Jul & Aug: Via Ortega 443
77 days around trees 🌲
What I’ve been doing
Learned to do SB (synthetic biology): I’d read all the books and papers, talked to the best of the best, done all the biohacking kits. Doing research at an academic lab was just a whole different beast. Part of the lab’s work is explained in detail here. Specifically I:
designed, built and tested a dozen different constructs over 1-10 iterations each
analyzed and managed CRISPR results through a simple biocomputational tool in the terminal
harvested and did phenotype analysis (sorting) of 20+ dozens of seed lines
conducted literature research on polycistronic expression of the CRISPR complex
Wrote things I am proud of:
Had fun: visited an astonishing redwoods park, met with friends in San Francisco, ate good food, took awesome photos, read great books, ran half a marathon on campus, ate lots of strawberries, listened to lots of podcasts, fasted, thought.
Without a doubt, this summer has been a transformational experience, one whose effects are just starting to grow in me. I am, once again, deeply grateful to everyone who has made this opportunity possible:
Tony Kulesa for suggesting that I took a chance on this experience in the first place and Tyler Cowen for making it financially possible through Emergent Ventures — an example of a relatively small amount of force applied at just the right place. You guys will see ; )
Jennifer Brophy for accepting me as a summer student to learn from the fantastic work that her team is doing, especially…
The best mentor I could have asked for. Thanking Vivian Zhong will take a whole letter that I have not written yet. The admiration I have for her and the impact she’s made on me cannot be overstated, and that’s all I can say for now.
My family for their constant excitement (over-protection? lol) to know how I’m doing; for those literal late-night conversations that helped me grow immensely as a person, for reminding me of the things I forget to do 🤫, and most importantly - for reminding me that the worst-case is not bad at all.
Isa, Mario, Bella, James, Janina, Vardaan, Soyeon, Daisy: thank you for making me feel like at home. Each of you is amazing and you’re building a great culture. Can’t wait to know what y’all are up to in 10 years from now :-)
What I’ve been thinking
Long list that goes from the broadest to the most specific, mostly philosophical, thoughts. You may as well read the headlines and dive into those that interest you the most. Also feel free to contact me to ask me whatever.
1. There are no solutions, only tradeoffs; and you try to get the best trade-off you can get, that’s all you can hope for — Thomas Sowell (economist)
I found this quote in the conclusions of a plant SB paper that we discussed in a lab meeting. Though the paper evaluated the feasibility and viability of solutions like biofuel and biofertilizers, the meaning started to really click while I was biking instead of reading.
The most meaningful things you cannot multi-task. Over these months I had to choose between staying home on the weekends to create and exploit or going out to consume and explore; between paying attention to false ideas about my abilities or what I was actually doing in the present to improve them. Certainly too, every time I ate at the ginormous Stanford dinning halls, where it’s unreasonable and earnestly risky to want it all yet the desire is still there.
2. Even if you’re going to live three thousand more years, or ten times that, remember: you cannot lose another life than the one you’re living now, or live another one than the one you’re losing. The longest amounts to the same as the shortest. The present is the same for everyone; its loss is the same for everyone — Marcus Aurelius
One of my slightly contrarian takes on life was that death does not give meaning to life, that life is valuable in of itself and thus, I would not have an existential crisis if I was to be granted immortality. “Life is extraordinary, the universe infinite”. This summer challenged that view.
I was supposed to be here for 2 months only, yet 2-3 weeks ago I realized I wanted to stay for longer. I wanted to add and capture a lot more value, which is still consistent with my world view. However, what is inconsistent is the actions I’d been taking towards adding/capturing value.
It feels that it’s only been until these last weeks that I’m actually pushing the hardest. Not only in the lab, doing more things, doing experiments at night and on the weekends, but also in my personal health by running more and eating more healthily (no more dinning halls, lol).
