Science

Yeah, that is where the conversation usually ends. I don't mean to scare anyone. I don't want to be right.

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Ahem. The transgenic shark has been jumped with all the wild eyed scaremongering going on. Personally I'm ready to post the tale of the toxic mind-controlling kombucha .... /sarc

Sent from my iPhone

> On May 28, 2019, at 5:35 PM, Matt Endrizzi <matt.endrizzi@gmail.com> wrote:
>
> We're adding drops to an ocean of genetic transformation, no doubt, but the drops we're adding are self-replicating in an environment covered with cellular life. We harvest sequences that already have high vector potential. We are now getting good at manipulating chromosomes directly. Transposase is a ubiquitous gene fragment in nature, and so probably our labs, and it could likely contaminate tubes that contain wildly different sources of genetic material and a ligase to connect the gene fragments. While there is some comfort in knowing nature has a much larger research budget than humans, I am not certain how blind evolution is. I know I am blind to where evolution will take us, so I feel an ethical need to act out of an abundance of caution.
>
> I pose that any single human-derived nucleic acid (as long or longer than the smallest SGE) that is not a replica or complement of a natural nucleic acid holds the potential to reboot evolution. We cannot know what a doomsday sequence is until it already exists. We should keep these recombinant nucleic acids out of the environment.
>
> I'm calling for precaution, not zero tolerance. If people handling recombinant nucleic acids shared my perspective, they would be more careful and attentive in the lab. Until there is a significantly better way to contain recombinant nucleic acids, this is the best I can hope for. For those of you who are careful, thank you! Expecting high school and middle school teachers to manage this with kids is a tall order we may want to put more thought into.
>
> Personally, from a moral perspective, I believe one is justified in manipulating nucleic acids if they respect its power and seek to alleviate suffering.
>
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We're adding drops to an ocean of genetic transformation, no doubt, but the drops we're adding are self-replicating in an environment covered with cellular life. We harvest sequences that already have high vector potential. We are now getting good at manipulating chromosomes directly. Transposase is a ubiquitous gene fragment in nature, and so probably our labs, and it could likely contaminate tubes that contain wildly different sources of genetic material and a ligase to connect the gene fragments. While there is some comfort in knowing nature has a much larger research budget than humans, I am not certain how blind evolution is. I know I am blind to where evolution will take us, so I feel an ethical need to act out of an abundance of caution.

I pose that any single human-derived nucleic acid (as long or longer than the smallest SGE) that is not a replica or complement of a natural nucleic acid holds the potential to reboot evolution. We cannot know what a doomsday sequence is until it already exists. We should keep these recombinant nucleic acids out of the environment.

I'm calling for precaution, not zero tolerance. If people handling recombinant nucleic acids shared my perspective, they would be more careful and attentive in the lab. Until there is a significantly better way to contain recombinant nucleic acids, this is the best I can hope for. For those of you who are careful, thank you! Expecting high school and middle school teachers to manage this with kids is a tall order we may want to put more thought into.

Personally, from a moral perspective, I believe one is justified in manipulating nucleic acids if they respect its power and seek to alleviate suffering.

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On 5/28/19, Tom Randall <tarandall@gmail.com> wrote:

> Given this has been
> going on over a billion years I don't see how humans, even if all DNA
> synthesis and cloning efforts were solely devoted to making and releasing
> novel sequences, could ever hope to catch up.
> ... Evolution is pretty blind.
>
> Tom

The difference is in yield. Evolution which creates one or two
strange mutations in an isolated geographical environment (small
yield) is different than humans artificially creating 1B clones of
with specifically engineered mutation as a target, of which 100M's of
those are released in various geographies globally (huge yield).
Evolution has been modifying highly localized flu viruses for
centuries in tiny populations but only fairly recently caused near
pandemic through worldwide, rapid globetrotting by humans.

Biologists have a weak argument and ingrained bias by frequently
reciting the improper analogy of, "Well, nature has been doing it for
millennia, so..." I can't say if the biosecurity idea in this
thread is valid but that defense is pretty thin. Nature creates
radioactive heavy metals sometimes, too: rarely and in single
molecules. In comparison, only humans could cause the high-yield
disaster of Chernobyl by mishandling massively concentrated elements.


