Were the DIY CRISPR kits contaminated?

[ukitel]

Were the DIY CRISPR kits contaminated?

Dear all,

We would like to give you an update on the situation regarding the possible contamination of the DIY Bacterial Gene Engineering CRIPSR kit distributed by The Odin online shop. We believe it is an issue that should be openly discussed as it can potentially affect the DIY biology community as a whole.

In March 2017, the authorities for health and food safety (LGL) of Bavaria, in Germany, issued a press release revealing their results of an investigation on the DIY Bacterial Gene Engineering CRIPSR kit supplied by The Odin, a company selling biotechnology reagents over the web. The LGL stated that the bacterial strain supplied in the kit was contaminated with potentially pathogenic species, such as Enterobacter species and Klebsiella pneumoniae. Based on these findings, the kit was subsequently banned from being used in Germany.

The press release came shortly after Rüdiger Trojok organized an event entitled “CRISPR kitchen”. LGL representatives requested the organizers from the Institute for Technology Assessment of Karlsruhe (KIT) to hand out a vial of the bacteria obtained from an Odin CRISPR kit, there on display. At the time, the LGL did not specify that they had already found a contamination in another sample.

After the press release, some people involved in activities of the DIYbio community of Europe felt that a proactive attitude was needed to address the issue in the most transparent manner and organized a volunteer committee.

It has been difficult to gather information from both the LGL and the Odin. The LGL press release did not contain any detailed information and we had only access to a leaked report containing a summary of their results. We managed to get some additional information about the methodology used from LGL, but we could not access any of the raw data. LGL researchers told us they would not release the data until their investigation is completed, and will only publish their results in a peer-reviewed journal at a later point.

The Odin produced blast mapping of the E.coli 16S sequence to their bacterial stock and showing 99% identity. They also showed that the strain was negative for lactose fermentation. Both these results were in contradiction with the findings described in the LGL report.

It was decided that gathering more information was necessary to evaluate the situation independently and start an open discussion on how we can promote safe and lawful use of these and other kits offered in and to the DIYbio community. The goal was to evaluate whether contamination was indeed a systematic problem or an isolated accident.

We gathered 3 samples independently from LGL and analyzed them. Two of these samples came from the incriminated CRISPR kit and the last one was an Escherichia coli HME63 strain identical to that included in the kits, all of them being sold by The Odin and shipped to European customers. To obtain high-quality DNA sequencing data, we secured a collaboration to sequence the samples at the European Molecular Biology Laboratory (EMBL) Genomics Core Facility in Heidelberg, Germany. We discussed with the authorities in Berlin (LAGESO, the LGL equivalent) how to safely handle the samples and shipped them to EMBL for analysis.

EMBL Genomics Core Facility collaborators were able to revive only one of the three samples, which showed bacterial growth both in liquid culture and on agar plate. From the 16 colonies grown on the agar plate, 10 colonies were chosen for library preparation and DNA sequencing on an Illumina platform (MiSeq). The sequencing reads have been uploaded at ENA database under the following ID PRJEB23486. We encourage everyone to go and analyze the data if interested. The Core Facility is analyzing the data, but we wanted to share with you some preliminary results:

The E.coli MG1655 strain is the closest strain relative to the E.coli HME63 supplied with the kit and whose complete genome is available. Therefore, we first aligned the sequencing reads to the E.coli MG1655 genome, but noticed that only 30% of the reads are mapping, which wouldn't be expected if the colonies contained E.coli HME63.

 

We then proceeded to assemble the unmapped reads in large sequences (>50 kb) and checked to which bacteria species they were matching. The analysis returned various Enterobacter species (aerogenes, cloacae and hormaechei), as well as Escherichia coli and Salmonella enterica. However, given the relative phylogenic proximity of these species, with this approach it was not possible to pin down the exact bacteria in the colonies. Nevertheless, it gave an indication of the possible bacteria identity.

 

Given the recurrence of Enterobacter species in the results, we aligned the reads this time to the genome of Enterobacter hormaechei subsp. Steigerwaltii and we could now see that 83% of the reads were mapping and corresponded to an expected good mapping rate on a specific genome. Notably, the presence of Enterobacter species was also mentioned in the LGL report.

