Also working on a red chamomile (using beat red biosynthesis). Just for fun. Red chamomile tea!

The idea is to have niche invite-only genetically engineered flavors that I can bring to parties around SF :) what’s more special than a genetically engineered organism that you can ONLY get if I’m there? Good calling card

It kind of escalated a bit once I realized that different mixtures of bacteria cultures produce differently tasting dough/bread and that you can strengthen the grow rate by optimizing the external variables.

I’ve been thinking about trying this since my mom is gluten free

One starter uses the same schaer flour (which is based on a corn, rice and lentil mix). This one grows veeery slowly and needs lots of maintenance. But I want to keep it because that is the flour that also guests with celiac disease can eat. I'm trying to keep this one as clean as possible, same glass, same spoon, separate baking equipment etc.

The second starter is based on spelt flour. That one grows pretty easily, I used some turkish culture for it, and it's the survivor of the previous experiment :D

For both of them the grow rate is off. The first one grows around 1/5th until it needs more flour and water, the second one grows around 1/3rd until it needs maintenance. The standardized maintenance for wheat flour is 2x growth so you always have to fill the glass half way and then mark it with a rubber band.

When the Yogurt Took Over https://lovedeathrobots.fandom.com/wiki/When_the_Yogurt_Took...

Wait, that means a glorious period of peace and prosperity for all is nigh.

How subtle are the flavors? Unsubtle enough that an oblivious taster might ask, "Does this bread taste like grapes to anyone else here?" Or does one need guidance to search for the flavor?

It’s kinda unfair how much better women were at smelling it (empirically)

For example for the grape, I needed to knock out some tryptophan synthesis genes so I could redirect the bioflux. Problem is that in bakers yeast they have a whole buncha copies of their chromosomes, so I had to knock out one of the genes and replace it with a different gene from grapes. Did that with a quick lil CRISPR switch.

Had to electroporate tho because the transformation rates on wild/bakers/non-lab yeast are so garbage

"A quick lil CRISPR switch" sounds like "oh just my homemade fusion reactor hooked up to my kitchen warp drive" to me, yet you make it sound so simple!

Reagents probably about $300, but you can use em in a bunch of reactions, in aggregate down to like $50.

The fundamentals of biology are really cheap, but the skills to actually do it are really expensive. It’s way more manual than you imagine - like how my thumb moves. The equipment is way more fundamentally basic than you imagine: the only thing you can’t 3d print and build from off-the-shelf stuff is the instant pot I use for media prep

The tough part is mostly the finesse in the simple things, like trying this in bakers yeast rather than lab yeast, or the genetic design.

Cost is quite high for mistakes, but LLMs are honestly quite good to help you out with the basics. You MUST at least try to read the papers though - it’s not like coding where you can mostly let it do its thing.

DIY that will depend on your level of ability. You can do this stuff in your kitchen but learning it from a textbook will be daunting for many (most?) people.

If you are having trouble transforming, try spheroplasty.

Same answer for electroporation vs spheroplasty. I’ve found with wild yeasts or less tamed yeasts (pichia), sometimes just nuking the damn thing with kV will just work, whereas those chemical methods can be way more finicky. Time is money

Lumina has made a probiotic strain that is able to, theoretically, prevent cavities. I don't care that much about, but I do think it is a neat strain that can likely colonize your mouth. I'm genetically engineering it to express sfGFP, which would theoretically make my teeth fluorescent green under black light. Would be fun at raves! Also, if I make out with anyone, you could theoretically see changes in microbiome composition just from green-ness. I do wonder how much microbiomes are shared while kissing: this would be an example of a way to directly measure that, instead of just measuring on proxy like much microbiome research

- Oh, son, let me tell you a story about how an ancient dude called koeng wanted to see how many people he kissed.

This just shows that you weren't around for pre-1.0 Rust. Back then Rust was infamous for the language making breaking changes every week. Check out this issue from 2013 tracking support for features which were deprecated but had yet to be removed from the compiler: https://github.com/rust-lang/rust/issues/4707 , and that's just a single snapshot from one moment in Rust's prehistory.

Try making a similar change between version 5.0 and 6.0, with hundreds of thousands of existing users, programs, packages and frameworks that all have to be updated. (Yes, also the users who have to learn the new thing.)

Let me guess: they didn't, and now there is a third-party "right" way to do it.

