How to advance a DIYBio lab beyond the basics.

[210jrd]

OK, we have built our lab, fairly well equipped (lots of ebay and purchases from China and India!) and done some basic PCR and electrophoresis testing and even done a small class in Transformation/recombination and a "crime" class with Electrophoresis.

 My question to DIYBio groups in general is where do we go to plan out future development of a DIYBio group and keep interest of members with practical ongoing projects (Basically non-commercial) so that we don't just sit looking at this lovely equipment and have meetings discussing aspects of microbiology?

The information on ongoing paths of DIYBio seems sparse at present and I for one would love to see more ideas coming in of a practical nature that will not break the bank. I do not wish to continually grow coloured e coli in Petri dishes.

Many of us do not have the luxury of a MSc or PhD team leader and must advance in small steps but some advice from those moving ahead would be great. Garage based DIYBio has got to the stage where most equipment (other than sequencers) is now easily obtained. Chemicals and microbes are a cost factor but ideas for the future pathways of DIYBio are seemingly either vague or lacking. Input welcome and if you can disdainfully prove me wrong,with evidence, I will happily admit this topic to have been a waste of time. John D

[Abizar Lakdawalla]

Hi John, see this as a key question. DIY Bio groups seem run out of steam once the initial honeymoon phase is over. 

Some of the projects take too long or are truly impossible or both. And there is very little guidance for the newbies at these sites. People just muddle around for a while.

I would divide viable potential projects into four broad groups

1. Eucation - teach new to bio how to do things.
   
2. Understand life (basic research) - why do we get an itch, how does a plant know where and when to put out flowers, what is the group dynamics amongst crows, can I interfere with dream states, amount of antibiotics in peoples urine (mapped on a google map)
   
3. Provide an alternative to commercial stuff (applied research) - instruments (PCR, sequencers), diagnostics (urine, blood drop, bacteria), drugs (recent example on malarial drug, testing natural remedies for efficacy), foods, ... 
   
4. Create new ground breaking stuff that does not exist yet (blue skies) e.g. an armband that monitors 16 vital signs continuously, machine human interfaces based on nerve signals, Science fiction books are a great source.
   

Abizar

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[Pieter Waag]

It really depends on the aim of your DIYBio group. What works well in our context is to create programs that have a societal impact, such as antibiotics or human enhancement. Also by offering educational programs that go beyond the basics and require some additional commitment from the participants helps in establishing a more vibrant community. In our BioHack Academy there is a strong emphasis on the development of new projects, so of which end up in galleries others become products or publications. It is really diverse, because biology so diverse. Setting a theme already helps a lot: nutrition, health, etc

[Sebastian S Cocioba]

I always recommend to begin with a question. A good way to advance is to let your passion drive you. Think of a specific question you have in biology and run with it. Immerse yourself in that field. Email authors of papers, attend lectures and events, talk to other folks interested, share your data, and build your lab around that question. The rest will unravel and come together as it should.

Sebastian S. Cocioba

CEO & Founder

New York Botanics, LLC

Blog: ATinyGreenCell.com

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[ukitel]

I am really interested in having such discussion.
I think that finding real applications for DIYbio in everyday life is crucial, otherwise I'm afraid the whole movement might soon end up like a soap bubble.

And this applies especially if you don't have, as you say, PhDs around which are motivated into carrying on a personal project.

1.The educational aspect of DIYbio is for sure valuable, but I guess it is not what people think when they hear DIYbio and biohacking.

2.Understanding life, I would redefine it as "exploratory" is closer to the hacker attitude, in that it tries to understand the functioning of a system that is normally unaccessible. Definitely a lot to do for hackers, however this requires some deeper understanding of the biology

3.4. is more about electronics rather than biology, which is good on one side because it is possible to convert skills that you already have, but on the other side I feel it's not dealing enough with biological matter.

The uncertain future of DIYbio I think is related to these 3 main challenges:

1. we are missing standardized parts. DIYbio misses the equivalent of nuts, bolts and electronic components. As a result it is much more difficult to build your own "devices" because you need to develop every single component.

2. we are missing applications. It requires a paradigm shift to start thinking in terms of biology and what biology can do for us. It is difficult because we are used to live in a world where electronics dominates.

3. we are missing specific regulations. Hacking, tinkering, making requires a design/build/test cycle and the same is true for biology. However, due to the inherent danger in tinkering with biology, the actual regulations in place which end up hindering this process because they are tuned on an industrial/academic environment. There is no defined legal space where people can try out things, test them, etc.

I think working on one of these challenges is crucial for the future of DIYbio.
In our small group in Heidelberg we are thinking a lot about interesting DIYbio project that can involve the maker community we are part of.