 

Moreover, as The Odin made available to us 16S sequence of the E.coli bacteria stock in their possession, we sought to determine if that sequence could be found in our reads. Unfortunately, the reads encompassing the 16S region showed again a much better match to Enterobacter hormaechei rather than E.coli.

 

This suggests that the bacteria in the colonies are most probably an Enterobacter species and not E.coli HME63. The 30% of reads mapping to E.coli are probably the result of cross mapping reads between E.coli and Enterobacter genomes.

 

We would like to mention a few words of caution. First, the methodology we used to obtain these results (whole genome sequencing) is different from the one employed by LGL (metabolic and phenotypic analyses). Second, the sample we analyzed was also different from theirs and a single occurrence could again be anecdotic. Third, we cannot guarantee that the samples were stored appropriately at all times before we collected them and ran the sequencing analysis. However, the fact still remains: both our results and the LGL investigation seem to confirm a contamination of the E. coli strain provided with the kit, possibly with the same bacterial species.

Even though the European Centre for Disease Prevention and Control (ECDC) has pointed out that the risk of infection using such contaminated kit is low, we believe it is not acceptable to have laypeople, often not skilled in laboratory techniques, as it may happen in DIYbio, unknowingly handling potentially harmful biological materials. We believe it is our responsibility to act responsibly, something that was explicitly stated in the DIYbio code of conduct and thus learn from this incident and inform the whole community about it. A failure to handle biomaterials appropriately is detrimental to the goals of the community to democratize the knowledge and technology of life sciences.

Authorities in the EU have to follow generally stricter rules than other parts of the world, including the US. Genetic engineering is particularly heavily regulated and only very few and specific educational experiments can be done outside of authorized laboratories. However, we want to stress here that our findings are not discussing the meaningfulness of European GMO laws. The problem we are concerned with is the shipping of living biological samples, which could contain unwanted bacteria or even potentially pathogenic ones due to insufficient quality assurance procedures. This problem not only unnecessarily endangers the customers, it also calls into question the ability of the DIYbio kit manufacturers.

We believe the value of educational kits needs to be stressed out and we want to support their safe distribution and use. We would like to start a discussion involving DIYbio practitioners, as well as the kit producers, academics, the authorities and the public, to collaboratively develop guidelines, or if necessary develop appropriate and efficient methods and procedures to guarantee the safety of the kits and their users.

We believe this should be a community effort in the spirit of the values of the DIYbio code of conduct and so this is also a call to all of you to get involved. If you have any questions regarding the analysis, please engage in the open discussion here on the google DIYbio mailing list.

Finally we would like to acknowledge the help provided by the EMBL Genomics Core Facility team, Vladimir Benes, Jonathan Landry and Anja Telzerow. Without their work and supportive attitude towards the community this work would have not been possible.

 

Best Regards,

 

Rüdiger Trojok

Marco R Cosenza

Julian Chollet

Luc Henry

[Nathan McCorkle]

It doesn't seem reasonable or credible to re-use samples that were already stored improperly, for months and months now... why didn't the experimenters simply re-order from the-odin? If they couldn't due to EU laws, they should have contracted/collaborated with someone outside the EU.

[Patrik D'haeseleer]

On Monday, December 11, 2017 at 8:55:16 AM UTC-8, ukitel wrote:

The LGL stated that the bacterial strain supplied in the kit was contaminated with potentially pathogenic species, such as Enterobacter species and Klebsiella pneumoniae.

Actually, it's worse than merely some contamination: they were not able to grow a single E. coli colony!

The Odin produced blast mapping of the E.coli 16S sequence to their bacterial stock and showing 99% identity.

Which is a test that is entirely useless to show the level of bacterial contamination in a sample - that only shows the identity of the dominant species.

I think it's pretty clear there was something seriously wrong with the sample LGL tested. And I don't doubt that you'd get a similar outcome if you tested the same sample again. One possibility is that the sample got overheated in transport or storage, and was mostly dead except for a few more robust contaminant bacteria. I don't think LGL ever reported what the CFU/g count of the culture was, for that matter.