Question for you: how do you actually make the most out of the middle part of an experience; that part when the time ahead feels infinite even though part of you knows it will be over? How do you push the hardest all the time? If you do…
3. Blessed is that who plants trees under whose shade they will never sit — Greek and Indian proverb
James was a fellow summer visitor from Oxford/Cambridge. The day he left everyone was saying how much they’d miss him. The day after it was as though he’d never existed (nothing against James, this is not about him haha :’)).
That showed me that soon I would also be that person who says goodbye and somehow fades into obscurity. James, however, left a legacy. Not only through his words and his work but through something he loves to do outside the lab: origami.
He is gone and yet that gorgeous swan made out of paper will live in Jenn’s office for who knows how many years so that anyone who visits says “Wow, that’s awesome! did you make it?” and then she’ll tell the story of James.
Question for you: why do you think that some of us (certainly including myself are so fixed in being remembered?
Living in places where I have new experiences and meet people and make things with them—start and close cycles—reminds me of life. The difference is that, while I’m still alive, I can wake up and feel the awe of knowing that it’s my last day here. Some day that will happen for real and I will not know it. All I can do meanwhile is to plant trees.
4. Don’t be grateful. Show it
Since I finished my first year at TKS I’ve been thinking that there’s no other way I can truly show my appreciation to those who’ve helped me than to make something wonderful.
Experiences like TKS and this summer are short-term experiences with a long-lasting impact. My job is to be as useful as possible in the present, make a small gift today, and never forget that the most important part, the best gift ever, will be to multiply it. To pay it forward to the rest of humankind, at scale.
5. What we owe the
What we owe the future is a book that informs XXI century people about the innumerable generations of human beings ahead of us, the fantastic future we could seed, if we tackle our world’s current biggest problems.
That’s nice but, to be honest, I always find it easier to be more compassionate of my past self (that 5-year-old kid I want to make proud) instead of my future self whose bones will hurt if I keep sitting like this.
Earnestly now, I’ve lately been fascinated by the idea of a genetic time machine. Hundreds of thousands of humans have lived their lives in very particular ways, leading to me metamorphosing my brainwaves into bits (i.e. writing this article). We sit beneath the trees they planted: we listen to their music, read their words, use their machines, see their bones in museums… study their genomes.
“The adaptations of an animal, its anatomical details, instincts, and internal biochemistry are a series of keys that exquisitely fit the locks that constituted its ancestral environments — they’re a key to reconstruct the environment they were in. If we could read the genome appropriately, we could get a negative imprint of ancient worlds, a description of the ancestral environments of the species: the genetic book of the dead”— Richard Dawkins is publishing a new book!
This topic deserves its own article (expect it soon). The way this makes sense to me is feeling grateful that everyone who’s ever existed, mainly my past family, have lived their lives in the way they did, without even knowing that it would allow someone (me) to be alive and with the opportunity to thrive today.
Another angle to the past two (trees gratefulness) points.
6. Is empathy ego looking at itself in the mirror?
One of the first deep questions I asked myself when arriving here. In my network it’s typical to hear people talk about the importance of networks: “everything is about people. Name one thing that does not involve interacting with others” — I was once prompted.
I realized that when I felt bad about myself, it was because I cared about the opinions of others and the same when I felt good. Even if I scratched deeper and looked for things that intrinsically made me happy, they somehow involved people. As mentioned before: make something wonderful… to be grateful to others.
Of course, this goes back to Mr. Dawkins: how does altruism relate to evolution? My very limited understanding lets me see as far as “we are kind to others because that feels good, so we’re still thinking about ourselves, in the end”.
That is all to question the initial assumption that my network suggests. Question for you: what do you think?
7. Think kinder
As slightly inferred in previous paragraphs, I was not having a kind internal narrative while learning new things here. “You’re supposed to know this already, you’ve been learning about biotech for years, how come are you even failing to sum and multiply, are you a kindergarten student? You must be so stupid, idiot”.
I know many people now look up to me for being the 776 fellow, Emergent Ventures winner, Stanford intern, and sick writer (the last one I don’t mind ;)). If you’ve compared yourself to me in any way, this is for you: I compare myself to others all the time too, I’ve talked bad to myself, I’ve failed to sum and multiply the simplest numbers (Vivian knows).
