Hack Chat Transcript, Part 1

A event log for Open Source Biology and Biohacking Hack Chat

Hacking carbon, oxygen and nitrogen, not just silicon

lutetiumLutetium 02/13/2019 at 21:080 Comments

Chuck.untulis11:58 AM
Is this the place for DIY biology chat?

anfractuosity11:59 AM

Dusan Petrovic11:59 AM
yes welcome!

konsgn11:59 AM
speaking of diy bio, How to?

Dan Maloney12:00 PM
@Chuck.untulis indeed it is. We'll get started in just a minute.

tocatrooper joined  the room.12:00 PM

Dan Maloney12:01 PM
Actually, it's noon, so let's get to it. Welcome to the Hack Chat! I'm really excited to have Justin Atkin here today...

thethoughtemporium12:01 PM
Hi Everyone!

Dan Maloney12:02 PM
He'll be under @thethoughtemporium handle for the chat, please welcome him and start asking questions about DIY biology

konsgn12:02 PM
ohhh pst is 3 hours off est no wonder it didn't start a couple hours ago

Dan Maloney12:02 PM
Time zones - getcha every time

Jarrett12:02 PM

Anthony joined  the room.12:02 PM

Jan12:02 PM
hi there!

Jarrett12:03 PM
I don't use timezones

Jarrett12:03 PM
they're just not that useful, to me

Dan Maloney12:03 PM
@thethoughtemporium - Maybe you can kick us off with a little bit about yourself, and how you got interested in DIY bio

lawrence_vpi12:03 PM
Hey, I am in Ontario and was wondering where you get your perishables?

tocatrooper12:03 PM
Best machines/tools for a start up lab? Cost? Best place?

thethoughtemporium12:04 PM
Ok will do! my background is pretty odd. Been experimenting in a home lab since I was in highschool. My current goal is to not only do fun and exciting research in a variety of fields, but to show that science can be done anywhere on any budget

thethoughtemporium12:05 PM
I've always been interested in bio because of the immense potential it holds. Bio is essentially the best way of converting one sort of matter into another so you can kind of do anything with it if you're clever and have enough time to mess with it.

lawrence_vpi12:05 PM
Hi Justin I to have been working in a home lab for quite awhile.

thethoughtemporium12:06 PM
It's everything I love about physics and chemistry, but applied at the smallest and largest scales at once.

Dan Maloney12:07 PM
The funny thing about biology is that for every "rule" there are a dozen exceptions. I always found that to drive the chemists and physicists crazy - they couldn't deal with the exceptions

thethoughtemporium12:08 PM
@lawrence_vpi I get my perishables from a variety of sources. And it really depends how perishable the item in question is. Most stuff I get on ebay and amazon honestly. It's crazy how much stuff is available. Anything specialty I have to get from the larger supply companies. If you set up a company and have a non residential address, you can order from them without issue.

Jan12:08 PM
so, we're talking petry dish biology here?

Dan Maloney12:10 PM
Really? Suppliers balk at residential addresses?

thethoughtemporium12:10 PM
@Jan Yes and no. Bio is interesting because most of it is moving small volumes of liquid around. But then you take that tiny starter and it can grow to kilometers wide depending on what the thing is. In my case I'm modifying yeast because then I can grow them in massive tanks to produce stuff

tocatrooper12:10 PM
Best diy molecular biology communities? Support/resources

Dan Maloney12:10 PM
I mean, I can see ordering radioisotopes as a problem, but enzymes and reagents?

Thomas Shaddack12:11 PM
why not lactobacilli?

OnlyOneCannolo12:11 PM
In your experience, what are the most cost-prohibitive aspects of diy bio that could benefit from more accessible equipment and tooling?

Jan12:11 PM
ah, I can relate! baking with a sourdough starter which I feed at least once a week for like ten years...

Dan Maloney12:11 PM
@Jan -- Mmmmm - sourdough...

Sina Booeshaghi joined  the room.12:12 PM

thethoughtemporium12:12 PM
@Dan Maloney Yup they're really picky. It's a bunch of paperwork for some companies like thermo or sigma. So most of the time I tend to go with smaller companies that don't care as much but may only ship to the US. Then you have to get it imported which is a bit of a hassle. That's the thing with doing this on your own or as a small company, learning to source stuff and building those networks is easily the most important part.

