Euphoria (Update)
This post is inspired by the two things I’m obsessed with: mass specs and mopeds. The vibe is up and stuck, forever.
Postdoc-level Moped Shit and Beyond
There are a lot of fucking hills in the La Jolla/Torrey Pines/UTC area. I thought I would be fine since before leaving the SF bay, I: geared down (from running a pw50 diff), added Boysen reeds, and upgraded to 40 lb clutch springs (Berkeley, I’m ready for our rematch). Unfortunately, it’s barely enough to hit the speed limit (45 mph) uphill. By moped standards this is amazing, and I am a serious contender for fastest moped in SD, but that’s not enough anymore. To safely ride in the CA streets, I want to hit 15 over the speed limit with ease. Since I am at the limit of aftermarket parts, I’m going to have to start ordering custom parts from machine shops: stuffy stroker cranks, custom cases, and a few other things.
I think this is blog-worthy because 1) I pay the bill for this website, and 2) I stopped mopeding during grad school and didn’t pick it back up during my first postdoc. This was partly due to time constraints, partly because I seized my shit, and partly because I wasn’t comfortable riding my moped above 40 mph*. Storing my bike for so many years felt bad, but during the worst year in my life, it kinda kept me alive. Since rebuilding the bike by myself, it feels like the risk-reward odds have skewed in my favor. In fact, the power-to-weight ratio that used to scare me now has me chasing faster speeds. I don’t care if it’s a 90 lb bike, never DNF.
Anyway, everyone tells me my bikes are magnificent, and they really are. The green goose is running, but since it has an LC50 crank/case, the stock qt50 exhaust doesn’t fit right and is acting like a rev limiter. I bought an A35 bi-turbo pipe, but have been too busy to grind out the mounting holes for proper fitment. I recently snagged one of the rarest Yamahopper parts of all time: the legendary leg shields for the MA50 (eurospec QT50.) I also picked up a European LC50 fuel meter and modified it to fit La Poderosa, but I want to order got one for the green goose before the import tariffs hit.
The green goose taking flight.
With La Poderosa, I almost went a full year with no breakdowns, but on the moped Wednesday before thanksgiving, my bike cut out at a stoplight. Turns out, one of my high-stall clutch springs broke, which mean that the transmission was constantly engaged (because centripetal force). Since clutch disengagement is basically my neutral, there was no way to keep the engine on (you can technical try to bump start but that would damage the transmission). It being a noped, I had to walk it to my car, but at least I was only 2 miles away. I was running the 40 lb springs before, and I tried the malossi scooter springs, but they didn’t fit, so I’m sticking to the 40 lb springs for now. On the plus side, my moped was the only one in the gang making enough power to climb the hill on 2000s block of B Street near downtown.
La Poderosa is still my baby and the green goose is still a work in progress, but I’m on the market for a more reliable daily motorbike. I’m thinking something like a Honda Super Cub/S90 or a ready to rally 1980s Vespa scooter. I’m open to sticking with 2stroke engines, but since I don’t really want another project, I wouldn’t be opposed to something like a Lifan’d Honda Passport.
“Learning” Bioinformatics
Insisting upon themselves smh.
As a grad student, and even during my first postdoc, I recognized that (gene-based) bioinformatics could be useful depending on the question. This is a general opinion I hold against all techniques: western blots, electrophysiology, protein modeling, ELISAs, CRISPR, etc. It was never a major or even minor component of my training, so I didn’t go out of my way to learn it any deeper than a respectful understanding. An aside: I feel like it’s frowned upon to admit that. I’m not saying it’s useless, I just never had a use for it, and I refuse to force the use of techniques when they’re not appropriate. Now that I’m in a proteomics lab, of course I need to use bioinformatics, so how is that going?
I’m not going to lie: it’s ok. The protein tools are the coolest, the gene ones are fine. I strongly prefer working at the bench, and I never see myself switching to only dry lab**. I had a little experience with python and R before/during grad school, so the concepts aren’t hard for me to grasp. I also don’t mind being on the hook for writing my own code/analysis either. My issue is that I see the limitations in coding vs the limitations in experimental design, and I prefer to pipette my problems away.
Anyway, I have nothing to add in this blog post R.E. general tips for learning (gene based) bioinformatics. Everyone learning to code and work with large datasets will tell you that you just search message boards and github and I’m no different. The most important lesson I’ve learned is that bioinformatics is the opposite of magic. This is a hard lesson for most people to learn, because it benefits novices and experts to treat it as such.