After realizing that the stories I was telling myself were a) only stories and b) false, I truly saw that I could be my greatest enemy or my biggest ally. Confidence befalls competence. You should always operate under the assumption that you can do anything you put your mind and soul to. You have no chance otherwise.
Free your mind from negative thoughts. Nobody is watching, nobody is talking except for you in your mind. Do your work and do it the best you can. That is the only way that you will.
Once I did that (took weeks) I stopped failing so much and started learning more. I took the courage to ask for what I wanted, like staying for longer or even longer (like long-term). And the response was completely the opposite to my negative mind: “Sure, why not! Let’s figure it out”.
8. Work with people who will break the brules for and with you
Stanford requires you to be a third-year student to intern with them as an international student in the summer — and yet I’m here, as someone who barely finished her freshman year of college.
This would not be possible without Vivian’s vision: she thought that rule was a bullshit rule (brule) and she simply talked to the right people in the right way to cut through it. Took a bit more of paperwork but nothing impossible. We did it. Work with people who will break the rules for and with you.
9. Many exceptional people are building themselves in private
I stopped using Twitter around 15 days ago. This is something I’d wanted to do for a while yet had been too coward to do. Thanks to Michael Raspuzzi for helping out with that!
I first found my desire to leave the app by reading a Naval phrase on my friend Sigil Wen’s website. Recently I saw my mentor Vivian fully embodying the phrase.
She — an amazing (not to say gifted) writer, well-educated in the history of our world and the most intricate details of peaches, capable of expressing herself through incredible dancing, while being an outstanding PhD bioengineering student — is not the person that thousands of others will follow on social media.
Her creative writing is carefully kept within private Google doc files, her extensive knowledge is even better guarded for private, in-person conversations. As someone so accustomed to sharing everything, from the simplest thoughts to my greatest achievements, I could not understand why.
Perhaps, again, it’s the trade-offs: I seek attention, she seeks knowledge. It might be impossible to have both, at the same time. I have not been this way all my life. In fact, my greatest periods of personal growth have been private; reading all those Synthego guides on CRISPR and doing all those biohacking kits instead of writing about them. Doing instead of talking.
If I were to give advice to someone younger, and in fact to myself in the next years, is that you can operate in cycles. Just keep in mind what my grandfather says: from the inside to the outside. Build yourself first, share it with the world next. That’s how you can make the most out of both.
10. First think, then search, then ask, then experiment, finally think again
For much I still see PhD students as “incredible question answering machines” — note that I’ve added ‘incredible’ lately — this summer I’ve learned that even when having them right next to you, it’s important that you don’t forget to answer your own questions when possible.
Thus, I came up with a personal framework for learning. Thinking of the question or problem on your own (no google no nothing, yourself) first gives you the privilege of being unbiased. In the base case, you find something no one else has before!
In our everyday modern life though, you may want to consult online sources then. I’ve found ChatGPT helpful when you want to know a summary of what exists and, of course, Google as a search engine will direct you to other sources to go more in depth. You can iterate through these first two steps of thinking and searching until…
Your questions are no longer found on Google. I reached this point when I started with my cotton project. No blog post, book or video could answer why we were not making cotton in the lab so I had to talk with people about them. Since then I knew that the best questions to ask interesting people are those that Google cannot answer.
Of course, after talking to many of these people, I also got to the point in which the answers would be given by nature itself, i.e., by experimenting.
I’ve run through similar cycles in the lab this summer: constructs don’t work, you think through the many things that could’ve gone wrong, you search random Reddit posts suggesting other reasons why, you think about that, you try stuff.
11. Experiments are a dialogue with nature, biotechnologists are using the equivalent of a telegram, and that's quite frankly depressing
I’ve designed, built, tested and learned. Witnessing the transformation of bits to atoms is utterly impressive. Being the agent of that transformation, knowing it works, is indescribable.
