We are currently pursuing the industrialization of biotech 🏭
In a new essay, I explore the following question:
What if we pursue the biologization of industry? 🧬
In the past few weeks, there's been an explosion of new tools for programming DNA and RNA 🧬
A thread with everything you need to know about these new results:
I've spent several years building software tools in genomics.
While the work couldn't be more exciting, there are unique challenges and tensions in the world of scientific software.
How does software in the life sciences actually work (and not work)?
It's dizzying keep up with BioML 🧬
Not one, not two, but THREE exciting papers from the
@MetaAI
Protein Team before the end of the year.
Here's what they released:
AlphaFold wouldn't have been possible without the PDB.
What will be the equivalent be for structure-based *drug discovery*?
Very cool new resource called MISATO: nearly 20,000 experimental structures of protein-ligand complexes + associated properties:
The {shiny} web framework is an incredibly powerful tool for
#rstats
users, and it's been really important for several of the scientific tools I've built.
After recently finishing the Mastering Shiny book by
@hadleywickham
, I thought I'd share a roadmap for learning Shiny: 👇🧵
Rocket science is hard.
Designing systems capable of launching materials—including humans—into orbit and then smoothly landing back on terrestrial ground is one of the greatest feats of engineering we’ve achieved.
But surviving in space will be even harder.
In his brilliant…
The Unreasonable Effectiveness of Language Models in Biology 🧬
A short preprint published earlier this month from the
@lab_berger
at
@MIT_CSAIL
showed that pre-trained language models are now state-of-the-art for drug-target interaction prediction.
No technology has ever improved more rapidly than DNA sequencing. The resulting explosion of genomic data has played a central role in transforming biology into an information science. We now browse genomes, search vast databases of biological annotations, and explore digital…
My final essay for 2022 🧬
The genomics revolution is now enabling a broad exploration across the Tree of Life.
Let's explore the wild world of Extreme Biology:
The Meta team modeled the metagenomic protein universe 🧬
More than 617 million new structure predictions of metagenomic proteins are now available. Predictions made using the largest protein language model to date. (15B params)
Now *that* is meta... 🤯
One of my absolute favorite quotes about science, by Peter Medawar who won the Nobel prize for discovery of immune tolerance 🧬
There is no monolithic Scientist, people join in the pursuit for many reasons.
From lab to approval in 11 years 🧬
And the thing is, medical applications of CRISPR are just getting started...
Just yesterday, the
@doudna_lab
released two juicy preprints on improved delivery methodologies for CRISPR editing machinery:
1. Lung and liver editing by lipid…
I am excited and a bit overwhelmed with emotion at the news of the approval of CASGEVY in the UK. Going from the lab to an approved
#CRISPR
therapy in just 11 years is a truly remarkable achievement. (1/3)
Distributed biomanufacturing is not sci-fi 🧬
It's already happening.
I want to share a few tangible recent examples of the *Atoms are Local* thesis in action:
The AlphaFold discourse is strange...
No, "AlphaFold won't revolutionize drug discovery" but neither did the Human Genome Project.
However: AlphaFold is arguably the first *major* empirical science win for AI after so much progress in games and virtual worlds.
Synthetic biology is maturing into a quantitative engineering discipline 🧬
Powerful ability to predict specific dose response curves (left), and engineer new mutations with expected outcomes (right) using ML.
A 3D printed DNA extraction device 🧬
How can we make biotechnology cheaper and more accessible? I talk a lot about the absurd genomics cost curve, and recently chronicled Illumina's journey towards making DNA sequencing ubiquitous.
But beyond DNA sequencing, what about the…
CRISPR screening + microscopy 🔬🧬
This past week,
@insitro
posted a new
@biorxivpreprint
detailing a screening platform that combines large-scale CRISPR screens with an optical readout.
Who is Insitro?
Founded in 2018 by
@DaphneKoller
, former Stanford professor and
@coursera
…
Tech investors: really like their vision, but kind of a red flag they didn't drop out of college to pursue this earlier 🤔
Biotech investors: they've spent the past decade doing their PhD and postdoc building this, but we need a leader with more experience 🤔
In the world outside of genomics, I had a major life milestone this week. I proposed to my girlfriend Kelda, who I have loved for nearly nine years (!!), since we were two high school kids in Seattle borrowing our parents cars to see each other 🥰 I couldn't feel more lucky!