Jan12:12 PM
@OnlyOneCannolo very interesting question!

anfractuosity12:14 PM
Hey, i'm just wondering, i've got an old electrophoresis PSU, i'm wondering, if i could use that + PCR to compare different brewers yeast? i watched your electrophoresis video the other day, which i found really interesting (i've never done pcr or electrophoresis before)

Thomas Shaddack12:15 PM
@thethoughtemporium thought. strains of easy to grow germs that make the most important ezymes. then we could just chromatoraphy-purify them without relying on orders.

thethoughtemporium12:15 PM
@OnlyOneCannolo It's kind of everything. Enzymes and reagents can be super expensive, but so can the hard ware. That's why bio projects are centered around detailed planning and sourcing well in advance. You get exactly what you need to save costs. But it's hard to really bring those costs that far down. Some of it is artificial and companies just overcharging, but some things like antibodies are just crazy expensive to produce at sufficent quality and there's no good ways around that.

thethoughtemporium12:18 PM
@anfractuosity Sure there's a variety of tests you can preform though most are pretty subjective. You could make PCR primers that target genes common to or present/absent in various yeast strains and then look at the results on a gel to see "finger" so to speak of the yeasts. Or you could just look at the distribution of proteins in the yeasts and see how that varies. I'm sure there's more but I'm not really an analytical biologist or microbiologist enough to say.

Dan Maloney12:18 PM
One of the biggest problems I see with setting up a home lab is the lack of a big centrifuge. We used our Sorvalls all the time - we had six in one lab I worked in - and each is the size of a washing machine and pretty pricey. Don't know that I've seen a DIY version that replaces a good centrifuge.

Jarrett12:18 PM
how's the lactose intolerance going?

Jarrett12:19 PM
and, why isn't that "fix" more common? Seems like a magic cure, no?

Dan Maloney12:19 PM


Large Capacity Centrifuges | Thermo Fisher Scientific - US

Reliable, reproducible separations for blood banking and large volume processing, our large capacity centrifuges can maximize your lab's productivity.

Read this on Thermofisher

thethoughtemporium12:20 PM
@Dan Maloney I use a cheap 15ml desktop model and a smaller one for my 1.5ml tubes and im totally content. I may pick up a 50ml at some point

anfractuosity12:20 PM
@thethoughtemporium thanks! i'll have to do more reading about PCR

badger12:22 PM
How feasible would it be in a home lab to detect the concentration of DNA fragments in the blood for early detection of cancer? As reported here:

Thomas Shaddack12:22 PM
small high-rpm multikilowatt motors are available at e.g. hobbyking as quadcopter motors. could work for centrifuges.

Tom Nardi12:22 PM
@Dan Maloney I had looked into building a DIY centrifuge, but in the end found that you can get desktop models pretty cheap on eBay if you're willing to wait for a good deal. The Eppendorf model I got only cost me $9

thethoughtemporium12:22 PM
@Jarrett Still good. I think it may have worn off ever so slightly as I can't shovel cream cheese into my face quite the same as I could a months or two after I took it, but I can still handle mil in foods and cheese and pizza and such so long as I don't go crazy. But that's like anyone really. It's not common because gene mods, even simple ones are very serious. I'm glad I did it, but before I'd ever let anyone else try it there's a lot of upgrades I'd want to make for the sake of added safety redundancies and improved performance.

OnlyOneCannolo12:22 PM
As a community of hardware hackers, I think most of us here are better equipped to tackle the hardware problems. So I'd like to hear specific examples from anyone regarding hardware. Centrifuge is one so far. @Dan Maloney Is it really necessary to have one as big as a washing machine?

Dan Maloney12:24 PM
@OnlyOneCannolo - Oh, no, definitely not. I'm just saying that we used these things all the time, and I kind of got spoiled. Just wondering what can replace it functionally without taking up too much space or $$.

anfractuosity12:24 PM
I think i read something about you doing something to do with yeast + silk iirc? I'm not sure i know the correct terminology, but how will you introduce the appropriate plasmid into the yeast, something like electroporation/...?

thethoughtemporium12:25 PM
@badger Depends how much you're willing to spend on setup and improving your technique enough to get accurate reads. There are lots of good kits for extracting floating DNA in blood, but the amount of DNA is small so it can be easily contaminated and it can be difficult to get enough to sequenece. But it's not impossible.

Jarrett12:25 PM
upgrades like how?

Jarrett12:25 PM
(re: home gene mods)

Dan Maloney12:25 PM
That said, big centrifuges can be terrifying. I've seen rotors on ultracentrifuges fail at 100k RPM. Not pretty.

thethoughtemporium12:25 PM
@anfractuosity Yup I actually just builts an electroporator. Gonna test it out next week

anfractuosity12:26 PM
oooh! nice, using capacitors ?

thethoughtemporium12:26 PM
nope! better

thethoughtemporium12:26 PM


A 2018 IGem team created the electropen which is an electroporator that uses a cheap BBQ ignitor piezo as the high voltage source. I've wanted an electroporator for a while now so made one of my own but with a few design tweaks. Can't wait to test this out!! #biohacking #biology #geneticengineering

94 Likes, 4 Comments - Justin Atkin (@thethoughtemporium) on Instagram: "A 2018 IGem team created the electropen which is an electroporator that uses a cheap BBQ ignitor..."

Read this on Instagram

anfractuosity12:26 PM
haha! nice!

badger12:26 PM
Re centrifuges: Up to 125,000 rpm, enough to separate plasma from blood in under two minutes and isolate malaria parasites in 15. Some versions of the device could cost as little as twenty cents and don’t require anything more exotic than paper and string.

