koeng

Recently got genomic DNA purification automated for yeast (plus have automated library prep for nanopore+ a promethion)! As part of the DNA purification task, I had to journey up to Healdsburg to buy some lysis enzyme (thank god for winemakers, 100x cheaper than the biotech grade stuff), and noticed catalogs of different yeast strains with all their flavor profiles and stuff characterized.

I'm thinking about buying all the strains and pushing them through my automated sequencing pipeline, and building a yeast genotype -> flavor converter. Then, I think it'd be neat if you could have someone try a bunch of wines to get their favorite, and then genetically engineer a yeast strain specifically for their favorite flavors. Think that could be neat.

I've worked in this field for many years. It's unfortunate that fears of AI have tarnished the field of synthetic cells so dramatically and yet so ignorantly. It's somewhat akin to believing we should ban charcoal because it is used to make (black) gunpowder, which is equally ridiculous

Another thing I’m working on: homemade linen.

Right now I just germinated a 4x8 bed with flax for fiber. The plan is to grow it for 100 days or so and then harvest, dry, ret, dry, and spin. I need a lot more to do anything serious, but I think it’d be awesome to have a scarf that I made with linen I grew and harvested myself

I’m smelting ore!

I got into creating my own rings, and I’d really like to create one with ore I harvest myself. Gold is too hard and silver can be kinda dangerous, but malachite is pretty safe and I can just drive to Copperopolis to pick some up.

Basically: smelt the malachite with flux and charcoal to get pure copper, flow that into an ingot mold, hammer it into shape. Then I’ll have my own ring, with metal I collected with my own hands

I met Craig about a year ago or so at a synthetic biology conference. Even though his institute was the one which created the first synthetic cell, he pretty much just talked about how disappointing it was that we couldn't engineer the ribosome more. Was a funny memory :) guess you always want more once you do something great.

I do some synthetic biology as a hobby - genetically engineered a baker’s yeast to produce grape aroma and then baked bread with it, and gave it to like 100 people at an event I was at.

Also do a few others - learned Esperanto (exclusively through listening and speaking with people), beekeeping, woodworking, etc.

if 10x the average amount of microplastics are showing changes that are approximately equivalent to hormonal or behavioral changes, it's not a significant factor to be worried about.

There are many times where unblinded experiments are still valid. And unfortunately, n=1 means that you can't have controls. The question: "did this intervention, in one person, cause a greater-than-normal increase in epigenetic changes, above baseline?"

eh, not that concerned

yes

Microplastics are bad. People are concerned that there are microplastics in your balls! And that this could epigenetically affect downstream generations. I want to test that theory with a real human, not an animal model.

My plan: collect my own sperm samples over time and do whole DNA preps + basic body metrics. Sperm regenerates approximately every 10w, so planning time series over 10w. Next, inject myself to ~10x the average amount of microplastics, directly into the bloodstream. Continue with the sperm collection, DNA preps, and basic body metrics. Nanopore sequence, and see if there actually ARE any epigenetic changes. Eventually I'll go back down to baseline - are there any lasting changes?

Of course, this is an N=1 experiment, but rather than a metastudy I'm directly changing one variable, so I think it is valuable. We should have more people doing controlled experiments on themselves for the sake of all of society - and as a biologist, I actually have the capacity to design the experiments and scientifically interpret the results. In a way, it's part of civic duty :)

I am also a fan of SQLite. One of the best parts during development is how easy it is to spin up and spin down databases for full integration tests without containers or anything. It also simplifies backups, and is probably good enough.

I don’t think it’s legal for me to sell it (it is a genetically modified organism used in food), but I’d like to figure out if I can just give it away

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