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No, I am not underestimating nature. I am pointing out that our activities are being underestimated. Nature will take its course and we can't do much about that. We can only control our own activity. One thing we should do is use biotech to defend ourselves. We're off and running in that department. The other thing we should do is not add to the problem, which we are grossly underestimating.

I will acknowledge that several of you in the DIYbio community have commented thoughtfully within a week. Only a handful of academics have commented in 17 years. Unfortunately, I believe the extreme competition for funding creates a selective pressure to remain silent. I also have concerns that an undereducated public would lash out at biotech if it engages in the debate. This is another reason a scientist might remain silent.

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I am not aware of anyone discovering a eukaryotic virus who knows for certain that some of that DNA came from a biotech experiment on bacteria. That would be very difficult to prove and would likely have to be done on purpose in order to be convincing. Again, I am talking about accidents.

Spilling oil vs. spilling a replicating molecule? The former risk is known and small. The latter risk is unknown and could be a lesser or far greater risk than the oil, depending on its nucleotide sequence.

High school labs have the infrastructure of a BSL1 lab but not necessarily the decontamination materials, but part of the definition of BSL1 are lab practices. Do not assume those are being met.

https://sspcdn.blob.core.windows.net/files/Documents/SEP/ISEF/Resources/BSL1-Checklist.pdf

Also, I can attest having started a high school biotech lab that no one told me I needed to maintain a certain level of safety. I did it because I knew better because of my 7 years in professional labs. Even with my knowledge of how things SHOULD run, some kids mess up. One example, a kid squirted another kid in the face with a solution of copper sulfate because he was annoying him.


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Or George Church printing a coded copy of his book on a tiny piece of paper using DNA. When Stephen Colbert tried to eat the paper, Dr. Church grabbed it from him.

Yes, awareness is as critical as following safety protocols. That is why I am reaching out to the DIYbio community - to check on this level of awareness. Based on the few responses I have received so far, it seems there is a sentiment that the "Pros" are doing way worse stuff than us, so we don't have to worry about it. Perhaps if the DIYbio community took the lead on communicating about safety of their own work, the general public might start to learn about risks associated with biotechnology. I have found, after 17 years of trying, that professionals using recombinant nucleic acids are not open to talking about this risk perspective anymore. They had that conversation, somewhat publicly, in the 1970s. Why bring attention to something a second time that might make the public nervous and only hurt research progress and biotech profits?

If the main purpose of DIYbio is to bring biotech to the masses and make it accessible to all, isn't public safety a good place to start?

Scientists by nature focus on speaking about what they have learned based on data and observations. That is another reason trying to talk scientifically about the risks of recombinant nucleic acids is problematic. The focus tends to be on human pathogens and related gene sequences that we know of. The danger with following this line of thinking ONLY is that we can miss plausible threats that are right under our nose that we are not even contemplating might be risky. It's a bit like some toddlers found dad's gun in the closet and are playing with it without anyone watching them. I would apply this analogy to both the Pros and the DIYs.

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rDNA stands for recombinant DNA. A more modern term would be synthetic nucleic acid (SNA), which covers more than just ligated DNA. The NIH distinguishes between SNAs that are copies/complements of natural DNA and SNAs that are not. My concern lies with the latter, mainly because the scientific community has moved on from their initial discussions that ended with a strategy to contain these nucleic acids in labs. The conversation may have faded but the risk is increasing.

We should worry about gene combinations we know are dangerous. Many advocate for this monitoring and I agree. The point I am trying to make is that we don't know enough to assume no novel genes or gene combinations will ever occur. Yes, nature could do this and so biotechnology might give us the tools to understand and defend ourselves from natural disasters. Bioterrorism is another issue. I'm not talking about either. I'm talking about unintended consequences. Because it seems like an existential threat is no reason to ignore it.

I'm glad you found Mr. Kozubek's article. I spoke with him after I read his book. The proposal to transplant containment off-planet is radical and I find it stifles the conversation, despite it making the point that containment is important - really important . Yes, it potentially creates a 'perfect is the enemy of good' situation.

Don't assume bleach or sterilization techniques destroy every single nucleic acid in a lab. We should assume some of these molecules are leaking into the environment via multiple vectors like accidental spills, malfunctioning autoclaves, and neglect.

