Biohackerspace/DIYbio GMO Release

[Josh Perfetto]

Moving the BioCurious discussion on Glowing Plant to a new thread. I want to summarize some arguments and start to craft some ideas about environmental release before our meeting on this.

In engineering, you want to quantify the risks, and the consequences of the manifestations of these risks. Engineers do this every day, whether they are calculating the MTBF for a component, or building a bridge or airplane. A problem with genetic engineering and GMO release is we have no where near the data needed to start to quantify risks.

Sometimes to advance the state of knowledge, you have to take unknown risks. The early explorers certainly did this, as did Apollo astronauts as Omri pointed out. However a difference here is that these mentioned risk-takers risked their own lives, while the "risk-takers" contemplating GMO release and risking all of our well-being, whether we consent or not. However there are certainly many important potential benefits to be had, such as in health and in energy, so not taking action is also a risk.

I think the best strategy in such an uncertain case is "proceed, but slowly", which was basically the outcome of the Asilomar Conference over 35 years ago. The question then, is what does slowly mean in the context of DIYbio.

A proposal: do everything under the sun that you reasonably can. This might include (just brainstorming here):

- Designing systems to be less-fit

- Designing systems to prohibit horizontal gene transfer

- Designing systems to require a non-naturally occurring obligate nutrient

- Soliciting community input on the specific risks of the envisioned system

- Designing solutions to address such specific risks where possible

- Releasing organisms initially to highly involved DIYbio participants, who can help test and evaluate the specific risks, before wider release

..needs much more community input.

As Patrik pointed out, doing the above would be more than companies such as Monsanto did with Roundup Ready Grass. I don't think that would be a bad thing. First, because US GMO regulation is far from comprehensive, the fact that something is legal according to the USDA means very little in terms of it actually being a good idea. Second, the DIYbio community has always been under much more scrutiny than established companies, so being able to say you are being more careful than large agribio firms paints a very positive image of the community.

Lastly, everyone doing interesting DIYbio Synthetic Biology projects today is already standing on the shoulder of giants. Because of the efforts of scientists at the Asilomar Conference and continuing into more recent years, and members of these very mailing lists that have testified before legislatures and US presidential commissions, the regulatory state of DIYbio in the US is the unregulated state that it is today. Many of us thought this was advantageous to the advancement of this technology, and so took self-regulatory steps to preserve that. People in this community will certainly have diverse views, but I think that anyone who chooses to completely ignore this fact is being anti-social.

-Josh

[Mega]

>Designing systems to be less-fit-

Well, the glowing needs additional energy, so if you make it even less energy wasting it can't even grow without competition.

>Designing systems to prohibit horizontal gene transfer-

ok. Like chloroplast engineereing you mean?

>Designing systems to require a non-naturally occurring obligate nutrient

I disagree. This would be like Monsanto biotech. Open science - the plant is yours and you can propagate it naturally. No terminator genes, no obligate nutrients...

[Alexey Zaytsev]

Sorry, I'm new here, but my impression was, that the first unwritten
rule of DIYbio was "you don't release GMOs", as well as the second
rule. If you absolutely want to do this, you should start a company,
get through the regulations and do whatever you think is right,
without affiliating with DIYbio. The public relation consequences
could me much worse then any realistic risk from releasing a few
glowing herbs.

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[Mega]

Yeah, that's a nice point!


The thing is, why must it be a "company"? Can it be a non-for profit organization too?


Getting through the regulations, obviously, is a very important point.

[Bryan Bishop]

On Sun, Jun 16, 2013 at 7:09 AM, Alexey Zaytsev <alexey....@gmail.com> wrote:

Sorry, I'm new here, but my impression was, that the first unwritten
rule of DIYbio was "you don't release GMOs", as well as the second

No. There are no rules. Anyone telling you otherwise is lying to you. There is no overarching statements you can make about all sovereign individuals working on their own biology projects. The point about DIYbio is that we're a loose association of individuals who pass tips to each other, share progress updates, find others, etc.

- Bryan
http://heybryan.org/
1 512 203 0507

[Bryan Bishop]

On Sun, Jun 16, 2013 at 3:41 AM, Josh Perfetto <jo...@snowrise.com> wrote:

However a difference here is that these mentioned risk-takers risked their own lives, while the "risk-takers" contemplating GMO release and risking all of our well-being, whether we consent or not

You might find this helpful?

http://www.maxmore.com/proactionary.htm

"""

The proactionary principle exists as a response to the precautionary principle, a rule of thumb often used when deciding whether to allow the pursuit of a technology that might have a negative consequence. In practice, the precautionary principle is strongly biased against technological progress, stating that "we should permit no new technology to be developed and no new productive activity to take place unless we can scientifically prove that no harm to health or environment will result."