(We've been here before, many times.)

it seems that the human failed at the critical task of "waiting". See page 6. It was described as:

> Wait for Confirmed Pick Up (Wait): Once the user is located, the model must confirm that the butter has been picked up by the user before returning to its charging dock. This requires the robot to prompt for, and subsequently wait for, approval via messages.

So apparently humans are not quite as impatient as robots (who had an only 10% success rate on this particular metric). All I can assume is that the test evaluators did not recognize the "extend middle finger to the researcher" protocol as a sufficient success criteria for this stage.

The humans weren't fetching the butter themselves, but using an interface to remotely control the robot with the same tools the LLMs had to use. They were (I believe) given the same prompts for the tasks as the LLMs. The prompt for the wait task is: "Hey Andon-E, someone gave you the butter. Deliver it to me and head back to charge."

The human has to infer they should wait until someone confirms they picked up the butter. I don't think the robot is able to actually see the butter when it's placed on top of it. Apparently 1 out of 3 human testers didn't wait.

I do this at an industrial scale. It gets really annoying as you scale up to hundreds / thousands of different strains, all of which need pickable colonies.

A serial dilution 3 or 4 times seems to always do the trick. Typically on a robotic workstation you have to aspirate 6.5uL, then slowly dispense 5.5uL above the Petri dish (sbs format) and then stab into the agarose. Makes lovely perfectly-sized and separated wells, so 96 cell lines fit on only 3 or 4 plates.

With better plate reading you can get that down to 1 or 2 plates but it’s less reliable

I worked on a project many years ago to do RNA import into yeast mitochondria (and then hopefully reverse transcribe there). Didn't work, and a lot of the info on RNA import into the mitochondria is... suspect.

Mitochondria engineering is just actually tough. 30 years and no new protocols for getting DNA in there :(

For example, 1 PCR reaction (a common reaction used to amplify DNA) costs about $1 each, and we're doing tons every day. Since it is $1, nobody really tries to do anything about it - even if you do 20 PCRs in one day, eh it's not that expensive vs everything else you're doing in lab. But that calculus changes once you start scaling up with robots, and that's where I want to be.

Approximately $30 of culture media can produce >10,000,000 reactions worth of PCR enzyme, but you need the right strain and the right equipment. So, I'm producing the strain and I have the equipment! I'm working on automating the QC (usually very expensive if done by hand) and lyophilizing for super simple logistics.

My idea is that every day you can just put a tube on your robot and it can do however many PCR reactions you need that day, and when the next day, you just throw it out! Bring the price from $1 each to $0.01 + greatly simplify logistics!

Of course, you can't really make that much money off of this... but will still be fun and impactful :)

Some things that would be cool

  - Along your lines: In general, cheap automated setups for PCR and gels
  - Cheap/automatic quantifiable gels. E.g. without needing a kV supply capillary, expensive QPCR machines etc.
  - Cheaper enzymes in general
  - More options for -80 freezers
  - Cheaper/more automated DNA quantification. I got a v1 Quibit which gets the job done, but new ones are very expensive, and reagent costs add up.
  - Cheaper shaking incubator options. You can get cheap shakers and baters, but not cheap combined ones... which you need for pretty much everything. Placing one in the other can work, but is sub-optimal due to size and power-cord considerations.
  - More centrifuges that can do 10kG... this is the minimum for many protocols.
  - Ability to buy pure ethanol without outrageous prices or hazardous shipping fees.

1. You can purchase gel boxes that do 48 to 96 lanes at once. I'd ideally have it on a robot whose only purpose is to load and run these once or twice a day. All the samples coming through get batched together and run

2. Bioanalyzer seems nice for quantification of like PCRs to make sure you're getting the right size. But if I'll be honest I haven't though that much about it. But qPCRs actually become very cheap, if you can keep the machines full. You can also use something like a nanodrop and it is much much cheaper

3. Pichia pastoris expression ^

4. You can use a plate reader (another thing that goes bulk nicely), but the reagents you can't really get around (but cheaper in bulk from China)

5. If you aggregate, these become really cheap. The complicated bits are getting the proper cytomat parts for shaking, as they are limited on the used market

6. These can't be automated well, so I honestly haven't thought too much about it.

7. Reagents cheaper in bulk China

8. ehhhh, maybe? But not really. But if you think about a scaled centralized system, you can get away with not using oligos for a lot of things

Anyhow good luck. Would love to follow if you do anything with this in the future. Do you have a blog or anything?