I don't think it's a big deal that there was a problem with a single sample - even the biggest commercial suppliers have a snafu every once in a while. Plus there's a good chance the problem actually occurred after the kit left The Odin.

I do think it would be in The Odin's best interest to have better QC and tracking for the cultures they send out. If they had been able to respond to the LGL report by saying "Oh, that kit was from batch 17, and here is the Certificate of Analysis showing that that batch contained <0.01% contaminant cells"... I think that would have been a much better comeback.

Having an independent facility test for bacterial contamination will add a bit to the price of the kits, but that can be spread out over larger batch sizes if necessary. Here's some very affordable testing services I came across recently for testing contamination in yeast or fermented beverages (just for illustration purposes - you'd obviously need something different to test a bacterial culture):

http://wildpitchyeast.com/lab-services/bacterial-contamination-analysis - $50/sample

https://www.whitelabs.com/other-products/ls6610-complete-microbiological-analysis - $148/sample

Patrik

[Ruediger Trojok]

Hey all,

here is a popular TV science show debating the topic and reporting on the contaminations found in the-ODIN kit. I was intereviewed there, too.

https://www.3sat.de/mediathek/?mode=play&obj=70680

the language is german.

Best,

Rüdiger

[Wolfgang Nellen]

When you inspect an alleged chicken farm and find that all animals have four legs and say „muh“ and none has feathers, you can certainly confirm your findings by a metagenome analysis. But it is pretty obvious that this is not a chicken farm!

 

I appreciate the efforts by some colleagues to do an in depth molecular analysis but the problem appears to be on a much more trivial level.
Contaminated bacterial samples were not an isolated incident. To my knowledge, at least four independently purchased samples were tested (by different, more or less sophisticated methods) and all tests came to the same result: Enterobacter, Klebsiella, no E. coli.

To check for a single contaminated batch was not possible because there are no batch numbers.

I assume (just my speculation!) that THE ODIN’s 16S analysis was done on their stock but not on the material that was shipped to the users.

 

There appear to be other problems with the kit – we are working on it at www.Sciencebridge.net  but are still reluctant to publish before we have fool-proof evidence.

 

We have to join efforts to clean up the mess! It is not useful to put pressure on the labs that contribute to the clean-up. We and others do not want to publish preliminary results before all controls are done. But the accumulating evidence is sufficient to ban the kit for the time being.

We are quite happy that the media coverage is (so far) reasonable and not blown out of proportion. We tried to contribute a bit (http://www.hr-fernsehen.de/sendungen-a-z/alles-wissen/sendungen/bio-hacking,bio-hacking-100.html).

 

Just a remark on the side: even though Strep resistance is not an environmental hazard, it is strategically bad to do editing on antibiotic resistance! It needs a lot of additional explanation for “normal” citizens and distracts from the core issue of editing. We need a different trait for editing!

Am Montag, 11. Dezember 2017 17:55:16 UTC+1 schrieb ukitel:

[Ruediger Trojok]

Hey everyone,

Alison Abbott from Nature participated in my event crispr.kitchen in Munich at UnternehmerTUM earlier this year.

 Since then, we kept contact. I explained her what was going on with the CRISPR kit from the ODIN

and the trouble it had caused us. I also informed her about our own investigation and results.

This is what she made out of it:

https://www.nature.com/articles/d41586-017-08807-z

Have nice christmas holidays and a happy new year!

Best,

Rüdiger

[Nathan McCorkle]

On Thu, Dec 21, 2017 at 7:13 AM, Ruediger Trojok <ruedi...@gmail.com> wrote:

Hey everyone,

Alison Abbott from Nature participated in my event crispr.kitchen in Munich at UnternehmerTUM earlier this year.

 Since then, we kept contact. I explained her what was going on with the CRISPR kit from the ODIN

and the trouble it had caused us. I also informed her about our own investigation and results.

This is what she made out of it:

https://www.nature.com/articles/d41586-017-08807-z

Have nice christmas holidays and a happy new year!

Best,

Rüdiger

I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.

--

-Nathan

[Patrik D'haeseleer]

On Thursday, December 21, 2017 at 2:20:55 PM UTC-8, Nathan McCorkle wrote:

I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.