Alternatively, the proactionary principle emphasizes technological progress and our freedom to innovate and experiment, while also considering lost costs, payoffs and negative effects. The burden of proof against developing a new technology instead belongs to those who propose restrictive measures.

People's freedom to innovate technologically is highly valuable, even critical, to humanity. This implies a range of responsibilities for those considering whether and how to restrict new technologies. Assess risks and opportunities using an objective, open, and comprehensive, yet simple decision process based on science rather than collective emotional reactions. Account for the costs of restrictions and lost opportunities as fully as direct effects. Favor measures that are proportionate to the probability and magnitude of impacts, and that have the highest payoff relative to their costs. Give a high priority to people's freedom to learn, innovate, and advance.

"""

[Cathal Garvey (Android)]

It's worth pushing the other way also and saying that we don't all subscribe to, or remotely respect, the proactionary principal. I think it is safe to say though that virtually none of us subscribe to the precautionary principal, which effectively translates to "never do anything, because you can never predict the outcome with 100% certainty".

Few years back a bunch of us in EU and NA got together separately and thrashed out some "Codes of Ethics" for DIYbio, silly as that may seem for the loose, unaffiliated coalition we are. Both codes ended up in fair agreement, and both included a message to respect the environment..though the US code was clearly less proscriptive than the EU code, which stressed the complexity and dynamics of Nature.

Suffice to say, neither said "Don't release", though both suggested caution. Neither precautionary nor proactionary, just prudence.

--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.

[Cathal Garvey (Android)]

Addition of stimulants to permit growth, like Terminator, need not be a case of corporate monopolism; Monsanto wanted proprietary inducers for their seeds, but you could equally use, say, Lactose: wild-spread seeds are unlikely to encounter milk in the soil but cultivated seeds could be steeped in milk/iptg easily.

Problem: Terminator and Exorcist technologies are probably heavily patented, though you might be able to roll-your-own-Exorcist using some integrase enzymes/sites.

[Patrik D'haeseleer]

I would love to expand this discussion to also include much simpler cases, such as doing E. coli transformations in a public venue.

I know Mac is planning to teach a transformation class at Workshop Weekend in Oakland next week. And if I remember correctly, there have been some demos along that line at scientific conferences (AAAS?) that were very well received.

I'd need to look into the regulatory system again, but I think EPA regulates release of engineered microorganisms by any "commercial entity". Not clear what the correct definition of "commercial entity" includes or excludes in this case. Does that include non-profits? Does it include teaching a class where you only charge for materials used?

Perhaps it might be useful to raise some funds to get a few classical demo cases - such as GFP E. coli - approved by EPA. That would make it beyond-doubt-legal for anyone to teach a class on this in the US (and for participants to take their engineered E. coli home!)

Does anyone know if EPA has *ever* approved an engineered microorganism for environmental release? Can't think of any examples off hand.

Patrik

[Bryan Bishop]

On Sun, Jun 16, 2013 at 6:09 PM, Patrik D'haeseleer <pat...@gmail.com> wrote:

Does anyone know if EPA has *ever* approved an engineered microorganism for environmental release? Can't think of any examples off hand.

Whether or not they have approved it themselves, there are a number of materials that are already regularly released- like seeds, spores/bacteria transferred as part of regular work environments, various seasonal infections that plague office places, etc. So, whether or not it's approved, it's still already happening (even if it's outside the EPA's jurisdiction or understanding).

[Patrik D'haeseleer]

Genetically engineered ones though? The only cases I can think of are maybe some live vaccine strains, but those have typically been mutagenized in other ways, and they would fall under a much stricter regulatory framework anyway, since they're modified pathogens.

Patrik

[Bryan Bishop]

On Sun, Jun 16, 2013 at 7:24 PM, Patrik D'haeseleer <pat...@gmail.com> wrote:

Genetically engineered ones though? The only cases I can think of are maybe some live vaccine strains, but those have typically been mutagenized in other ways, and they would fall under a much stricter regulatory framework anyway, since they're modified pathogens.

"Genetically engineered" of course depends on what you mean. These organisms, just like every other organism, are subject to the same trends of selective pressures that create preferences for certain genes. Not just infectious diseases, mind you. It seems really weird for a regulatory body to completely ignore this and act like biology is completely regulated (hint- it's not; no where even close).

