Hack Chat Transcript, Part 2

A event log for Open Source Biology and Biohacking Hack Chat

Hacking carbon, oxygen and nitrogen, not just silicon

lutetiumLutetium 02/21/2019 at 16:420 Comments

thethoughtemporiumFeb-13 12:39 PM
you can already use lots of plants for that. it just won't be quite so magically effective

JarrettFeb-13 12:39 PM

thethoughtemporiumFeb-13 12:40 PM
Come spring I'm planning on filling the space I work in with plants and air filters

thethoughtemporiumFeb-13 12:40 PM
And putting algae growing tubing over the windows

Dan MaloneyFeb-13 12:40 PM
Looks like the DIY biodiesel crowd is big into making their own centrifuges to spin down waste frying oil. Found one video where they cast a big continuous flow rotor from aluminum alloy wheels and machined it into shape.

Thomas ShaddackFeb-13 12:41 PM
there's a genemodded germ that acts as immunization against tooth decay. modded streptococcus mutans. not on the market due to some paperwork/lawyer wrangling. any chance of getting it done by alternative channels if the sequences can be found in literature?

thethoughtemporiumFeb-13 12:41 PM
I have some in my fridge XD

thethoughtemporiumFeb-13 12:42 PM
Been tinkering with it in the background

JarrettFeb-13 12:42 PM
I'd definitely be interesting in the algae growing tubes

thethoughtemporiumFeb-13 12:42 PM
I also have the same plasmid that the crispr baby guy used basically

Thomas ShaddackFeb-13 12:42 PM

Thomas ShaddackFeb-13 12:43 PM

thethoughtemporiumFeb-13 12:43 PM
I mean it's a pretty crappy plasmid as these things go, but it's funny to have

thethoughtemporiumFeb-13 12:45 PM
The other fun one I can think of is one we're testing to see if it'll make plants grow faster.

Thomas ShaddackFeb-13 12:45 PM
what about making the plants more tolerant to drought or saltwater or other stressors?

thethoughtemporiumFeb-13 12:46 PM
Very doable, sometimes it's onyl 1 gene you need to kick, but it depends one the stressor

sparkrisp joined  the room.Feb-13 12:47 PM

Thomas ShaddackFeb-13 12:47 PM
another thought.very simple. modded fish that has melanine gene expressing in bones.

thethoughtemporiumFeb-13 12:47 PM
The thing is we have the tech to do all kinds of weird stuff to plants to make them super tough and more nutritous and such, but it freaks people out so we don't do it. It's one of those things where you could make apples that taste like lemons and are rich in vitamin A, but that'd be too weird for people to handle

Thomas ShaddackFeb-13 12:47 PM
making the bloody bones more visible.

Thomas ShaddackFeb-13 12:47 PM
screw the people!

Andrew SmartFeb-13 12:48 PM
@OnlyOneCannolo I suppose one opportunity would be microwave assisted digestion vessels, they're pricey.

I can see a technique to digest samples in a household microwave (instead of a $$$ lab microwave) using a thicker PFTE vessel:

But I suppose there may be other uses for "microwave-assisted liquefaction":

Dan MaloneyFeb-13 12:48 PM
@thethoughtemporium - Do you find that access to current literature is hampered by paywalls on journal sites? Any tips for getting around them?

Thomas ShaddackFeb-13 12:48 PM
we don't need the people's opinions. we need enough underground labs to just get the things done.

Thomas ShaddackFeb-13 12:48 PM
re papers, sci-hub does the trick.

Andrew SmartFeb-13 12:48 PM
#OnlyOneCannolo More DIY instrument ideas:

There is also the recently released Chemputer (open-source), the syringe pumps and 6-way valves are all DIY 3D printed (PFTE filament for chemical contact parts). Seriously an outstanding marvel, but I expect there would be hardware-hacking utility to bring part costs down (computer controllable rotovap & hotplate). Author estimates total cost is $10k, and idea is to use inexpensive off the shelf parts as much as possible:

thethoughtemporiumFeb-13 12:49 PM
*cough* *cough*

Thomas ShaddackFeb-13 12:49 PM


Sci-Hub: устраняя преграды на пути распространения знаний

Первый в мире пиратский ресурс, который открыл массовый доступ к десяткам миллионов научных статей

Read this on Sci-hub

Dan MaloneyFeb-13 12:49 PM

Thomas ShaddackFeb-13 12:49 PM
...that one.

thethoughtemporiumFeb-13 12:49 PM
what paywalls XD

Thomas ShaddackFeb-13 12:50 PM
i am just now assigned to some r&d on 3d-printing uv resins. may be suitable for lab parts, as the material is crosslinked and more resistant chemically, and there's more accuracy and better ways to control the material properties as you can just mix liquids instead of bothering with precision extrusion of filaments.

