Synthetic Biologist - Foundry Theorist - American Wetware - stay humble biodesigners
Cambridge, MA
- Tweets 13,221
- Following 425
- Followers 17,492
- Likes 46,482
One wrong mutation and your beautiful daisy transforms into an eldrich horror. Stay humble biodesigners.
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Somehow my reviewers always needed 3 months of convincing about the choice of Kruskal–Wallis versus Wilcoxon Rank-Sum as the test of statistical significance for supplementary figure 7j but giant AI generated rat balls just sails right though sure why not
Erm, how did Figure 1 get past a peer reviewer?! frontiersin.org/articles/10.… H/T @aero_anna
ALT AI image mouse with giant testicle sack and nonsense labels. Terrifying.
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I can’t explain it but this image makes me want to go to a conference where people exchange tiny posters with QR codes on the back to the full poster
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When the prestige journal transfers your manuscript to a more specialized journal within the same publishing group.
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When the PI decides to help out in lab after being away from the bench for a few years.
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Europeans: sterile conditions for microbiology were maintained by performing all manipulations within a laminar flow cabinet
Americans:
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Lab interns take note if you add thymine instead of thiamine as a media supplement even one time your cells turn into one of these
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If you’re looking for a prank gift for that biologist you hate consider 96 individually wrapped pipette tips
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When the PI hasn't worked in at the bench in years but needs to do something in the lab for a photoshoot
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I miss the lab so much that today I put some clear liquid in a cup then poured it into another cup
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I know that the mRNA is larger than the protein it codes for but I don't believe it
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Ladies if you go to his apartment and his fridge is full of sequencing primers for his plasmid collection you DO NOT date him you deserve a man who does whole plasmid sequencing
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"Activation of NF-κB pathway in DCs via TLR4 signaling upregulates pro-inflammatory TNF-α, IL-6, and IL-1β, which enhances Th17 differentiation through IL-23R engagement while inflammasome activation drives IL-18 secretion and recruits neutrophils..."
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Many scientists are proud of their craft and the highly specialized skills they hone at the bench
But nobody hates Western Blots more than the people who have to do them
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Focused, hydrated, in my shell, filter feeding, growing my nacre, secreting my byssus, foot strong
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Every synthetic biologist, every biochemist, when they dream, will sometimes hear a voice calling
A whisper on the wind, as impossible as infinity, as sweet as the ambrosia of the very Gods
"Engineer RuBisCo"
And this paper takes us one step closer
nature.com/articles/s41586-0…
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When I ran my first agarose gel 175 years ago I was all like this janky ass contraption will be obsolete in six months there is no way this is how a high tech field handles DNA
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My favorite kinds of scientists are
1) Crazy enough to publish a paper where you give ecstasy to octopuses and study their social behavior
2) Detail-oriented enough to specify in the figure that 30 minutes is exactly 1800 seconds
cell.com/current-biology/ful…
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If the superconductor thing pans out we biologists need to come up with something pretty dope to make sure we keep winning the nobel prize in chemistry like we always do
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Protein engineering mfers will be like “see it works like this” and then show you the most broken slinky ass looking pile of random squiggles ever to appear in a scientific figure
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ppl who think that biomaterials will be hard to scale up should know that most things are already made of crabs
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This pretty much settles it: we're entering the era of low-cost, on-demand binders for everything
Excited to see what people build now that "inject a llama with some junk and bleed it a month later" is no longer the cutting-edge tech
nature.com/articles/s41586-0…
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When another scientist gives you a tour of their lab they're always like "here's the regular equipment I know you've seen it a million times so boring" but I genuinely love land snorkeling through other people's labs and noticing tiny details about how they organize things
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Human engineers: "Let's separate this problem into several well-defined subproblems then solve each one using the most appropriate tool for that job."
Biology:
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Success in academia means becoming a PI and “leaving the bench”
PhDs are trained in this culture. Actual lab work is for junior mentees. Important people don’t do that
So naturally biologists in industry scramble to leave the bench and biotech is bloated with middle managers
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The tipping point was 2012. After silicon-based DNA synthesis and Crispr, the synbio toolbox became too complex for the way we work.
The future of biotech isn’t "the same labs but with more tools." It takes a new level of organization, a foundry, to use the tools effectively.
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I’m proud of biotech’s culture of understatement but we do pay a price for not hyping our accomplishments
Imagine if a tech startup achieved something 1% as cool as this the levels of self-promotion and circlejerking would break the spacetime continuum
newatlas.com/disease/gene-th…
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The emerging blackpill scenario for the next 5 years in biopharma is 8000 techbio startups using AI to make antibody drugs for the same 12 targets and fucking nothing else
Arena BioWorks, a Boston-area biotech that launched w/a bold $500M bet on the drug R&D model in January 2024, laid off staff on Thursday, its second such move this year
A spokesperson told @endpts that Arena is cutting back on cell & gene therapy work
endpoints.news/arena-biowork…
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Some personal news: today is my last day at Ginkgo Bioworks
After 3 years telling people about the cool things they can build with biology, maybe it was inevitable that I would evangelize myself
I’m starting a new project with an old friend that I hope to post more about soon
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If human wounds heal 3x slower than every other non-human primate it seems reasonable to expect that a relatively simple intervention exists that can triple the human would healing rate
royalsocietypublishing.org/d…
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That labmate who you catch taking the good pens off your bench because they don't wan't to walk to the supply closet
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The wolf of wall street except they do biotech and for the "sell me this pen" scene the leonardo dicaprio character busts out one of these babies
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Real talk: why do we store so many lab enzymes at -20 when they are apparently shelf stable? Are we stupid?