Still I have a couple of questions: why are there two unused OpenTrons in Drew Endy’s lab? Why do brilliant scientists at Stanford and elsewhere (especially my mentor) spend most of their waking hours repeating the same movements with their hands? Why in heavens does every single freaking lab bench look like the same mess it looked like 50 years ago?
The fact that I’m a newbie means that I can see these things differently and it also means that I could be asking the wrong questions. I stay firm though: this needs to change.
"Progress in science depends on new techniques, new discoveries and new ideas, probably in that order" — Sydney Brenner, Nobel Laurette, African biologist
Chatting with Niko McCarty changed how I weight the importance of SB tools vs apps. Once a biosimp, his thinking seems more based: we are, still, in the dark era of SB. How could we not be if the answer to why we use this genetic part from potato is “because it’s the only one available, the only one people have characterized”?! I felt as if Steve Jobs had asked people why they use a BlackBerry. They knew nothing better.
If no one in our building is using the liquid handling devices, the problem I see is clearly not solved. Many interesting people say that it’s rather multiplexing, running several experiments at once, that is freeing scientists the most.
I would rather use the word enabling. Running more experiments simultaneously enables you to find more things faster. Still you need to run those experiments.
Niko’s vision looks more like "What if we completely modeled cells on a computer to know exactly how they would react, to design them and know exactly how our designs will work?” Design, build, and it works the first time. Just like a bridge.
Guess what? That requires data! Wooohooo!
12. Physics x bio
Not only understanding life behavior through a physics lens but building a seamless transition for discoveries from the physics department directly into the bioengineering and biology department. There are tons of examples: X-Ray crystallography, all of microscopy, microfluidics, mass spectrometry, flow cytometry, MRIs, cryo-electron microscopes… I want to see more!
The solution to me not counting seeds under a microscope and separating them using toothpicks might look more like a filter of the right size that can sort seeds based on fluorescence (aka flow cytometry) instead of a seed-picking robot.
We don’t have flying cars but we have FaceTime. The computer didn’t start with transistors but jumped to them from vacuum tubes. We don’t have a physical C-3PO but we have chatGPT. We didn’t get faster horses but we got cars. We know what we want but we don’t know how that will materialize.
Yet another article to explore in greater depth.
13. I’m more impulsive and less disciplined than I thought. It’s late and I will just finish by sharing a list of other thoughts
Pros follow protocols and get the right thing every time. Artists break them and get a new thing every time.
Leo was right in that, after too much thinking, you can’t do too much. I didn’t gain much from reading about a PCR vs actually doing it.
Almost everything is a language. You want to become fluent in it and understand the learning curve. It applies to SB too.
After this internship - is biology a computer or a burrito? Biology might be computers that we simply don’t know enough about yet to be able to program like computers.
Be in the present, there’s joy in there. When doing experiments, when traveling to San Francisco, when riding a bike hands-free. It’s not about “putting your mind in blank”. That just happens. It’s wonderful.
Energy makes a ton of a difference. BRING IN THE ENERGY!
Most tweets fade into obscurity, most content you consume is forgotten just as most thoughts are too.
Keep asking for more. More feedback, more practice, more things to do. Stay hungry!
The main difference between research here and elsewhere is ambition and how enabled people are to pursue. I am almost convinced that financial capital is a greater barrier than human capital.
Complacency kills more people than hunger and Stanford is a very comfortable place.
Manu and Da Vinci: stay curious. Question literally everything, especially the simplest things. For example, why do kids have so much more energy than adults? Following the tree lesson, Manu is one of the true tree growers I’ve seen in our times. I appreciate his existence a lot and I’m chatting with him tomorrow?! :D
Why are papers so complicated to read? It’s literally a whole different thing when people present their work in a ppt, explaining in plain words, slide by slide, figure by figure, what they’re doing and thinking.
Ideas are very dangerous. Act upon them so you don’t sink in them.
I have a love-hate relationship with writing.
Not being smart enough is not an excuse. I don’t give a f*ck about brains. I care about people who do.
A good memory comes from a good attention, which comes from caring enough about the thing
Fish are not thinking about swimming, they just do it. If you were born to do it, you’ve already done it.