We are building up a panel of PCR protocols to help people to test food/plants/genes (there is quite some interest in it)

We are exploring the possibility of tinkering old food fermentation processes thanks to the modern knowledge in biology

We plan to build aquaponics systems and to enhance plant growth by selecting/evolving microbial strains involved in nitrogen fixation

We plan to start playing with bacterial fuel cells

[210jrd]

Some good replies in there, I hope as people do come up with novel (and cheap) ways to expand our DIYBio horizons that they will share some details.  I think in general, even in cities, we are talking about small numbers of keen members. Most exciting have been the development of Amino Labs and Bento Labs, both of which will be focussing on practical kits and education so that buyers can proceed further. We are still at the parallel of the early stage of Arduino and pretty soon it took off with many many kits and useful devices following the basic board. Thx to those that answered.

[Josiah Zayner]

Hey John,

     Check out our website(http://the-odin.com) we have lots of new kits and projects and inexpensive reagents. If you need anything let me know and I will do my best to help you.

Thanks,

     Josiah Zayner, Ph.D.

     The ODIN, Founder & CEO

     http://the-odin.com

[Mega [Andreas Stuermer]]

What is this "inherent danger in tinkering with biology". Mostly when I hear this phrase it comes from poeple without a background in biology.

There are certain experiments, where you can reasonably predict the outcome, especially if hundreds of labs have done it before. Like GFP or, say, vanillin biosynthesis. At least if you do it in a contained environment where everything is autoclaved that leaves the lab, I am yet to hear any reasonable explanation why this is not unregulated or there is not some whitelist.

 




On Saturday, December 3, 2016 at 5:22:49 PM UTC+1, 210jrd wrote:

[cathal...@cathalgarvey.me]

Kinda like saying there are "inherent dangers" in electronics, because high voltage experiments can backfire, or you could make interference that might jam a medical device, or... but how often does this actually happen when people get into hobby electronics? :)

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[ukitel]

I actually have a background in biology (10+ years now)

Now, I agree that if you keep it to hobby level and do experiments "where you can reasonably predict the outcome", there aren't many things that can go wrong. And I'm all in favor for better regulation and whitelists.

But I have to say that I've had lab accidents and I have collegues which have had lab accidents.

Just some examples from the top of my head:

splashing stuff on yourself (did it with blood, cells and mutagenic chemicals)
inhaling stuff (happened to me while weighing chemicals)

injecting something in your fingers (surprisingly common when you work with needles)

allergy or even anaphilactic reaction to chemicals (rare but I know at least 1 story like this)

weird inflammation reaction in lymphnodes (collegue working with bacteria and got surgery to remove it)

None of these things caused a permanent damage, but what if that happened during a DIYbio workshop to one of the participants?

Are we waiting for the first anaphilactic reaction in a workshop with mushrooms or are we starting to talk together about how to handle/tackle/prevent this?

I don't think that the rarity of these events is a sufficient justification to ignore their possibility.

Especially because if this movement gets much bigger, as I hope, these unfortunate events will happen no matter how rare.

[Josiah Zayner]

Wow, you must be pretty accident prone or work around accident prone people!

What you posted is extremely anecdotal.

Instead let's look at reality

99.9% of chemicals(if people run PAGE gels acrylamide is toxic when it isn't crosslinked which occurs if they make their own gels but that's about all I can think of) and materials used in molecular biology are non-hazardous in most reasonable quantities(sure you can hurt yourself if you eat too much NaCl but the LD50 is >12g/kg!!!). From running PCR to cloning genes to growing bacteria and yeast you could literally eat everything even the plastic and nothing bad would happen.

Biohackers and DIYBio people don't work with needles usually and even if they do it is rarely or never in the case of using them on mammals. 

Berkeley Lab Accident statistics for the past 6 months http://www2.lbl.gov/ehs/safety/accidentStatistics.pdf

22 people of > 3,200 (most of them ergonomic injuries(using the keyboard too much) or slips and falls!) 0 accidents or injuries reported for Biosciences

You are seriously doing something wrong if all that shit is happening to you and your colleagues.

Finally, what you are saying is that people are allergic to stuff and so we shouldn't do stuff. Because people are allergic to stuff does that mean they shouldn't goto restaurants? the gym? Cook(because they might inhale stuff, ya' know, that they might be allergic to).

Please stop your fear mongering.

Josiah Zayner, Ph.D.

The ODIN, Founder & CEO

http://the-odin.com

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[Winnie Poncelet]

I would find a discussion on 'how big are the risks in a DIYbio lab?', more interesting. I feel like this discussion has been about 'do I classify the amount of risk as dangerous or not dangerous?'. As this is very subjective, it's no surprise that there are very different opinions. The risk someone is willing to take is different for everyone. I could be fine with having 10% chance of dying in traffic on my motorcycle, someone else might shiver at 3%. I'll call it fine, the other will call it dangerous.

So, how big are the risks in a DIYbio lab?

Our data: I can't recall anything happening in the last 1,5 years. I reckon we must have had 2-3 smaller injuries like a small cut or minor burn, as is expected during any activity involving cutting and cooking stuff. There was also one small acid spill that could have ruined some clothes but didn't, and was quickly cleaned up with the spill kit.

We don't do much molecular biology, but lots of microbiology.

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[ukitel]

I already agreed that "if you keep it to hobby level and do experiments "where you can reasonably predict the outcome", there aren't many things that can go wrong." (verbatim from my last post).