pubmed.ncbi.nlm.nih.gov/1099…
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My pubmed alert for "photosynthetic mammals" has been quiet for a while but it paid off big today
jstage.jst.go.jp/article/pja…
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This paper on de novo luciferase design is mind blowing in in 7648 ways, but here's one part I'm watching with special interest:
How many designs do you need to test before you hit an ML-generated enzyme that works?
nature.com/articles/s41586-0…
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I can't shake this sense that biologists were crazier in the past and that this craziness was a net positive for the rate of discovery
the recent peptide craze reminds me of how nobel prize winner rita levi-montalcini (who discovered of nerve growth factor) reportedly took eye drops of NGF daily
ALT According to Pietro Calissano, who collaborated with the professor on an article for Scientific American in which she announced her discovery in 1979, NGF may have played a direct role in her amazing vitality. "Every day, she takes NGF in the form of eye drops," he said, "but I can't say for sure if this is her secret. At the start, it seemed this molecule's effect was restricted to acting on the peripheral nervous system, but then it emerged that it has a very important role in the brain. Contrary to what was believed, the brain does not have a rigid structure but is in continuous movement, and NGF helps neurons – which we begin to lose between 10 and 15 years old – survive."
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ML for bio is fed all the DNA sequences of nature and makes a beautiful glowing enzyme
ML for tech is fed all the content from the internet and makes a toxic psycho chatbot
As you choose your next career moves remember that you have to live in the world you build
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The endgame of biology as a self-assembling nanometer-scale precision manufacturing technology hasn’t arrived until we can tattoo the waterbear
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Working as a lab tech before your PhD is basically leveling up on the side missions then speed running the main quest
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PCR, restriction cloning, Golden Gate. So many core DNA techniques started with a natural enzyme then figured out a use for it
Has anyone tried to reverse engineer this? Is there a wishlist of plausible DNA enzyme activities that, if they existed, would be the next CRISPR?
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TIL when you sort the codon wheel by the second base the quadrants align with the properties of the amino acids being coded for and also it looks like the mystic sigil of the coven of the four bases
journals.asm.org/doi/pdf/10.…
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By this tweet I hereby announce my new role at @Ginkgo - Developer Evangelist
Here's what I need: I need hundreds and hundreds of new startups making sweet biotech and obsoleting shitty petroleum products
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When you're trying to sequence the gene for alkaline phosphatase in 1987 and you notice 5 homologous sequences of 29 nucleotides arranged as direct repeats with 32 nucleotides as spacing
ncbi.nlm.nih.gov/pmc/article…
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It seems obvious to me that the dire wolf thing could never have happened in academia or traditional biopharma
I wonder if we're seeing the emergence of a new kind of thing: well-funded biotech R&D that lives outside of the traditional incentives and institutional gatekeepers
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People who can unscrew Falcon tubes with one hand how does it feel to be on top of the food chain?
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Any scientist can generate a high resolution AI figure with no thought and no effort. Big whoop.
Give me an image that shows a human mind at work. Give me a hand-drawn diagram from an improvised chalk talk.
The future of technical communication is "human signaling."
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Since nobody uses light bulbs anymore I propose we make this thing the new symbol for having an idea
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10 years ago, a biotech startup would never have open-sourced a method for antibody design. It would have been antithetical to all biopharma incentives
Today it seems ... totally rational? I'm curious to see how far AI pushes biotech toward open-source
biorxiv.org/content/10.1101/…
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Biotech can expect a culture shift as:
• Applications get more diverse and interesting
• Start-up costs and timelines fall
• VCs gatekeep less
• Academic postdocs continue to suck
PhDs will simply prefer to become founders and the cultural heart of bio will move to industry
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As a biologist, I've tried many Electronic Lab Notebooks and never found true love
It could be the inherent complexity and messiness of biology. Or it could be that all creative work is hard to document
Curious if software people see note-taking as a (mostly) solved problem?
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To face the future with the confidence and grace of this crab riding a coconut into the sunset
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You might think all the good fruit is already domesticated but in fact earth’s genetic biodiversity encodes whimsical delight at an average density of one willy wonka chocolate factory per square kilometer
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When you publish an important result in a mouse model and science twitter is about to absolutely obliterate you but you remembered to add “in mice” to the title
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When you ask the right question and design the perfect experiment but you still don't learn shit because nature hates us
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People who complain about the accuracy of your nanodrop have you considered just getting good at doing DNA preps
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I would like to read a 1000-page case study explaining why we still use serum for cell culture in biotech
- expensive
- poorly defined
- ground up cow fetuses are bad vibes
- replacing it seems super doable
And yet decades pass with no progress. Are we stupid?
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