self-discipline.

After the talks, we each received a commemorative DGL 70 T-shirt and a 3D-printed model of one of Bill’s de novo proteins🥳, then headed to the dinner party at Taksim (564 4th St, San Francisco, CA 94107). Professor Yong-Ho Kim from SKKU arrived with six of his students, and the current Korean post-doc in the lab (Yong-Ho’s very first student) joined us as well. We enjoyed a two-course meal plus dessert, which was quite satisfying. We all surprised Bill with a “wholesome” cake and a tablecloth signed by everyone. Bill made a point of visiting every table and talking to each person; his energy and warmth were soooo and wholesome.

The evening wrapped up after nine. I’d been helping with setup since early morning, so I came home exhausted and fell asleep almost immediately, but with a head full of new ideas and a heart full of admiration.

Thursday, June 26

🏃🏻 Done (3/6) | ★★★★

Maybe I pushed myself too hard yesterday. I woke up at dawn coughing and felt off all day, so I only stopped by the lab briefly and did most of my work from home. After a quick workout, I went to a Chinese restaurant (Z & Y Restaurant, 655 Jackson St, San Francisco, CA 94133) in Chinatown for dinner. The fried rice was fine, but the beef pancake and the chili-oil fish fillet were fantastic. The pancake’s combination of cilantro, cucumber, and thinly sliced beef shank was perfect, and the fish fillet reminded me of the flavor I tasted at Shanghai Disneyland. Totally satisfying. Determined not to lie down on a full stomach, I walked home and went to bed early.

Lately, I’ve been rating my days on a five-point scale. Technically, 2.5 is average, but I find it hard to give myself below a 4🫠 maybe I should grade more strictly…?

Friday, June 27

167.0 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6) | ★★★★

At 10 am, I grabbed coffee with a fifth-year student in the DeGrado Lab, technically one of my seniors in the CCB program. She shared the realistic challenges of a PhD: experiments rarely work the first time, unexpected results are normal, and the key is to trust your mentors (and yourself) and keep working hard. We also discussed a potential thesis idea I wanted to do, and she helped me organize my thoughts a lot!

After the coffee chat, I headed to UCSF Bayfront urgent care. I woke up at 2–3 am due to severe coughing, so I booked an urgent-care slot. Fortunately, the doctor ruled out pneumonia by a clear chest X-ray result, and there was no wheezing, so asthma seems unlikely. The doctor prescribed 1. Famotidine (an H2-receptor antagonist) for possible GERD (gastroesophageal reflux disease) / 2. Fluticasone nasal spray for allergy-related inflammation. If I’m not better in a week, she’ll add Cetirizine (an antihistamine); if that still fails, we might try an inhaled corticosteroid. I felt a bit reassured leaving the clinic, grabbed a quick cafeteria lunch, and took the first doses.

Once I got back home, I published my latest blog post and then spent some time doing background reading for my thesis. I’m leaning toward a different direction from my advisor’s original idea, so I need to schedule a meeting to discuss it. In the evening, I squeezed in a quick gym session. My dinner plans with a friend were cancelled at the last minute, so I just meal-prepped some chicken thighs and jasmine rice at home and unwound with a few 침착맨 YouTube videos🙃

Saturday, June 28

167.7 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★★☆

I’m happy that I slept straight through the night, no mid-sleep coughing! I got up early and did have a bad coughing spell after I woke up, but that’s still better than being jolted awake at 3 a.m. If I keep taking my meds consistently, I’m sure things will keep improving. I grabbed a quick breakfast and wrote a blog post. After hitting the gym with a friend. Today I felt like I needed a serious focus block, so I skipped the public library (too many distractions, sometimes even somewhat threatening people) and tried a new study spot instead: Mechanics’ Institute (57 Post St, San Francisco, CA 94104)

It was fantastic! quiet, cozy desks tucked between bookshelves, and even a chess room that gives off a slight Harry-Potter vibe. I was so impressed that I signed up for a student membership on the spot: $80 a year versus $15 per day, totally worth it (should be😁). Unfortunately, it’s closed on Sundays, but I’ll make it my regular Saturday haunt. I spent the afternoon polishing an old side-project manuscript. It probably won’t make it into a journal on its own, so the plan is to post it on bioRxiv and later combine the data with a bigger study. AI models that can run this kind of analysis are improving rapidly, so the sooner we upload, the better. I didn’t finish all the revisions, so tomorrow will be another sprint.

For dinner, we tried Chipotle nearby. My friend showed me the “shake the closed bowl like crazy” trick😂, and it was surprisingly good. Big portions, decent taste, fair price! Too bad there isn’t one near campus. Instead of going back home, I headed straight to Hub to keep working. I still need feedback on my potential thesis project; hopefully, I can nail down the direction before my trip to Korea🥹