Hi Nathan. I have to admit I don't really understand this comment. What behavior are you objecting to here? 

Patrik

[Jonathan Ferooz]

Nathan I think you are wrong, in Belgium we are very interested to collaborate with other groups (and I'm sure in other EU countries too). But in contrast with some other groups we are a small group with no funding.
What do you think we can do?
We are pushing, at our level, to show what is the DIYbio and hope that we'll can adapt our laws to facilitate the DIYbio.
In europe just have the right to put GFP in a genome it's a fight with the authorities.
If other groups want to collaborate with us in Belgium, we are open.
We are not making the show on TV, Nature or other, but yes, we are there.

[Vanessa lorenzo toquero]

Hi,

I introduce myself. Vanessa Lorenzo from Hackuarium biohackerspace in Renens, Switzerland, co-leading it together with Rachel Aronoff and the board,

Just to inform that we had a kit from the Odin at the lab. We decided to get in contact with the German authorities who suggested that our kit might also be contaminated. We sent them the kit.

We also got better informed on how our community could contribute better to the DIY Bio movement. A more dynamic dialogue between the authorities and the affected peers of the DIY Bio movement would had been more desirable but we are now navigating between different landscapes with different time scales and communication protocols. We should push for a better more transparent ones, and of course our door is literally transparent and always open on Wednesdays or on appointment (basically cause we are volunteers and have side jobs or even lives!). Having a constructive and responsible attitude towards the issues we face could help shaping the science we dream of.

Best regards

Vanessa

[Nathan McCorkle]

There's no conversation going on here... and it seems like shoddy and misleading work.

If hamburgers were illegal to eat in the EU, and I mailed a hamburger to some food-hacker there... and they cut open the gamma-sterilized vacuum-sealed bag I sent it in, but only smelled it... so they wouldn't break the law. Then months later the hamburger-police show up demanding that now-rotten hamburger, take it to their lab and test it, only to declare "we couldn't find any beef DNA, only flesh-eating bacteria, thus there must have never been any beef at all and only flesh eating bacteria". Then these food-hackers decide they want to double-check the hamburger-police's lab work... so they do their own DNA test on the rotten-hamburger, to discover the same horrific results!

Let me tell you... I would have ordered a fresh hamburger for any re-testing of hamburgers pre and post rotting. Of course if there is hamburger flesh, flesh-eating bacteria will gladly show up and start eating away/ Of course these bacteria will release nucleases, and other reactive waste products that will destroy any detectable trace of beef evidence.

I don't know what's going on here... but something is shady.

[Julian Chollet]

Bacteria are not hamburgers. Much better shelf life. If I put E. coli in a tube (under more or less sterile conditions) there are still be some viable bugs in there after a few months, usually even years… this is my personal experience – but I’m looking forward to be contradicted.

Re-testing a fresh sample makes total sense - if we want to see if the problem was fixed in the meantime. Any volunteer with a sequencer?

[BraveScience]

As soon as chain of custody of a given material is interrupted (material is open, seal is broken) how can a company be blamed for the state of it?

Here Nathan's analogy fits, that's the common practice in the whole food industry (in EU at least).

The "indignation" of the authority seems out of place and procedures applied non conforming to standard procedures in matter of sampling. Again, if you want to make sure that goods are free of contamination you should check an "untouched" lot before this reaches the customer.

On the other hand hinting to "EU biohackers" is IMHO not the correct way to frame this and a generalization. EU is not USA, there are many different countries here, the fact happened in Germany, that's a whole different story if compared to Denmark, Netherlands, Italy or whatever.

[ukitel]

Hello Nathan,

Maybe there is a misunderstanding going on or we didn't make it clear enough in the post.
The samples analyzed were independently collected from the german authorities. We're talking of two different samples. Actually three, because the bavarian LGL claimed to have analyzed two samples.
Wolfgang Nellen also mentioned that to his knowledge other samples were tested.
In all cases there seemed to be a contamination.