Getting my reSPECt
Omics, and specifically mass spec based proteomics, is kind of a hard field to get into after you “start” your career in grad school. Thermo’s flagship mass spectrometer, the Astral orbitrap, is a multimillion dollar instrument; who is going to trust you to design experiments if you don’t have a lot of experience? Smart people (my PI) who recognize other smart people (me) but this is an exceptionally rare thing. In my opinion, electrophysiology and proteomics as tools are like vectors, and they’re similar in magnitude (i.e. difficult to get good at), but have opposite directions: electrophysiologists have way worse career prospects than mass spectrometrists, and face an impossible challenge when trying to change therapeutic areas.
Proteomics labs are highly productive and well regarded by design; they have many millions of dollars invested which means they have to emphasize volume and collaborations. This makes it hard for them to change gears and single-handedly explore areas of biology that they have little/no experience working in. The flip side is that you have old school biologists that are hyper-focused on one target/disease/thing who straight up do not understand how the mass spec works, how the stats are different, or how to work with large datasets.
I saw this first-hand being in the most hyper-focused field of all: alcohol research. After switching fields to proteomics, I find the scientific curiosity, creativity, and freedom super refreshing. I get to spend my time thinking about how software works, the limitations of statistical inference, the laws of chemistry/physics, and how all this can be exploited for drugging… or to understand biology if that’s your thing.
Birthday and Blogiversary
I celebrated my 33rd birthday last December with my family in Dodge. If you know anything about Kansas, you know that there’s nothing to do there during the winter, and nothing I did: mostly just chilled out with my family. It was great hanging out with my little brother: we watched/finished Trigun (90s version), we went to the gym, and I taught him and my mom how to play board games. Plus, I continued the tradition of making them my signature holiday ham (with fixin’s.)
I also visited my beloved 1986 Nissan 300zx, which I decided will be my next project. Again, I taught myself mopeds and I switched fields to proteomics; the temptation to use that power to build a fire-breathing burnout machine is too strong. Hurdles to overcome: it’s 1200 miles away, 16+ years of ridding it dirty, no garage , it hasn’t started since 2014, and postdocs make shit money. I’ll figure it out though.
In other news, my blog turned 6! My most popular post by far is still How to run DNA/RNA gels faster, although the form and function has shifted. Posts are longer and more personal, but consistency dropped in 2023. Again fuck that year, worst period in my life. I didn’t blog much in 2024 because I was busy learning, but also because I was un-burning out and rebuilding my life. I also have to admit that I’m not 100% sure how I’ll be blogging forward; I just know that I won’t stop. I might try miniblogs to get things out faster. I’m inspired by https://proteomicsnews.blogspot.com/ to post about things I feel are dope.
Imaginary Scientists
Three things:
It’s always been about love and hate
1) In my opinion, you are a good scientist if you can pick up new things. This could be working on a new assay, switching to a new disease area, or learning a new field. Unknown risk is a force multiplier and a better measure of scientific ability than raw deliverables. Sadly, I don’t think many people are really like that. The converse is also true: I’m disappointed to hear about people who play it safe and are unwilling to adapt. I think that might be why I got so many final round interviews despite being labeled an electrophysiologist. Some of the feedback from hiring managers was “your personality makes you hard to reject, and your skills make it harder to hire you”. I’m open to the possibility that this is the wrong attitude. I do have some preliminary data: the difference in how people treat me as a mass spectrometrist vs how I was treated as an electrophysiologist is incredible. For background, read this.
2) It’s nice to finally postdoc in a lab that is the opposite of industry hostile! You can read about the lab’s previous experience with starting (and successfully selling) companies here. My main project is working with a proteomics-based AI CRO, and our lab has 3-ish startups spinning out. This is very different from my 1st postdoc lab where I was told I was “paid to work in the lab” and “think on your own time not mine” by my old PI (brazy).
To be clear***, while I’m enjoying my new postdoc experience, I haven’t lost sight of my goal of working in the pharmaceutical industry. However, the job market is a dumpster fire and I see the party lasting another year or two. I base that off of my experience in the 22-23 job market bubble and crash, and not for nothing: all of those companies have announced layoffs (and a few of them may go out of business in 2025). So look down on me for being an academic postdoc if you want; being able take risks while everyone else is on scary time is euphoric.
3) the “Imaginary Scientists” heading is inspired the decentralized science “movement”. 2020-2022 was a very stupid time to be alive and many dumb things around biotech/pharma received funding (and have blown up). To be clear, the sentiment isn’t bad, but the cultural undertones in that community are fascist, the execution is unserious, and I don’t respect handwaving. I guess that’s the default for the whole world now, but idc; I have to call it out. it’s the same feeling I got back during the NFT craze of 21, with the same weird racial undertones.
To be clear, I’m always on team patient, and scammers/idiots/techevangelists are the opps.
*turns out, my handlebar mount was cracked at the base, which is why it was so hard to control
** I’m neither a techevangalist nor a luddite; I’m just pragmatic.
*** I tolerate postdoctoral poverty; I don’t LIKE it