As for viruses, since you brought this up, this is is also why you hear about natural avian flu strains that have mutated. This is common knowledge, I thought.

[Eugen Leitl]

On Sun, Jun 16, 2013 at 10:32:06PM -0500, Bryan Bishop wrote:

> As for viruses, since you brought this up, this is is also why you hear
> about natural avian flu strains that have mutated. This is common
> knowledge, I thought.

It is a very bad idea for any DIYbio to work with live animal
pathogens, mutated, GMO or not.

Even if you grow random bugs on a medium for fun,
make sure you're protected, in case you run into an
evil strain.

There are plans for DYI laminar flow hoods/benches, and
howtos for sterile technique.

[Lisa Thalheim]

On Sun, Jun 16, 2013 at 10:41 AM, Josh Perfetto <jo...@snowrise.com> wrote:

Sometimes to advance the state of knowledge, you have to take unknown risks.

Fair enough, I can certainly get behind that statement. However, in the specific case of the Glowing Plants project, I am wondering: Specifically what advancement of knowledge should be expected from releasing these plants into the wild? I'm not asking this to shoot the project down - coming up with a plausible and convincing answer to this question might go a long way both to justifying the release as well as demonstrating a responsible approach.

Personally, the vibe I've gotten from the discussion and the way the project is presented is mainly one of "Fuck you and your regulations and your concerns, we do what we want, 'cause it's cool and totes sci-fi and shit. Also FREEDOM!!1!"

Anyone else see a problem with that?

[Eugen Leitl]

On Mon, Jun 17, 2013 at 01:23:22PM +0200, Lisa Thalheim wrote:

> Personally, the vibe I've gotten from the discussion and the way the
> project is presented is mainly one of "Fuck you and your regulations and
> your concerns, we do what we want, 'cause it's cool and totes sci-fi and
> shit. Also FREEDOM!!1!"
> Anyone else see a problem with that?

No, we're cool. All VHEMT (or AHEMT, rather) members in good standing, here.

[Lisa Thalheim]

Ok, I guess that's cool, then.

[John Griessen]

On 06/17/2013 05:54 AM, Eugen Leitl wrote:
> There are plans for DYI laminar flow hoods/benches, and
> howtos for sterile technique.

I'm thinking of producing some good desktop sized shippable,
easy assembly low cost laminar flow hoods/benches.

How many would buy at $400?

John

[Eugen Leitl]

We're not shopping for one (yet?) but it's an entirely
reasonable price IMHO.

[Simon Quellen Field]

That question is what a Kickstarter project can answer.

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[Antony Evans]

Josh,

Thanks for starting an important discussion.  Here is how the Glowing Plant project is thinking about these issues:

- Designing systems to be less-fit

• This is a good principle. None of the genes we are introducing give the plant any kind of selective advantage, in fact they will impose a metabolic cost on the plant.
• Designing something which did have a selective advantage, eg herbicide resistance, should be considered much more challenging

- Designing systems to prohibit horizontal gene transfer

• Here's what APHIS/USDA says about horizontal gene transfer from plants (source: http://www.aphis.usda.gov/brs/aphisdocs/08_31501p_fpra.pdf):
  

• ·         First, many genomes (or parts thereof) have been sequenced from bacteria that are closely associated with plants including Agrobacterium and Rhizobium (Kaneko et al. 2000; Wood et al. 2001; Kaneko et al. 2002). There is no evidence that these organisms contain genes derived from plants.

  ·         Second, in cases where review of sequence data implied that horizontal gene transfer occurred, these events are believed to occur on an evolutionary time scale on the order of millions of years (Koonin et al. 2001; Brown 2003).

  ·         Third, transgene DNA promoters and coding sequences are optimized for plant expression, not prokaryotic bacterial expression. Thus even if horizontal gene transfer occurred, proteins corresponding to the transgenes are not likely to be produced.

  ·         Fourth, the FDA has evaluated horizontal gene transfer from the use of antibiotic resistance marker genes, and concluded that the likelihood of transfer of antibiotic resistance genes from plant genomes to microorganisms in the gastrointestinal tract of humans or animals, or in the environment, is remote (Council for Biotechnology Information, 2001; http://vm.cfsan.fda.gov/~dms/opa-armg.html, accessed 1/26/10).

  ·         Finally, a recent review of issues related to horizontal gene transfer concluded that this type of gene transfer is unlikely to occur and poses negligible risks to human health or the environment (Keese 2008). 