Single-cell genomics, without the microfluidics 👀
While single-cell has enormous power, people have been working to tackle the microfluidics bottleneck (scalability, cost, simplicity).
This emulsification-based approach seems promising 🧬
Implementing neural networks... in DNA 🧬
Neural networks are an example of a bio-inspired algorithm. We used neuroscience as an intuition pump for making learning systems.
But what if we took our C.S. innovation in neural nets, and... implemented that using biology?
How would…
Organ-on-a-chip for CAR-T cell therapy 🧬
I've been digging into the current state-of-the-art for new in-vitro drug discovery models for an essay I'm currently writing 👀
For small molecule discovery, Big Pharma companies like Roche have announced major investments in this…
Protein-protein interactions seem like an obvious frontier for protein science in a post-AlphaFold world.
Excited to see a new study with some of the top minds in BioML and protein science working together to build a scalable sequencing-based measurement platform 🧬
The fact that we can hot-wire a patients own T cells to attack certain types of tumors is absolutely incredible.
And the thing is, we're just scratching the surface when it comes to cell therapy.
BioConvert: a comprehensive format converter for life sciences
Bioinformaticians shouldn't worry about being replaced by ChatGPT.
This is the real threat!
A structure/sequence representation for Protein Language Models 🧬
To date, Protein Language Models (PLMs) have been trained on large databases of protein sequences, primarily with the trained objective being to predict masked amino acids.
Simultaneously, with incredibly fast…
Bugs as drugs 🦠🧬
Engineering edible microbes (spirulina) to produce acetaminophen (Tylenol)
POC for "small molecule production derived from CO2, H2O, and light in an edible host for bioavailable, oral drug delivery" 🤯
We can program cells to produce drugs, perform logic operations, and attack tumors.
What does it take to write a new cellular program? Trial and error, of course. Biology is complicated, and we shouldn’t ever expect our designs to work the first time. Individual genes interact…
The future is going to be really weird.
In April, I traveled to Montenegro for the
@SynBioBeta
"Blockchain Meets Bio" Summit. This event was held at Zuzalu, a pop-up city experimenting with crypto citizenship.
Key leaders of both technology communities spent several days…
Beyond Steel Tanks 🏭
It's been fascinating to watch the growth of GLP-1 drugs.
For the first time, a bioproduct could outsell the iPhone.
But we can't make anywhere near enough of these medicines to meet demand right now in the United States—let alone globally.
I was…
Transferrin Receptor Targeting Chimeras (TransTACs) 🧬
The field of targeted protein degradation is going through a renaissance. The core idea: use a bifunctional molecule to bring a protein in proximity to a degrader.
The first wave (PROTACs) primarily used E3 ligases as the…
Biopharma is a strange business. Drug candidates routinely fail in clinical trials at a rate that would be unacceptable in most other industries. Why should we accept this as the norm? What if we could produce medicines in such a reliable way that their clinical success was…
Moved to SF this past weekend 🌊
We’re closer to the school where my wife teaches, and the ocean!
I’m also enjoying the little office nook I’ve fashioned for myself.
We are living through a renaissance in the field of computational protein science. This has enormous implications for biotechnology at large. Check out my COB highlight of the amazing recent work from
@UWproteindesign
on protein binders:
Excited to be back with another essay 🧬
I normally focus on *what* is happening: a biotech revolution. I also focus on *how* scientists and engineers in this space are building the future.
Here's *why* I view it is a moral and aesthetic imperative to pursue biotechnology:
Internal Pharma AI efforts at Sanofi 🧬
It can be easy to paint a caricature of Big Pharma companies as Leviathan institutions that aren't capable of internal innovation. Yes, many of the top companies are hundreds of years old (seriously: ), but that…
A genomic smart watch 🧬
@JShendure
is one of the most creative scientists in the field of genomics. My time working at the
@uwgenome
was extremely formative for understanding the enormous potential of the NGS revolution beyond personalized health.
He believes that NGS is…
This year's Nobel Prize announcement has stirred up a lot of conversation about institutional blindspots that hinder great work.