Thomas ShaddackFeb-13 12:51 PM
and i saw a paper about curcumin working as a biocompatible photoinitiator or photosensitizer.

thethoughtemporiumFeb-13 12:51 PM
I don't even feel bad because the scientists aren't even getting paid. Most of the time if you just email a researcher they'd give you a copy of the paper anyway as is their right. So why waste their time?

Thomas ShaddackFeb-13 12:52 PM
@thethoughtemporium and they can get cited and that improves their standing, too.

thethoughtemporiumFeb-13 12:53 PM

Andrew SmartFeb-13 12:53 PM
@OnlyOneCannolo Oops forgot links to the Chemputer paper:

Thomas ShaddackFeb-13 12:54 PM
the chemputer-like thingy could be very handy for peptide or dna sequence synthesis.

thethoughtemporiumFeb-13 12:55 PM
Ya microfludics is amazing. Some local researchers I know study it and do all kinds of weird lab on a chip stuff. If I ever get an SLA printer I plan on playing around with it. I really want to do complex 3d bioprinting and a microfludic nozel for smoothly adjusting the extruded polymer composition on the fly would be amazing.

Thomas ShaddackFeb-13 12:56 PM

Thomas ShaddackFeb-13 12:56 PM
i am aiming in that direction with my materials. the guys want to target to model kit makers, but i am tacking on some of my own thoughts into the pipeline.

Dan MaloneyFeb-13 12:56 PM
@thethoughtemporium - About how many square feet (or square meters, if you prefer) would you say your lab occupies? I've only got about 60 sqaure feet to work with, wondering what I can accomplish with it.

Thomas ShaddackFeb-13 12:57 PM
sla printers are going down FAST with price. i just now have anycubic photon here.

thethoughtemporiumFeb-13 12:57 PM
The bio part of the lab is about 7'X12'

OnlyOneCannoloFeb-13 12:57 PM
@Andrew Smart I hadn't heard of most of those things before - very cool. $10k is definitely beyond most DIY budgets, so there's definitely opportunity for improvement there.

OnlyOneCannoloFeb-13 12:57 PM
@Andrew Smart and thank you for the links. I'll check them out after work :-)

thethoughtemporiumFeb-13 12:58 PM
I mean I used to be in the fusion community and 10k is about what people would end up spending on their reactors and detection and shielding setups. Bio isn't much cheaper. The mammalian lab I collaberate with cost about 100k to setup, but that's small potatos compared to a university budget

Thomas ShaddackFeb-13 12:58 PM
i am going to experiment with silicone composite, sol-gel silicone from methyltrimethoxysilane with hex boron nitride, for nonstick printer nozzle coatings. polycarbonate is a PITA to print otherwise.

Andrew SmartFeb-13 1:00 PM
Oops I meant PTFE filimant, not "PFTE".

OnlyOneCannoloFeb-13 1:00 PM
Haha I figured - it was close enough

Thomas ShaddackFeb-13 1:00 PM
@Andrew Smart it will be FEP or so. PTFE won't melt before decomposing.

Thomas ShaddackFeb-13 1:01 PM
what about sol-gel glass or ceramics surfaces for inert layers on the printed devices?

Dan MaloneyFeb-13 1:02 PM
So we're getting up to 1:00 here in PST-land, which means our official time is about up. But I don't want to disrupt the conversation, so feel free to stay online and chat for as long as @thethoughtemporium wants to stick around.

thethoughtemporiumFeb-13 1:03 PM
Today is video editing day for me so I'm happy to keep this tab open for a while if anymore has any more questions

Thomas ShaddackFeb-13 1:03 PM
@thethoughtemporium feel free to mail me or pm me or whatever to discuss materials/polymers/crazy things.

Thomas ShaddackFeb-13 1:03 PM
@thethoughtemporium anytime.

Dan MaloneyFeb-13 1:03 PM
I just want to say thanks to Justin for hosting this chat, and for fielding all our questions. I really enjoyed this one, and I feel like I'm going to be looking for space to build out a lab at home...

Andrew SmartFeb-13 1:03 PM
@Thomas Shaddack Oh, thanks. I assumed it was 3D printed just like FEP. Teflon is nasty stuff.

Thomas ShaddackFeb-13 1:03 PM
@Andrew Smart teflon is NEAT. but has its limitations.