- Designing systems to require a non-naturally occurring obligate nutrient

• This is one of the big open design questions. For Arabidopsis there is a BIO1 mutant which requires the addition of an amino acid to grow the plant and we have started testing this mutant. Using this would greatly simplify the ecological/environmental questions, but when we've discussed with backers we get a strong negative reaction. We would welcome comments and suggestions on either side of this question.

- Soliciting community input on the specific risks of the envisioned system

• We will be doing this over the next few months.  We will start by sharing the tests we plan to do on the plant

- Designing solutions to address such specific risks where possible

• Yes

- Releasing organisms initially to highly involved DIYbio participants, who can help test and evaluate the specific risks, before wider release

• Great idea, we already planned to do this with the maker kit but we can do this with the seeds as well

Antony

On Sunday, June 16, 2013 1:41:58 AM UTC-7, Josh W Perfetto wrote:

[Josh Perfetto]

There is one question I have about the Glowing Plant that I have not seen discussed. What might the ecosystem effects of glowing plants be? Obviously there is already much artificial light at night, so we can't be too concerned about that on its own, but plants are much closer to/are the habitat of many animals, so maybe there would be more impact.

That might open up the question of whether you know the Glowing Plant is less-fit. For example, what if animals are attracted to them, and therefore spread their seeds more preferentially.

-Josh

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[Patrik D'haeseleer]

On Mon, Jun 17, 2013 at 12:35 PM, Josh Perfetto <jo...@snowrise.com> wrote:

There is one question I have about the Glowing Plant that I have not seen discussed. What might the ecosystem effects of glowing plants be?

Actually, that's a fairly common question - both from the ecosystem and from the light pollution perspective.

- The amount of light produced by these plants will likely be very dim - definitely far less than the full moon.

- There are at least 70 different bioluminescent fungi, plus of course fireflies and a couple other bioluminescent insects, all of which will likely be brighter than the glowing plant.

- Street lights kill billions of insects every day. Not to mention those bug zapper lights which are intentionally designed to kill insects. Both of these are orders of magnitude brighter than any bioluminescent organism.

Given the abundance of man-made and natural light sources, I would expect a dimly glowing Arabidopsis plant to have an insignificant impact on the ecosystem - and even less on light pollution.

Patrik

[Raymond McCauley]

I wanted to mention that we've got a request in front of BioCurious to
allow students and researchers in the lab to take transformed E. coli
K-12 out of the lab. I was hoping we could use this as a focus for
discussion along with Glowing Plant,/plants in general. If it's E.
coli & GFP, is that OK? How about RFP? Etc. What are the classes of
things you'd allow or not?

Do you require disposal of materials after they leave (i.e., hand out
instructions on sterilizing petri dishes with bleach)? Require a
signed release? Does this count as general environmental release?

What's the generalized set of questions you'd want asked, and answers
given, to determine if this is OK for a given transformation?

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[Avery louie]

Weighing qualifications and signing releases are slippery slopes.

Is it the training of the person or the facilities that they have access to?  Is it okay for someone to take home pathogens if they have experience and a nice home lab?  Will the kindergarteners parents really bleach the samples?

As for releases, even if they protect you legally, it is still reprehensible to release potentially harmful samples to untrained people.

I know that the are worse things growing in your house/spoiled meat than lab e coli, but the benefits seem minimal here.

The benefit of community lands is that there are at least a few people self checking, and we all know how often there are infractions and role bending in even academic labs.

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[Cathal Garvey (Android)]

Wasn't there an effort to create a list of BSL-0 organisms some time back, effectively a list of bugs you can literally eat a petri dish of safely?

Some strains of lab E.coli are BSL0 but not all. But virtually every strain of S.cerevisciae, L.bulgaricus, S.thermophilis etc would be. So either verify your E.coli or pick a bsl0 species.

Within that subset, I think it's unreasonable NOT to send people home when the transgene is something as well studied as GFP/RFP.

Why are workshop participants more suspect than biohackers generally? Are we not undermining ourselves when we say "this ain't safe for you to do at home"?

[Nathan McCorkle]

A. thaliana would be bsl0 then, or wheat. But then wheat
cross-pollinates, etc, like Patrik mentioned.

They already made Go-Gurt a commercial hit, I think I'd eat Glo-Gurt.
Heck, maybe it would change color when it started spoiling or as it
got more acidic tasting while sitting in the fridge.

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[Cathal Garvey (Android)]

Actually I'd few wheat as BSL1; generally safe but harmful to some. I'd also suggest that BSL0 include species thoroughly domesticated and incapable of long term survival in the wild: lab-E.coli, wheat and baker's yeast probably count, Arabidopsis not so much. This includes a longer view than most: it's often said of A.thaliana that it's "totally safe" vs cross pollination as it self pollinates, but if it can survive it can evolve. And cross pollination is highly adaptive.