Dr. Katalin Karikó struggled for years to pursue her foundational research program that ultimately enabled the global dissemination of mRNA vaccines…
The claim by
@lpachter
that "hardly anyone reads papers anymore" is super interesting, and has generated a lot of discussion.
I think that there is a lot going on here...
On biotech platform strategy 🧬
For biotech founders and investors, not all types of risk are the same. Opinions vary, but three major buckets of risk are scientific/technical risk, team/execution risk, and market risk.
In other words, how likely is it that the technology will…
Biology as technology 🧬
Moving up the ladder of complexity from designing individual proteins to extendable protein multiplexes.
The rate of progress in the Baker Lab is insane.
Delivering the delivery vector 🧬
Gene therapies aim to reprogram diseased cells by delivering nucleic acids or gene-editing machinery.
A central bottleneck is precise delivery to the targeted cell type while evading the immune system.
To date, adeno-associated viruses (AAVs)…
How can we learn to rapidly compose new genetic circuits?
In a new essay, I explore recent work from the frontier of ML-driven biodesign 🧬
We're expanding from models of genetic parts, to models of genetic circuits:
When Mark Zuckerberg and Priscilla Chan announced their philanthropic efforts to “cure, prevent, or manage all diseases by the end of the century” in 2016, they were ridiculed. Skeptical scientists leaned back from their lab benches and groaned collectively. More tech money…
Illumina announced they will pursue their own drug discovery efforts this month 🧬
What product companies have successfully become discovery companies?
It turns out another valid question is: what major pharma companies *didn't* start selling products?
Nanopore Sequencing x Single Cell Biology 🧬
A new technique (scNanoGPS) from the
@Ruli_Gao
Lab was able to detect expression and isoform differences (the phenotype) *and* mutations (the genotype) in single cells—without short read information.
Some thoughts on Agency.
What is Agency? The belief that you can change the world around you.
One of my favorite quotes comes from
@pmarca
:
“The world is a very malleable place. If you know what you want, and you go for it with maximum energy and drive and passion, the world…
It was my birthday yesterday.
To celebrate, my wife and I walked the SF Crosstown Trail—a diagonal route through the city connecting many of the parks, gardens, and greenways 🌳🌱
It was a really cool 17-mile journey:
What are some of the major recent biotech advances? 🧬
CRISPR. Next-gen sequencing. CAR-T therapy.
Does the creation of bioRxiv count? I think it should:
Extreme Biology goes mainstream 🧬
Paratus Sciences recently raised $100M from top biotech investors to build a comparative biology platform to understand bat biology.
Wow! The T2T crew (team that produced first gapless human genome assembly) is back at it...
Were able to complete a nearly perfect assembly of the human genome (plus tomato and maize) using only one sequencing technology:
Oxford Nanopore Tech.
This is big!
If you haven’t read this deeply researched primer on biomaterials by
@tsungxu
yet… you should now 🧬
Packed with information and ideas, I ended up reading twice.
A new preprint introduced:
1. A new RNA database
2. A language model architecture for RNA
3. Experimental demonstration of in silico predictions for mutations increasing ribosomal thermostability
All started from a Berkeley hackathon w/ undergrad participation!
Very evocative figure.
"We present an alternative to Graph Neural Networks (GNNs) termed Graph Structured Neural Networks (GSNN), which uses cell signaling knowledge, encoded as a graph data structure, to add inductive biases to deep learning."
Experimental biology revolves around a central process:
Manipulating small volumes of liquid.
Researchers at Cornell recently invented a new system for doing this, called SPOTs. The idea is to use a liquid-repelling coating organized in precise geometries—no pipettes needed.
From the cutting room floor of my most recent essay:
The cost of precision fermentation is falling exponentially.
This should expand the set of commercially competitive bioproducts—even in sectors where previous efforts have failed.
A big milestone: I joined my thesis lab this week!
I can’t wait to keep working with
@sbmontgom
at the intersection of human genetics and multi-omics 🧬
Progress in reading, writing, and editing DNA has been relentless.
With all of these new tools, why haven't we successfully cured every disease with a genetic basis?