Of course one could argue that the "cold chain" got broken in every single case. IMHO, unlikely that it happened independently many times, but for the sake of the argument, let's assume that some kind of improper storage it is what happened:
even so, maybe there should be a note in the user manual about it, maybe kits should be delivered at cold temperature, maybe the bacteria should be kept in an "air-tight" vial, maybe there could be an "expiry date", maybe there could be an internal control helping the user to know if the kit is still usable...
These are all solution that IMHO could help improving the kit. Not necessarily that kit, but any kit that might include bacteria.

This is the type of discussion that I would wish to see. Instead of turning the face the other way, dismissing the claims, or even suggesting some kind of hidden agenda, let's use this incident to learn and make this stuff better. Because in the end, you might still experiment with those kits in US, but don't forget that's us in Germany (and possibly Europe) that don't have those tools available.

[ukitel]

I like the food analogy but that's also flawed.

Of course if the chain of custody is interrupted then a company cannot be blamed.
But that's not always the case here (for example for the LGL), please do not forget that we are talking about different samples.

Let's look at the food analogy: what does it happen normally when some people get sick with a product bought at the supermarket? the entire lot gets withdrawn and all the people that have bought it are informed (when possible) and asked to return their product. You take a moment of pause, check everything, point down where the contamination happened. If there's something to fix, fix it and then start over.
IMHO, this would be a wonderful resolution for the this case.

Of course food doesn't have to be sterile, but there are thresholds, which are more or less strict depending on the danger connected to the contaminant. The problem is that the LGL and us did not find e.coli at all there. But let's not focus on this kit alone and think generally about such kits: do we need similar thresholds here? The product has to be devoid of any contaminant or not? Can we design a kit so that even if contamination is present, it is eliminated by some kind of selective media?

[Wolfgang Nellen]

I agree with ukitel. We got the real bacteria from the original source and they're fine (so we are not too stupid to grow bugs without contamination).But there seems to be another problem with the protocol: the two vectors transform with very different efficiency and it is difficult to get them both in at the same time.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/307d48d0-7ddc-48e4-adc4-00ddad319825%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Wolfgang Nellen]

Did you get any response from the Germans yet?
Concerning communication: is there anything like a Facebook site where all communities could talk to each other and discuss issues like the kit? I guess the authorities do not have a clue where the DIY communities are!

--

-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/1fc60b5a-ee58-463d-8076-99c4d4c3e515%40googlegroups.com.

[August Pamplona]

On Tuesday, December 26, 2017 at 9:01:47 AM UTC-5, Wolfgang Nellen wrote:

Did you get any response from the Germans yet?
Concerning communication: is there anything like a Facebook site where all communities could talk to each other and discuss issues like the kit? I guess the authorities do not have a clue where the DIY communities are!

Hi,

        There are some. Try https://www.facebook.com/groups/diybio/ and https://www.facebook.com/groups/769326966539324/ . This might be relevant too: https://www.facebook.com/groups/biohackacademy/ 

        Also, if you are into fungi these might be sort of relevant: https://www.facebook.com/groups/FungalSequencing/ & https://www.facebook.com/groups/fungalmaterials/

        There are many other possible matches.

August

[Wolfgang Nellen]

From the Germans (science bridge): still the same. Got  new bacteria from Don Court, we get StrepR but no correct editing. Our post on Odiham Page is not released. Zayner does not respond to mail.

--

-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/98af9aa6-a23e-4d44-a17d-5fcfe63f2bb8%40googlegroups.com.

[Josiah Zayner]

Hey All,

     Quick comment. 

     The contamination that is suggested to have happened occurred over a year ago(1.5 years ago we sent the kit to Bavaria). The EU put out responses and we put out responses also around a year ago, this is like digging up dead bacteria. We don't even work at the same facility we did then, we now ship the bacteria in a different manner. Even so contamination can happen. I have gotten contaminated stabs from other companies and they just send a replacement. This isn't food and as the EU said that if you did somehow manage to eat the bacteria they are not considered deadly and there are common treatments. They also said even if the kit was contaminated kit it was very low risk. I don't know what else I can say in response?