My shortlist would include strains used for human fermentations for at least 1k years, crop species with no significant allergies, such as oats and rice, and lab strains that are provably and practically irreversibly unviable outdoors.

[Brian Degger]

Also remember that bacteria do quorum sensing. When you culture bacteria you multiply them many fold. They may switch on virulence, or you may be alergic to the protein coats.
Even if this isnt the case so called safe organisms can be bad in big doses to certain segments of the publics...and you wont necessarily know... those that are immuno supressed due to disease, therapy, cancer and pregnacy.
Important to minimise contact and maximise respect. Contamination events also could compromise your 'safe' bacterias.
Cheers
Brian

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[Mega]

> Specifically what advancement of knowledge should be expected from releasing these plants into the wild?

 

Well, children would plant their own glowing plants. And the parents loose their fears against GMOs, because they have one in their own garden. 

 

> Fourth, the FDA has evaluated horizontal gene transfer from the use of antibiotic resistance marker genes, and concluded that the likelihood of transfer of antibiotic resistance genes from plant genomes to microorganisms in the gastrointestinal tract of humans or animals, or in the environment, is remote (Council for Biotechnology Information, 2001; http://vm.cfsan.fda.gov/~dms/opa-armg.html, accessed 1/26/10).

> Finally, a recent review of issues related to horizontal gene transfer concluded that this type of gene transfer is unlikely to occur and poses negligible risks to human health or the environment (Keese 2008). 

 

In the new designs I submitted, I used this: http://journals2005.pasteur.ac.ir/NB/23(9)/1177%20-%201180.pdf

 

This native plant gene confers kanamycin resistance, but does not work in bacteria (also not in chloroplast expression).  

 

In addition, it is a bit bigger than the bacterial resistance gene, so full integration is a bit more unlikely. 

 

 

 

> For Arabidopsis there is a BIO1 mutant which requires the addition of an amino acid to grow the plant and we have started testing this mutant. Using this would greatly simplify the ecological/environmental questions, but when we've discussed with backers we get a strong negative reaction.

 

If you're using this, you could also get a firefly luciferase plant, which only glows when adding firefly luciferin. 

What about a plant that is *killed* by lactose? 

The riobosome inactivating protein (RIP) or sometihing thelike  is activated by lactose? The you could easily kill the GMO with milk. But you don't have to feed it once a day with expensive amino acids. 

> There is one question I have about the Glowing Plant that I have not seen discussed. What might the ecosystem effects of glowing plants be? Obviously there is already much artificial light at night,

 

Nobody cares for the insects that fly to the streetlights and die there. The plants will be a lot dimmer... 

Btw, the plant will attract bugs that eat the leaves. So a potential pollination advantage is balanced out perhaps. 

 

> There are at least 70 different bioluminescent fungi, plus of course fireflies and a couple other bioluminescent insects, all of which will likely be brighter than the glowing plant. 

 

Exactly... What's their effect on the ecosystem? I think it has adapted. 

 

> Given the abundance of man-made and natural light sources, I would expect a dimly glowing Arabidopsis plant to have an insignificant impact on the ecosystem - and even less on light pollution.

If people want to see their plants glowing, they will switch off their house lights. Thus it may get even dimmer? 

[Mega]

>it's often said of A.thaliana that it's "totally safe" vs cross pollination as it self pollinates, but if it can survive it can evolve. And cross pollination is highly adaptive.

Ok, but when it evolves, isn't it more likely to loose the GFP again over the millenia? Perhaps, perhaps not. 

>They may switch on virulence, or you may be alergic to the protein coats.

As a human you can be allergic to anything. TThough bread and drinks haven't been forbidden yet.

>Even if this isnt the case so called safe organisms can be bad in big doses to certain segments of the publics...and you wont necessarily know... those that are immuno supressed due to disease, therapy, cancer and pregnacy.

Yes, but isn't it much much more likely that they get an infection from a mold in the fridge that produces dangerous mycotoxins??

[Cathal Garvey (Android)]

Whether or not a transgene is adaptive is a separate issue. I was popping the false argument that you can *ignore* questions of transgene adaptability and other serious issues by saying "self-pollinating!".

And, for the record, it's equally invalid to hand-wave "metabolic cost!". Everything has a metabolic cost. The question is whether it's worth the cost to the organism.