There are several reasons—including financing the cost of clinical development for rare diseases—but there is a…
Epic start to the Founder-led Biotech Summit 🧬
After a great overview from
@kulesatony
, we got to hear the founding story of
@TwistBioscience
directly from
@EmilyLeproust
. Next founder up is
@srikosuri
.
Also a cool cellular visualization of the founder-led ecosystem 🤯
On a recent trip to NYC, I spent time thinking about the staggering complexity of maintaining all of the manmade infrastructure that we rely on.
What if our tunnels, subways, and buildings could grow and regenerate like biology? 🧬
Big milestone: 1M+ researchers have now made use of
#AlphaFold
in their vital work, in the 18 months since we made it freely available.
From antibiotic resistance to crop sustainability, it's been amazing to see the impact of ‘Science at Digital Speed’:
SF is a living embodiment of one of
@GreatDismal
’s core themes:
The future crawls clumsily out of the past.
Victorians with dual monitor workstations in their bay windows. Driverless cars silently traversing streets along the Pacific lined with Spanish row homes.
This week on The Century of Biology, I highlight the really impressive new work led by
@Avsecz
,
@vagar112
,
@drklly
, and Daniel Visentin.
A short thread 🧵:
Hot take: the recent acquisition of Prometheus Biosciences by Merck for $11B should be counted as a win for TechBio 👀
You may be saying: that's not TechBio!1!1 😖
Consider suspending skepticism for this analysis:
Lot's of debate and questions about what is and isn't TechBio 🤔
In my view, it's biotech all the way down.
TechBio is useful for describing a subset of companies with new founders/investors/tech/biz models. Over time, it will be an irrelevant distinction like molecular bio 🧬
Single-cell atlases aim to "create comprehensive reference maps of all human cells" 🧬
Read about a powerful new bridge between these atlases and diverse single-cell omics technologies:
It was a blockbuster biotech breakthrough when Genentech successfully synthesized human insulin in 1978.
Now, many dream of an entire economy where *everything* is
@BuiltWithBio
What technology will enable this revolution?
Just a matter of decades ago, a PhD in genetics often consisted of sequencing *a* gene. Now, graduate students can carry out massive functional studies perturbing every gene in the genome.
What has changed to make this possible?
Books are phenomenal bioproducts.
Thin sheets of processed cellulose fibres transduce neural signals between apes across space and time.
They are a memetic portal to our ancestors. A record of our civilizational conversation.
I will never take this for granted.
Engineers love general solutions.
Normally, biotechs focus all their efforts on a set of specific solutions.
These solutions are what create value.
But the engineer's central urge is to improve *the way* that we arrive at these solutions. It's a really long-term bet.
The success rates for antibodies are going up across nearly every clinical phase transition.
Figure shows "rates for antibody therapeutics for any therapeutic area that entered clinical study during 3 periods."
Very exciting, compared to industry benchmarks across modalities.
Impressive recent
@PacBio
preprint 🧬
SMN1 is a gene that plays a central role in spinal muscular atrophy. It's tough to analyze because it has a very similar paralog SMN2 (below).
They were able to detect both, call phased variants, assess copy number.
Lipid nanoparticles are very inflammatory.
This makes them a great vaccine adjuvant, but a difficult vector for universal delivery of nucleic acids.
A recent study showed that endosomal escape—the mechanism for RNA delivery—is also the driver of this inflammation.
This increasingly worries me. It too greatly resembles the initial conditions for “The Jackpot”
@GreatDismal
has written about: a future where systemic problems (stagnation, pandemics, climate) collapse all but 20% of society who survive w/ godlike tech (1/2)
Stark dissonance between what I hear from folks at the edge of their fields imagining the future and assessing our current trajectory.
There's crazy stuff going on that will change the world for good in the short term, but at the same time the world is increasingly on fire
More bugs as drugs 🧬🦠
This study led by
@yerinchen
from
@mfgrp
lab (my lab) absolutely blew me away the first time I saw the data.
Engineering commensal skin microbes to express cancer antigens leads to highly effective T-cell mediated cancer killing.
Base editors, with an on-switch 🧬
By using a molecular glue—a technology that triggers protein degradation—it's possible to program the half-life of Cas-based gene editing therapies.
The pace of progress in the CRISPR field is only rivaled by AI right now.