Thomas Shaddack12:27 PM
@thethoughtemporium any thoughtsabout single-molecule techniques?

thethoughtemporium12:27 PM
@Thomas Shaddack in what context? Like DNA sequencing? Or..?

anfractuosity12:27 PM
@thethoughtemporium were do you get the plasmids from out of interest?

Thomas Shaddack12:27 PM
@thethoughtemporium mostly dna sequencing.

Dan Maloney12:28 PM
@badger - Thanks, I had forgotten about that

thethoughtemporium12:28 PM
@anfractuosity Variety of places. Friends, addgene, other researchers if you ask them nicely

anfractuosity12:28 PM

thethoughtemporium12:29 PM
@Thomas Shaddack I mean nanopore sequencing is pretty amazing, as are the tethered polymerase thing. Blanking on the name. But haven't really used either personally

OnlyOneCannolo12:29 PM
@Dan Maloney re: centrifuge size -- gotcha. I wasn't sure if there was a situation where a desktop model just wouldn't cut it. Thanks!

Dan Maloney12:30 PM
It seems like a lot of analytical/synthetic stuff (sequencing, primer synthesis, etc.) is available as a service these days, whereas we used to have to do all that stuff in house. Is that true? Can you just send a sample away for sequencing or order primers online?

thethoughtemporium12:31 PM
re: centrifuges - unless you need more than a 50ml fuge, there's really no need. My lab is tiny, I couldn't afford to waste space on a huge fuge unless I absolutely needed one. One person I know in the diybio crowd that has one is David Ishee because he's processing ecoli from a 5 gallon bioreactor

Thomas Shaddack12:32 PM
@thethoughtemporium i am nurturing a thought of light-controlled dna or rna printing. a variant on transcription, but with light pulses to energize the given nucleotide addition. it's a bit far in the left field, kind of an artificial anoparticle/"enzyme" that'd absorb at five wavelenghs, have one for each nucleotide (add to the growing chain on illumination), and one for reset (to prevent longer light intervals from making polynucleotides).

Dan Maloney12:33 PM
@thethoughtemporium - See, that's a use case I could see needing a big Sorvall for, and one that I might be coming up against. I wonder if there are any compact or DIY flow centrifuges, so you wouldn't have to spin in batches with big 500 mL bottles.

thethoughtemporium12:33 PM
@Dan Maloney Yup! you never do anything yourself if you don't have to. For some of the work we don't even build the plasmids. We just order the pieces from one company, send them to another company for assembly, then we get it and throw it into some cells. Same with tests. Why spend 100-500k on a machine when you can pay 150 bucks to use someone elses

Thomas Shaddack12:33 PM
@thethoughtemporium if it could work as directly inserted into the cells, we'd have effectively light-programmable biosynthesis.

thethoughtemporium12:35 PM
@Thomas Shaddack what you''re describing is incredibly hard. Not to say it's impossible, but it's very hard. I encourage you to try because if it works it'll be great, but just know it's hard going in.

anfractuosity12:35 PM
I saw you've grown glowing yeast which looked really cool, are you planning anything else with yeast soon? I think i saw about people getting 'hop-like' flavours from yeast which i was intrigued by

Dan Maloney12:36 PM


How To Build Your Own DIY Centrifuge

For any garage-ista ready to tackle molecular biology, the centrifuge is an essential laboratory tool. Its super-rapid spin supplies the right G-forces to neatly separate biological materials-including cells, proteins, and DNA-from a liquid. University-grade centrifuges sell for about $2,000, but synthetic biology enthusiast and inventor Cathal Garvey figured out how to build one with a Dremel tool and a 3-D-printed wheel.

Read this on Popular Science

thethoughtemporium12:36 PM
@Dan Maloney I mean I've been toying with the idea of using a reverse osmosis filter setup to concentrate stuff. Not sure how well it would work yet though.

Jarrett12:36 PM
Thoughts on the GM Pothos that can break down chloroform?

Jarrett12:37 PM
I've sent that link through your contact form, but you should totally try to replicate it :P

thethoughtemporium12:37 PM
also those DIY fuges suck. A lot. For the 50-100 bucks it costs for a fuge, there's no reason to ever make one of those unless you absolutely can't find one

anfractuosity12:38 PM
i'd worry the tube things would fall out of that diy centrigue?

Tom Nardi12:38 PM
I blew up a 3D printed rotor like that spinning up a couple tubes in a Dremel. Would not recommend...

anfractuosity12:38 PM
heh eek

thethoughtemporium12:38 PM
@Jarrett I've seen that article. Looked cool. I don't think I'd want to replicate it but I'd love a sample of the plant. If I ever got a sample of the DNA I'd happily throw it into a plant. Been wanting to mess with some plant bio. Currently looking at protoplast fusion to make weird fusion plants

Thomas Shaddack12:38 PM
@thethoughtemporium yay weird plants!

Jarrett12:39 PM
I really really want it for my hackspace, it's basically ideal