Biosecurity

[Matt Endrizzi]

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?

[S James Parsons Jr]

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

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[Reginald Smith]

Honestly, besides PPE (personal protective equipment) I am pretty sure this varies widely. I don't do recombinant DNA at this time, mostly barcoding, phylogenetic and evolutionary research on bacteria and nematodes, so I don't have the need for such things but I can see why it is an issue. Regarding the rDNA being safe, I remember articles on plasmid population genetics from the 70s trying to predict the probability engineered plasmids could propagate widely in the ecological community. As you say, nothing happened so people feel safe.

My biggest concern, at least now, is people hurting themselves. While not impugning anyone's motives or knowledge I think actual knowledge and effective DIY Bio has still to catch up with enthusiasm in many quarters. Biohackers compare genetic engineering to computer programming but that's pretty strained in my opinion especially as programming is today. Maybe you can compare it to the programming in the 70s and 80s where you needed to know assembly and the workings of computer memory, CPU, bus, etc. to make it work. Getting a CRISPR-Cas9 kit and some synthesized DNA is not going to get much without much more detailed knowledge and hopefully people with that knowledge will take precautions.

I do think we could all see a chilling effect though if someone does something bad or dangerous. I have been in amateur science for a bit and remember over at the amateur chemistry site, Sciencemadness.org how everyone was aghast when the Norwegian terrorist Anders Behring Breivik referenced the site and other sources for chemical supplies in his manifesto on how to make explosives. If someone even tried to do something illegal or damaging we would feel the blowback, no matter how much ethics we try to push and this list is pretty ethical from what I have seen. 

But none of us have enforcement power, we can just give recommendations and tips as far as I know. Worst comes to worst, we would need to understand if we would ever have to report someone for doing anything completely dangerous.

[Niles Donegan]

That reminds me of a poster presentation I saw at a conference fifteen years ago, where a PI at a NYU tuberculosis lab put an undergrad on a summer research project where they were supposed to use phage transduction to move vancomycin resistance into methicillin-resistant S. aureus (MRSA) strains.  

Shockingly bad idea on SO many levels.

I asked the undergrad if they knew what they were trying to accomplish and the danger it posed, and the student said it was all cool because ultimately the phage transduction didn't work.

[Nick Fackler]

1) "rDNA" is a very broad topic built on many methods. I believe the safety is more related to the DNA inputs (i.g. genes) than the recombinant aspect of genome engineering. The government and nucleic acid providers monitor sequences and look for potentially biohazardous purchases. 

2) Can you elaborate on how synthetic nucleic acids in humans will alter the environment? I believe this is possible but I think the statement is more bigger than you imagine and it is not intrinsically dangerous/bad. 

3/4) Bleach destroys DNA. Please, be more specific about "rDNA". 

I believe you don't understand what "recombinant DNA" means these days. I hope you educate yourself before making more statements like this, "Matthew Endrizzi, a biology teacher in New Hampshire, suggested recombinant DNA research—including CRISPR—was dangerous enough in theory that he has proposed to move it all to the moon (he has not yet secured the funding or political will to do this). "

Try reading this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5178364/

https://blogs.scientificamerican.com/observations/science-and-morality/

[Jonathan Cline]

diybio is the tiniest drop in the tiniest bucket compared to nonsense that goes on in academia and industry, like this:   (re-creation of nativity scene in a lab, in celebration?!) 

-- quote --

"World’s first living organism with fully redesigned DNA created"

...

More than 18,000 edits later, the scientists [at Medical Research Council’s Laboratory of Molecular Biology in Cambridge] had removed every occurrence of the three codons from the bug’s genome. The redesigned genetic code was then chemically synthesised and, piece by piece, added to E coli where it replaced the organism’s natural genome. The result, reported in Nature, is a microbe with a completely synthetic and radically altered DNA code. Known as Syn61, the bug is a little longer than normal, and grows more slowly, but survives nonetheless.