I did not say human sequences might affect the environment. I did suggest human-created (engineered) sequences could affect the environment. I will not spell out specific mechanisms on the internet, and so I understand I might not be able to convince people through this medium that what they are doing by creating SNAs that are novel is potentially dangerous. The analogy that I use is the Megabucks lottery. The chances any one new SNA will lead to a catastrophe is almost zero, but someone wins the lottery almost every week. The risk is not in any one molecule. The risk of something really bad happening increases as we make more SNAs. The risk also increases with time new sequences have to evolve.

The majority of molecular biologists who first considered risks associated with creating recombinant DNA said they had concerns novel viral or pathogenic materials might be created inadvertently and so they sounded the alarm. That should give us all pause, especially if we are the ones making the stuff.

https://profiles.nlm.nih.gov/ps/access/CDBBCF.pdf

So, my message is please be careful and at the very least meet BSL1 standards and follow the NIH Guidelines on rDNA research.

If you don't comprehend what I am saying here, perhaps you should consider giving up your hobby.


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You should worry about super bugs and other known hazards. My post is focused on unknown consequences. Sequences that nature would not create hold the potential for novel functions far more detrimental than a human pathogen.

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I'm more worried about the experts in academia and hospitals growing super bugs.

> On May 22, 2019, at 3:26 PM, Matt Endrizzi <matt.endrizzi@gmail.com> wrote:
>
> I hope folks might comment on the security measures taken by the DIYbio community to ensure containment of recombinant DNA. My background is in molecular biology at Florida State, Harvard Med, and the Whitehead Institute (currently Broad). I have several concerns:
>
> 1) The biological community in general seems to have concluded that rDNA is not hazardous because nothing noticeably bad has happened in the last 40 years. Look at figure 2 in this paper:
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5898234/
>
> In short, it has been shown through viral sequence analysis that plasmid DNA and other bacterial DNA can evolve into a eukaryotic virus. So plasmids we make today can contribute to viruses in the future. Risk increases with time as well as trials.
>
> 40 years is not long enough to conclude rDNA is safe.
>
> 2) Bioethics conversations focus on CRISPR application in humans. Should we be considering how our synthetic nucleic acids might affect the ecosystem that supports us? We are making nucleotide sequences that nature would likely never make.
>
> 3) I have taught high schoolers now for 15 years. If you want to know how an experiment can fail, have high schoolers do it. Whether through malice or inattention, students often make mistakes making solutions, much less performing ligation reactions or bacterial transformations. They are also not good at cleaning up. What is the competency level in your DIY lab?
>
> 4) What assurances can the DIYbio community give that BSL1 safety levels are being met and that rDNA and everything it touches are being sterilized properly?
>
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I hope folks might comment on the security measures taken by the DIYbio community to ensure containment of recombinant DNA. My background is in molecular biology at Florida State, Harvard Med, and the Whitehead Institute (currently Broad). I have several concerns:

1) The biological community in general seems to have concluded that rDNA is not hazardous because nothing noticeably bad has happened in the last 40 years. Look at figure 2 in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5898234/

In short, it has been shown through viral sequence analysis that plasmid DNA and other bacterial DNA can evolve into a eukaryotic virus. So plasmids we make today can contribute to viruses in the future. Risk increases with time as well as trials.

40 years is not long enough to conclude rDNA is safe.

2) Bioethics conversations focus on CRISPR application in humans. Should we be considering how our synthetic nucleic acids might affect the ecosystem that supports us? We are making nucleotide sequences that nature would likely never make.

3) I have taught high schoolers now for 15 years. If you want to know how an experiment can fail, have high schoolers do it. Whether through malice or inattention, students often make mistakes making solutions, much less performing ligation reactions or bacterial transformations. They are also not good at cleaning up. What is the competency level in your DIY lab?

4) What assurances can the DIYbio community give that BSL1 safety levels are being met and that rDNA and everything it touches are being sterilized properly?

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Hi Yoshi,

I should clarify that they just sent us reagents and primers (not equipment like pipettors or thermal cyclers) but still hugely helpful in getting us started. I just reached out to the general contact form on https://www.dnabarcoding101.org/ expressing interest in their barcoding program and asking what it would take to get involved. One of the program leads reached out and said they were happy to help us out and send us some starting materials. They were super great to work with and happy to answer any questions we had along the way.

I'm happy to give you the contact information to the person I was working with. Just shoot me a DM.

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