Now let's follow your reply and let's assume for the sake of argument, that you are right and if me/people I know are doing it wrong in an academic environment. What ensures that every single biohacker will do it right? Especially given the case that there are people (as you say, like me) that don't do it right? I'm also doing DIYbio. If I behave the same way, according to your opinion, I'll hurt myself, won't I?

The truth is of those accidents that I am aware of only few were reported.

That's because if there is a small accidents a there are no consequences, no one cares, not even the victim.

"Biohackers and DIYBio people don't work with needles usually" <--- that's the point. What is that word doing there? I tell you: you know of instances were needles were used... And, for example, I know one workshop were needles and syringes were employed for lack of pipettes. Nothing bad happened, sure. Could it or could it not?

Please, don't take it as fear mongering.

I am all in favor of letting anyone do this stuff: I organized a PCR workshop where people of all ages took part to it. And together with other DIYbio people we are making a PCR machine available for everyone to use in our makerspace.

This to say that I believe that DIYbio can be done in a safe way.

But from your words it seems that for you the potential dangers are negligible, for me it isn't so and I think there's the need to talk about it. And I'm not alone: the sticky post in this google group is "ask a biosafety expert", because other biohackers recognize that too.

Let's have an honest discussion instead of ignoring the topic because of the "fear of fear mongering".

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[John Griessen]

On 01/11/2017 02:27 AM, ukitel wrote:
>
> But from your words it seems that for you the potential dangers are negligible, for me it isn't so and I think there's the need to
> talk about it. And I'm not alone: the sticky post in this google group is "ask a biosafety expert", because other biohackers
> recognize that too.
>
> Let's have an honest discussion

It's certainly good to talk about practical exposure levels that could cause allergy attacks.
Doctors that treat people have shock reactions to injected allergen treatments at a rate of 2 or 4 per thousand,
fluctuating monthly in that range, said one I know. They make people stay for 20 minutes after injections
so remedies can be done easily if an attack happens.

What would be reasonable in a teaching biohackerspace?

[ukitel]

Already asking ourselves whether it makes sense to keep a first aid kit or a chemical spill kit instead of dismissing the possibility that some things could happen would be great.

Regarding allergens: I'm in germany. Working with fungi constitutes an S1* activity. Because some fungi can produce spores, which can cause severe allergy. This means that spaces where this can happen have to comply to all S1 requirements, plus they must have ensure air circulation.
That's how the law it's written. This means that here, if you are producing cheese, which might have mold growing on it then you must comply to S1* standards: such example is given in the appendix to the law concerning handling of biological material.

Now, is it exaggerated? I have no idea.

[210jrd]

HI Josiah, yes I did already get some stuff and kits from you and I applaud what you are doing, also kudos to Cathal because I now he was trying to do the same.  But thumbs down to the side trackers that want this discussion to be about safety in DIYBio labs. That is a totally separate discussion. necessary yes but not relevant here. Having been a physician for 40+ years I know plenty about labs and needles and allergies etc. But it is off target on this topic, which is to get feedback on ways  to encourage and advance DIYBio beyond the usual meeting where 10 people show up and only one or two at subsequent ones. So it is what we can all do in a practical sense (without being top academics) to enhance the "fun" and educational aspects of this subject that interests me. Quite happy to sit on a committee to discuss safety but not here. And yes I keep a first aid kit handy, it was already in my electronics lab. And you can buy needle disposal boxes and a local hospital will likely dispose of them, or a friendly medical clinic! I would also say that there was less danger at our DNA transformation seminar than at our weekly electronics teaching for kids where they dig around inside computers! But I digress as I am trying to point out.

[Raphael Laurenceau]

Hi John,
As you ask I will answer here to your very first email, how to advance a DIYbio lab beyond the basics.
You say that you don't have the luxury of having a MSc or PhD person in your team, well I think that is what you should try to focus on. I personally think DIYbio lab are a great place to mix scientists and non-scientists. And it might actually be easier than you think to get one in your team. Try posting adds around, so that people in universities or biotechs can see it. There are plenty of scientists who have never heard about DIYbio movement and instantly want to engage in it when they hear about it. Someone with training in microbiology / synthetic biology could help you push projects much further, just sharing their expertise. They will tell you what's unfeasible and what's a good idea, what sort of cloning strategy you should use, what plasmid you can buy, etc.

I'm part of Boslab in the Boston area, and we have tons of scientists coming at very event we organize. We are definitely lucky to be surrounded by biotechs and big universities. But my point is that there is a real interest among scientists. Even people working everyday in a synthetic biology lab come here, they're eager to help democratize these technologies and more generally to 'have fun' with it, to escape the requirements of preparing projects month in advance, and simply start tinkering around with some random ideas they have.

I bet you can find that for your team, good luck!

Raphael

[210jrd]

Hi Raphael, thx and yes I have and am trying very hard to find qualified and interested members, but living in a small skiing town in the Canadian Rockies makes it much harder than you would imagine. There is no University here, but I will persist i looking for other interested parties don't worry. For now everything comes from online data.  J