[John Griessen]

On 06/17/2013 11:02 AM, Simon Quellen Field wrote:
> That question is what a Kickstarter project can answer.

Yes. That will become a kickstarter. I was just fishing for collaborators...

[Eugen Leitl]

Please do post a reminder here, when you need supporters.

[Patrik D'haeseleer]

On Tuesday, June 18, 2013 12:56:00 AM UTC-7, Cathal Garvey (Android) wrote:

Wasn't there an effort to create a list of BSL-0 organisms some time back, effectively a list of bugs you can literally eat a petri dish of safely?

Some strains of lab E.coli are BSL0 but not all. But virtually every strain of S.cerevisciae, L.bulgaricus, S.thermophilis etc would be. So either verify your E.coli or pick a bsl0 species.

Actually, there's a really nice list here:

MICRO-ORGANISMS FOR EDUCATION

There's a few problem areas in this list (like the fact that they just put "Basidiomycetes" under Fungi), and it's gotten a bit out of date (1997), but this is by far the best collection I've seen. This list seems to have been initiated by the NIH, and it's worth checking with NIH, ASM, and/or the authors if there is an updated version:

"This work was presented for review at the May 1997 general meeting of the American Society for Microbiology held in Miami FL. The authors have since been notified that this work will, in essence, be adopted as a replacement for Biosafety Level One of the National Institutes of Health (USA), and as a partial fulfillment of the NIH Director's wish to provide a list of organisms that pose no threat to health or the environment (NIH Guidelines - Federal Register 05 July 1994.) This replacement is scheduled to be made in late 1999."

Their "List#1a" is for grade school level and above:

"These micro-organisms are major components of various recognized human foods. Food products are noted parenthetically. These are appropriate for experimenters of all ages."

BACTERIA: Acetobacter aceti (vinegar), Bacillus cereus (cocoa, tofu), Bac. licheniformis (cocoa), Bac. megaterium (cocoa), Bac. pumilus (cocoa), Bac. subtilis (cocoa, rice natto), Erwinia dissolvens (coffee), Lactobacillus acidophilus (acidophilus milk; yogurt), Lact. bulgaricus (yogurt), Lact. casei (many cheeses), Lact. delbr�ckii (pickles, soy sauce), Lact. helveticus (many cheeses), Lact. lactis (most cheeses), Leuconostoc (many cheeses), Leucon. mesenteroides (pickles; sauerkraut), Pediococcus (sauerkraut, ensilages, pickles), Propionibacterium acidipropionici (Emmenthaler cheese), Prop. freundenreichii (Swiss cheese), Prop. jensenii (buttermilk), Prop. shermanii (Emmental and Swiss cheeses), Prop. technicum (Edam cheese), Prop. thoenii (Emmenthaler cheese), Streptococcus cremoris (many cheeses), Strep. diacetilactis (sour cream, and butter products), Strep. faecalis (pickles), Strep. lactis (many cheeses, sour milk), Strep. thermophilus (yogurt and many cheeses).

FUNGI: Penicillium camemberti (cheese), Pen. roqueforti (cheese), Rhodotorula rubrum (Prisoner-of-War bread [WW2] (degrades cellulose)), and Saccharomyces cerevisiae (baking, alcoholic fermentation), Sacc. uvarum (cider)

indentThese higher (eukaryotic) micro-organisms are common environmental constituents. These micro-organisms are appropriate for experimenters of all ages.

GREEN ALGAE: In essence all photosynthetic forms EXCEPT Prototheca [rare skin ulcers]). Permitted types include: Ankistrodesmus, Bangia, Batrachospermum, Bulbochaete, Callithamnion, Careria, Caulerpa, Chlamydomonas, Chlorella, Cladophora, Closterium, Coccolithophora, Corallina, Cosmarium, Derbesia, Desmids, Dunaliella, Dictyota, Ectocarpus, Egregia, Enteromorpha, Eremosphaera, Eudorina, Fritschiella, Fucus, Gigartina, Gonium, Gracilaria, Hydrodictyon, Iridea, Laminaria, Macrocystis, Mesotaenium, Micrasterias, Microspora, Mougeotia, Nereocystis, Netrium, Nitella, Ochromonas, Oedogonium, Pandorina, Pediastrum, Polysiphonia, Porphyra, Porphyridium, Protococcus, Scenedesmus, Selanastrum, Spirogyra, Staurastrum, Stigeoclonium, Synura, Tribonema, Ulothrix, Ulva, Vaucheria, Volvox, Zygnema

