Microbiologist and Scientist exploring climate-tech. Cat dude, mediocre drummer. Formerly Berkeley/Amyris/Harvard/Wyss Inst.

He/him
Joined July 2018
New preprint: Cyanobacteria isolated from marine volcanic seeps display rapid sinking and robust, high density growth. Thanks to U Palermo and Two Frontiers Project, we got unique samples from Vulcano, Italy, where CO2 bubbles into the shallow ocean, 24-7! biorxiv.org/content/10.1101/…
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How do you publish this tree and claim it's a success???!!!
We are releasing Carbon: a crazy fast DNA model Carbon is 275x faster than the next best model. So fast you can process the whole human genome on a single GPU in <2 days. Here are the tricks we used: When modelling DNA sequences a lot of the performance comes down to tokenizing the sequences in a smart way. BPE tokenizer struggle because there are no whitespaces and character (called base in DNA) level tokenizers waste a lot of compute on too many tokens. Carbon is built with a unique tokenizer: we split sequences in chunks of 6 bases, but during both training and inference we can work with single base resolution. That's similar to having word tokens but resolving them at the character level. All possible thanks to the DNA tokens unique structure. The architecture combined with the tokenizer makes the model 275x faster than the previous SoTA (Evo2) at this size. We built an interactive demo so you can explore how the model can generate DNA sequences, investigate the structure of genes, predict the effect of mutations, generate and fold proteins and even reconstruct parts of the tree of life. huggingface.co/spaces/Huggin…
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This tube is a library of bacteria with every single-base-pair genome mutation, all DNA-barcoded.🧪Growth + barcode sequencing = data on millions of mutations. 📄 Report: biorxiv.org/content/10.64898… Retweet if you want more data, and read on if you want to use the library! 🧵
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An international coalition of scientists discovered a novel cyanobacteria strain adept at “eating” CO2 and sinking in water. It is a prime candidate for biologically-based carbon sequestration projects & bioproduction of valuable commodities. wyss.harvard.edu/news/newly-…
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Once again seems to have aged poorly, this time recent Nobel News.
C. elegans. They wiggle forward. They wiggle backwards. And occasionally they fuck themselves. That’s it.
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Can we settle once and for all how to pronounce "-mycin" antibiotics?
100%Spectinomycin, Rapamycin.
0%'Spectinomy*i*cin' etc
0%don't care/ show me
3 votes • Final results
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Garden Grants: Very cool approach toward more collaborative problem-solving and funding exploratory climate-relevant science
🌱 Today is a special day for Homeworld: We are publishing over 50 proposals from Homeworld’s first Garden Grants program focused on protein engineering. 1/
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So @nanopore discovered something a few days ago - and it has to do with light. And they posted this image (sorry, too good not to share off the community). Yes, that’s 469% increased output. So, we decided to give it a shot and …
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I would recommend opening up your laptop and cleaning the dust off your fans. Improves lappy cooling, and a sobering meditation on the lingering requirement for hardware and moving parts (!) and the fight against entropy.
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Great opportunity for Climate-relevant projects looking to pursue translation from within academic labs!
1/ Solutions to the climate crisis are already here. But they're stuck in academic labs. Often, after the basic science is done, there’s just a little more work needed to show the science has commercial potential. But no one funds this! Introducing Manifest Climate!
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Five days left if anyone wishes to donate to my fundraiser! Making a ultra cheap turbidostat for use in experimental evolution. Fund go toward bringing these tools into the classroom. Every penny counts! 💚 experiment.com/projects/affo…
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