     Wolfgang, we don't even use the same plasmids or bacteria that were shipped to you in 2016. We changed the system completely so it has higher efficiency. Sorry, it didn't work for you. I didn't respond to whatever email you sent because I didn't know what you were looking for in a response? I didn't know how I could help? The old kit and DNA was based exactly off a published paper which we verified the results of. So even if you blame our kit you are also saying the peer reviewed paper is wrong. Maybe it is? Who knows? If you feel slighted by us and want a refund I will give it to you.

     We are working on a new kit that should be out soon that inserts GFP into the genome. We know the antibiotic resistance thing is weird to non-scientists and are trying to change that.

You all tell me what it would take to resolve these things and I will see what I can do. Please let me know how I can help.

Thanks,

     Josiah

 

-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en

Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.

To unsubscribe from this group and all its topics, send an email to diybio+un...@googlegroups.com.

[Ruediger Trojok]

Hey Josiah,

your apology for sending out contaminated materials comes 1.5 years late. I remember well how you responded when bavarian authorities pointed out the kit you sent me was contaminated. It was not exactly what i would call adequate customer support. And blame shifting is also not what is to be expected from a distributor of molecular and microbiology reagents. Your production system at that point in my jdugement was significantly flawed and seemingly no quality control was done.  For the sake of the other customers I hope you improved this by now. 

As its not so easy to detect contamination customers need to be able to trust on the integrity of the producer. Generally I am not recommending anyone to buy from your shop any longer, as you lack this reliability.

By the way, i meanwhile isolated 5 phages which can eliminate the multidrugresistant pathogens you shipped around. 

@all, please let me know if you need the-odin pathogen antidote (phage cocktail).

Best,

Rüdiger

[ukitel]

Hello Josiah,

I wanted to start by saying that I'm very happy you've engaged in the conversation.

I just want to make a clarification, before entering the discussion, since it seems that this point was confused again:

we're talking about different samples, which were also found to be contaminated. The one we sequenced in collaboration with EMBL is different from the one sent to Bavaria. In addition, Wolfgang Nellen also mentioned that other groups in Germany have done similar analysis on their own samples and found a contamination. So we're not talking of an isolated case, but here we have at least 2 cases.

I also wanted to point that your response now is very different from the one you had at that time, which was dismissive of the claims, to say the least. However, I welcome the current approach, more open to discussion and to feedback. Moreover, from what you say, now the production has changed in many ways, and if the situation has improved, that's good for everyone.

It seems to me that you want to restrict what has happened to a mistake in the QA, that can happen of course, but I think it goes beyond that and I care here for a broader discussion:

What biohackers (or DIYbio) are, as a community, is grounded on the actions of every single member. And biohackers are an heterogeneous community, so people very different in their ideas share a common label. Sometimes someone does something and we get all labeled that way, like it or not. You can see it with what has happened recently in DIY gene therapies. I've read your comment of facebook, you protested because the approach of Ascend Biotech was infringing, and I'm quoting, "number one rule of biohacking", that is "never put another person's life at risk". And of course you don't want to share the label of biohackers with them, because you care, and that's why you call them "not legit".

This applies when you or me do something as well. Different story but same reasoning, try to apply it to the DIY CRISPR kits. Maybe it was a tiny mistake, maybe it was a sistematic contamination, but the authorities in Germany thought that the kit was putting people at risk and promptly stopped it. Now, you might have improved the production, but here biohackers are labeled *also* on the basis of that event as "those people that don't know what they're working with".

The ban is still in place, virtually the authorities don't know if the situation has improved or not. And biohackers might pay the consequences of that action, your action, for long time. Hopefully, with what we have done has helped a bit to make things better. It was certainly a way to show how things can be done differently, more responsibly.

If the community cares about what it gets associated with under this big umbrella term that is "biohacking", there's only one way and that is "rules", like the one you were citing. Of course that rule is not written anywhere, but we do have, luckily, the DIYbio code of conduct. Maybe it's not perfect, but that's a start. And that's looking at that code that we decided to take action.

Otherwise we might well start distributing white hats and black hats.

So, I'd like to invite you to rethink what happened with the DIY CRISPR kits, in the same way you have done regarding you self-experimentation on myostatin. You wrote regarding that "I want to apologize, in that I could have inspired people to think I was doing things on a whim when I was not". Well, it looked the same with the DIY CRISPR kits.