Dan MaloneyFeb-13 1:04 PM
And don't forget that next week we'll be talking about X-Rays and High-Voltage experiments with Fran Piernas -

thethoughtemporiumFeb-13 1:04 PM

thethoughtemporiumFeb-13 1:05 PM
For those curious, this is a still from this weeks video. I spent the last couple days extracting red fluorescent protein from some bacteria to try and use in a glowstick

Dan MaloneyFeb-13 1:05 PM

thethoughtemporiumFeb-13 1:06 PM
@Dan Maloney Thanks for having me, this was fun :)

Thomas ShaddackFeb-13 1:06 PM
polymethylsilsesquioxane - another material of interest. from said methyltrimethoxysilane, can withstand up to 500'c without decomposition. teflon, eat your heart out!

thethoughtemporiumFeb-13 1:07 PM
The bioreactor I built and grew the bacteria in

thethoughtemporiumFeb-13 1:07 PM

Thomas ShaddackFeb-13 1:07 PM
i love that!

Thomas ShaddackFeb-13 1:08 PM


Thomas ShaddackFeb-13 1:08 PM
this is a glovebox that won me a bet i can build one for $50 or less.

Thomas ShaddackFeb-13 1:08 PM
note the airlock from two silicone-sealed food storage boxes.

thethoughtemporiumFeb-13 1:08 PM

Thomas ShaddackFeb-13 1:09 PM
newer versions hsould have glove ports 3d-printed.

tocatrooperFeb-13 1:09 PM
PDF for that?

thethoughtemporiumFeb-13 1:10 PM
Been thinking that in about a year I'm gonna double the size of my lab so I can do mammalian and plant work. Looking forward to a nice flow hood.

Thomas ShaddackFeb-13 1:10 PM
would make the design to easil scale from a big train of ones to a little box with one glove.

thethoughtemporiumFeb-13 1:10 PM
@tocatrooper pdf for what?

tocatrooperFeb-13 1:12 PM
For a 3D printed glove box but I guess I’m being to ambitious

Thomas ShaddackFeb-13 1:13 PM
@tocatrooper no pdf yet. the photo is of a manually assembled unit. glove ports aren't properly designed yet, but a suitably big kossel xl printer was acquired exactly with that purpose in mind.

tocatrooperFeb-13 1:15 PM
Understandable brilliant engineering on both your guys part not just the glove box but the bioreactor too

thethoughtemporiumFeb-13 1:16 PM

Thomas ShaddackFeb-13 1:16 PM
indeed, it's pretty!

thethoughtemporiumFeb-13 1:17 PM
For anyone interested, my channel is:

Got lots more like the bioreactor and electroporator there

JarrettFeb-13 1:18 PM
thanks for chatting, Justin

tocatrooperFeb-13 1:18 PM
So one more thing any recommendations on where to find individuals like yourself I mean on any platform I’m definitely gonna watch all the thought emporium videos on YouTube

Thomas ShaddackFeb-13 1:20 PM
youtube. here goes my life!

thethoughtemporiumFeb-13 1:22 PM
There's a couple large group on facebook (biohackin and design,, diybio and others) and a bunch of good channels on youtube. But right now there isn't a good centralized hub to find people as everyone is spread out and in their own little bubbles. Some good ones are: David Ishee (youtube), Sebastian Cocioba (atinygreencell on instagram), Gabriel Licina and,

thethoughtemporiumFeb-13 1:24 PM
once you get into those groups you'll see people posting about their various spaces and projects. There's labs all over the place so there's lots of content. Also Igem teams often make great content to show off their work

neil k. sheridan joined  the room.Feb-13 1:24 PM

anfractuosityFeb-13 1:24 PM
Have you ever looked at synthesizers out of interest, sometimes they seem to turn up on ebay from what i heard, but it sounds like thre chemicals are very very expensive?

thethoughtemporiumFeb-13 1:26 PM
ya a few times. The chemicals actually aren't that bad. But the machines are suuuuuper finicky. Things like air humidiity can have a huge effect on performance. So it can be iffy to get them working well. But they're useful if you've got them.

anfractuosityFeb-13 1:26 PM
ah yeah the chemicals expire fast don't they?

anfractuosityFeb-13 1:26 PM
cool, you've used them, what did you make with one?

Thomas ShaddackFeb-13 1:28 PM
would a glovebox around the machine, with temp/humi control inside, work? or put the mchine into a larger cigar humidor?

thethoughtemporiumFeb-13 1:28 PM
Never use don personally. One of my professors was one of the world leaders in apatamers and would remind us how awful it was to use the thing any time we asked to. SO we'd just order the DNA instead. It's cheap and fast and hassle free.

thethoughtemporiumFeb-13 1:28 PM
*used one

anfractuosityFeb-13 1:28 PM

JarrettFeb-13 1:28 PM
like: why would you ever etch your own PCB? ;)

anfractuosityFeb-13 1:29 PM

anfractuosityFeb-13 1:29 PM that looked interesting

thethoughtemporiumFeb-13 1:29 PM
the guy I mentioned, sebastian, uses those to sequence and publish new genomes. he's currently working on sequencing one of the most radiation resistant microbes