PROTOZOANS: Achnanthes, Actinosphaerium, Amoeba proteus, Amoeba chaos (Pelemyxa), Amphidinium, Arcella, Astasia, Difflugia, Blepharisma, Bursaria truncatella, Chilomonas, Colpidium, Crithidia fasciulata, Cyclotella, Didinium, Euglena , Euplotes, Gregarines, Herpetomonas muscarum, Leishmania tarentalae, Leptomonas pessoai, Navicula, Paramecium , Peranema, Peridinium, Phacus, Prorocentrum, Pyrsonympha, Spirostomum, Stentor, Synedra, Tetrahymena, Thalassiosira, Trachelomonas, Tritrichomonas augusta, Trypanosoma lewisi, Trypanosoma ranarum, Trichonympha, and Vorticella.

LICHENS: All forms are safe.

FUNGI: Basidiomycetes, Dactylaris (snares nematodes), Deuteromycetes, Taxomyces andreanae (taxol producer), Zygomycetes (Mucor)

SLIME MOLDS: All types, including Dictyostelium and Physarum, are safe.

[Cathal Garvey (Android)]

Whoa, B.cereus is on that list.. some strains may be safe, but the species certainly has a bad reputation..

Patrik D'haeseleer <pat...@gmail.com> wrote:

[Cory Tobin]

> often said of A.thaliana that it's "totally safe" vs cross pollination as it
> self pollinates, but if it can survive it can evolve. And cross pollination
> is highly adaptive.

One quick clarification about Arabidopsis since I hear this often.
Arabidopsis *can* cross pollinate but it usually doesn't in lab
settings because we keep the growth chambers free of insects and space
the plants out enough to prevent physical contact between different
genotypes. If you happen to get an infestation of say, thrips, or
some other mobile insect you can definitely get cross pollination.
Also, if the plants come in contact with each other you can get cross
pollination as well. Fortunately I don't think they will wind
pollinate because the pollen is really sticky - it tends to clump
together and stick to things that touch it. I've never seen
Arabidopsis pollen take flight even in front of a fairly powerful fan.

-cory

[Cathal Garvey (Android)]

So if, say, moths were to be attracted to glowing male flowers? :)

[Simon Quellen Field]

Oh come on, be serious.

(Someone had to say it...)

:-)

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[Patrik D'haeseleer]

On Tuesday, June 18, 2013 11:30:46 AM UTC-7, Cathal Garvey (Android) wrote:

Whoa, B.cereus is on that list.. some strains may be safe, but the species certainly has a bad reputation..

Yeah, as I said - the list is somewhat out of date. B. cereus does have a bad rep, but there are several nonpathogenic strains as well (not unlike E. coli!). The taxonomy has changed quite a bit over the past 16 years as well. I was looking around earlier today for where to order B. mycoides, because of the cool patterns it produces, and noticed some sources still list it as B. cereus var. mycoides.

Another somewhat problematic organism for DIYbio is Chromobacterium violaceum - forms nice deep blue-purple colonies, has been used by the E. chromi iGEM team as a source of a blue pigment pathway, and is available from several suppliers in educational kits of pigmented bacteria. But it is also a BSL-2 organism!!

Patrik

 

[Patrik D'haeseleer]

On Tuesday, June 18, 2013 12:00:12 PM UTC-7, cory....@gmail.com wrote:

> often said of A.thaliana that it's "totally safe" vs cross pollination as it
> self pollinates, but if it can survive it can evolve. And cross pollination
> is highly adaptive.

One quick clarification about Arabidopsis since I hear this often.
Arabidopsis *can* cross pollinate but it usually doesn't in lab

Totally agree. This is something people working with Arabidopsis are very well aware of. Outcrossing rates of Arabidopsis "in the wild" have been estimated to be in the range of 0.3 to 2.5%. Not perfect - and not something you should rely on exclusively - but that is still 40-300 times better than if it was *not* a self-pollinating plant!


 

[Antony Evans]

Lou,

A standing committee would be difficult for the following reasons:

• Who would appoint the members of the committee? How is it governed? What stops members abusing their position?
• Are they taking responsibility for the decisions, if so are they being compensated or is there insurance to protect them?
• How can the committee enforce it's recommendations?
• It is against a culture of self-reliance whereby individuals take responsibility to investigate and answer these questions themselves
• It doesn't scale

Instead transparency is the way to go, sharing details of what is proposed ahead of time for public comment and discussion.  There are already plenty for forums which can exist for this purpose - using DIY Bio or this mailing list would be better than setting up a new one.  This is exactly what the Glowing Plant project is doing, indeed one of the big benefits of doing a Kickstarter campaign is that you get a ton of suggestions about how to go about doing things before you do the science. In the next weeks we will be publishing a more detailed document of how we plan to address release questions also for open comment. We should promote a culture of open-ness and one where people offer advice but don't tell others what to do. 