It seems now that you are willing to improve the kit and making it safer, better. That's great.
Maybe, we could arrange a common discussion, so that the whole community might gain from these thoughts.

Best,

Marco

[Wolfgang Nellen]

Hi Josiah,
I largely agree with Rüdiger and Marco.

A refund does not help a lot. It would just be nice if critical reviews of the kit were also published on your website and allow to talk about problems. Our comments on the kit (Science Bridge, Jörg Klug) were never released. (This was a kit ordered independently from the two by LGL, Rüdiger and others). This could have started the discussion a lot earlier prevented a lot of damage to the community.

Wolfgang

Am Montag, 11. Dezember 2017 17:55:16 UTC+1 schrieb ukitel:

[Nathan McCorkle]

On Thu, Feb 8, 2018 at 6:54 PM, 'Wolfgang Nellen' via DIYbio
<diy...@googlegroups.com> wrote:
> Our comments on the kit (Science Bridge, Jörg Klug) were never released.

Sounds like that is your fault. Why didn't you post them online publicly?

In the computer security industry there's a common practice known as
"Responsible disclosure", where you let a company know they messed up
and give them ~6 months to try fixing their issues before going
public.
https://en.wikipedia.org/wiki/Responsible_disclosure

Sounds like it's well past time to release your comments publicly.

[Rachel Aronoff]

After just catching up on this discussion, in its many interesting permutations, I feel I should just add that your solution, Rüdiger, is not only of great interest but also quite topical, as we are just organising a public event about phage therapy at Hackuarium.  (We had another a while ago, apparently, but that was before my time...)

So, anyway, if there is any chance people might be around Lausanne at the end of next month (28march), you are invited to join us, and we can discuss this all further (possibly around a beer!).  The event is already up in the Hackuarium web page.

Just to get back on topic, I applaud all who contributed to solving this issue of the 'banned odin kit,' and hope to see more collaborative efforts and less hype in the future.  DIT Research is the way forward, imho...  (Of course we are very keen on the diybio.org code of conduct, too!)  It seems to me that those who bundle together transhumanism with biohacking are not generally helping, but that is another story, and I am very new to all this.

I would add that I personally am quite interested in trying the non-cutting crispr to probe sub-nuclear dynamics, so if anyone else has great tools for that, please let me know!

Thank you very much!

best wishes!

Rachel

[Rachel Aronoff]

oops, the facebook page (and the wiki).

here is one...

https://www.facebook.com/events/527517820982197/

best,

RA

[Wolfgang Nellen]

Well, Jörg posted on the comments site of The Odin. Apparently they decided that this was not a good comment.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en

Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.

To unsubscribe from this group and all its topics, send an email to diybio+unsubscribe@googlegroups.com.

To post to this group, send email to diy...@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CA%2B82U9JY7nN4rC34ROy7ntRFXkyZiuPhBsmy%3DzH%3DyHPB52qYyg%40mail.gmail.com.

[Wolfgang Nellen]

There is one thing that is not really discussed here: the HM68 cells barely grow at37. When you try to grow up at 37 C, you actually select for even minor contaminations.

--

-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/7edeb40b-343b-42a3-a9f7-d6067a2e9049%40googlegroups.com.

[ukitel]

Well, it's not really a difficult to find information... the strain was known and the relevant information can be found everywhere, including the protocol provided together with the kit which says to grow at 30°C or RT.

Wolfgang wrote above that his group tried, with success, to grow the strain from another commercial source (I guess ATCC). Moreover, on an article appeared on Laborjournal (a german magazine for biologists) Wolfgang's version of the story is described in more detail. There, if I remember well, there was also an interview to the scientist who developed the strain and mentioned exactly the fact that the strain cannot grow well at 37°C due to heat-shock driven expression of phage proteins, that could be possibly triggered even with the short the heat-shock included in the transformation protocol.

He was suggesting that as a possible source of the kit contamination, but I don't agree. I can't speak for everyone but, from what I've seen, the Odin as well as all the people involved here are aware the behavior of this strain and worked accordingly.

-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en

Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.

To unsubscribe from this group and all its topics, send an email to diybio+un...@googlegroups.com.