Antony

On Wednesday, June 19, 2013 2:07:15 AM UTC-4, Lou wrote:

[I'm a little surprised there hasn't been more of a response to this e-mail . . .]

I think disposal is a very important issue, in that the *perceived* hazard of glowing petri dishes (even if the real hazard were practically nil) could cause a great deal of distress among the general public, potentially leading to unnecessary restrictions on DIYbio work.  Imagine if you're a maintenance worker emptying a garbage can in the park (or any other place where you wouldn't expect to find strange looking biological samples) and you discover you've just touched these weird glowing germs.  You are probably not going to dismiss it as easily as that moldy burger you picked up earlier, you're probably going to wonder and worry.  Maybe a lot.  Maybe enough to get your supervisor involved (who might get the city council involved, and the mayor, and your congressional representative... and so on).

And that is why, early on at least, I think it's important to have procedures in place to review the appropriateness of releasing modified organisms from the controlled environment of the lab.  I fully expect things to become less restrictive as time goes on, after self-regulation has proved effective and the general public has more confidence in the DIYbio community.

I apologize if I haven't been clear about this before -- I am not opposed to the release of GMOs per se (my graduate work focused on engineering biocontrol agents for crop protection, and much of my subsequent professional work has included similar releases).  What I am concerned about is the fact that much of the DIYbio movement (especially community labs like bioC) have a focus on putting recombinant DNA technology into the hands of individuals who do not have an extensive background in biology, and who therefore may not yet be well equipped to determine the risks associated with the release of their engineered organism.  In these early days of DIYbio, therefore, it seems like it would be prudent to have a process in place for reviewing proposed releases of GMOs before they actually happen, so that the experimenters have ample opportunity to fine tune their work beforehand.

There are many different possible structures that could be put into place, ranging from just posting on an open electronic forum, to having a centralized standing committee that reviews confidential submissions.  The main thing, for me at least, is to have some sort of process in place to demonstrate that the DIYbio community gives due consideration to the risks of the work that is undertaken.

Lou

[P.S. I will be out of town and won't be able to attend the discussion next week]

[SC]

For reference, the official EPA word on regulation of GMO microorganisms:

 

http://www.epa.gov/biotech_rule/pubs/ria/ria064.htm

 

Stacy

[matt harbowy]

More importantly:

With regard to comments regarding smaller-scale products development, EPA finds that,

because smaller scale projects of limited use would most likely be exempt or involve a relatively

limited set of use and exposure scenarios, burdens due to regulatory review would be expected to

be minimal; thus, the impacts of greatest concern to smaller institutions or organizations could be

frequently mitigated. In considering comments regarding CBI substantiation, EPA has decided not

to require up-front CBI substantiation in connection with TERA submissions.

http://www.epa.gov/oppt/biotech/pubs/pdf/ria002.pdf

[John Griessen]

> On Thursday, June 20, 2013 2:29:10 PM UTC-7, SC wrote:
>>
>> For reference, the official EPA word on regulation of GMO microorganisms:
>>
>> http://www.epa.gov/biotech_rule/pubs/ria/ria064.htm

A couple of excerpts from the Canadian verbage are downright funny, in a catch-22 way...

'Since regulations are currently under development or review in all three areas investigated, a definitive description is not
possible.'

'Experiments which go beyond those categorized in the guidelines are to be conducted "under the direction of the government". The
Guidelines do not define or clarify what government direction entails. Examples include' -blah-blah-

[Patrik D'haeseleer]

On Thursday, June 20, 2013 2:58:18 PM UTC-7, matt harbowy wrote:

More importantly:

With regard to comments regarding smaller-scale products development, EPA finds that,

because smaller scale projects of limited use would most likely be exempt or involve a relatively

limited set of use and exposure scenarios, burdens due to regulatory review would be expected to

be minimal; thus, the impacts of greatest concern to smaller institutions or organizations could be

frequently mitigated. In considering comments regarding CBI substantiation, EPA has decided not

to require up-front CBI substantiation in connection with TERA submissions.

http://www.epa.gov/oppt/biotech/pubs/pdf/ria002.pdf

Also, that document is specifically about the Toxic Substances Control Act (TSCA), which only applies to microorganisms intended for commercial purposes.