“It’s pretty amazing,” said Chin. When the bug was created, shortly before Christmas, the research team had a photo taken in the lab with a plate of the microbes as the central figure in a recreation of the nativity.

-- end quote --

Biosecurity means more than simply inactivating the materials used.  It also means there is an awareness of overriding sensitivities to the experiments being performed and an associated level of professionalism related to all  conduct associated with the work.

On Wednesday, May 22, 2019 at 1:36:57 PM UTC-7, Matt Endrizzi 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:

 

-- 

## Jonathan Cline

## jcl...@ieee.org

## Mobile: +1-805-617-0223

########################

[Matt Endrizzi]

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.

[Matt Endrizzi]

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.

[Matt Endrizzi]

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.

[Dakota Hamill]

Most DIYBio folks I've met follow general lab safety protocol, I'm sure there are some out there who do not either out of ignorance of how to properly dispose of waste, or just laziness.  The same could be said for every single hobby or job in existence.  

Some people bring their spent break fluid to be discarded of properly after a break job.  Most probably dump it in the back yard, down the drain, or fill up a coke bottle and throw it in the trash.   Likewise I'm sure some people have used a GFP kit from Carolina and thrown those petri dishes in the trash.  What's worse? 

Every science classroom in America at least 9th-12th grade is considered a BSL1 lab.

I'm not aware of very many DIYBio people creating custom Gblocks and dropping a few grand at IDT.  And if there are, I imagine they have bleach and an autoclave. 

Your point about the unknown consequences is valid, probably because people really don't know yet.  I'm not well read up enough on the topic to take a stance either way.  Throughout human history there has been many unintended consequences of various inventions, but in this case is there enough evidence to warrant a halt on the invention process?

I don't have an answer for that one.  

Figure 2 from the original paper, if I'm reading it correctly, basically says that genetic information from prokaryotes can be passed to eukaryotes via a viral vector.   Has there been any scenarios where synthetic DNA created for use in bacteria by humans has been found in viruses or in eukaryotes?

On Fri, May 24, 2019 at 8:44 PM Matt Endrizzi <matt.e...@gmail.com> wrote:

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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[Matt Endrizzi]

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.

[Patrik D'haeseleer]

On Friday, May 24, 2019 at 5:45:00 PM UTC-7, Matt Endrizzi wrote:

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.

I think you hugely underestimate the dangers that Nature throws at us, in comparison to what humans are able to engineer.

There are an estimated 10^31 phages and viruses on earth - all of which are constantly reshuffling and mutating existing genes or even creating new genes from scratch. We may never be able to sequence all genes on earth, because the rate at which new genes are generated by phages dwarfs the speed at which we can find and sequence them. In comparison to that torrent of trial-and-error, the little amount of tinkering humanity has managed to do so far is rather puny.

That is not to argue that we don't need bioethics and biosafety - in fact, I have seen far *more* discussion of those issues within the DIYbio community than I've seen in any academic or commercial biotech setting.

But yeah, I think you are seriously underestimating Nature...

[Matt Endrizzi]

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.

[doctor.perkins]

Here is a good resource on biosafety and biosecurity training, including responsible conduct in the life sciences research, at:

https://ebsaweb.eu/sites/default/files/culture_training_catalogue-final-27march2019.pdf

dp

On Wednesday, May 22, 2019 at 4:36:57 PM UTC-4, Matt Endrizzi wrote:

[Tom Randall]

I recently read a paper (Marine DNA Viral Macro- and Microdiversity from Pole to Pole; Cell 177: 1, 2019) which claimed this: "Beyond mortality, viruses can alter evolutionary trajectories of microbial communities by transferring 10^29 genes per day globally (Paul, 1999)". The Paul citation is attached. If this is plausible, and considering it only refers to oceanic viruses, not all of the other inter-bacterial and other sequence exchanges that must be occurring on the earth I would have to agree Patrik. 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.

@Matt. From this conversation and our private exchange it just sounds like you are advocating almost a zero tolerance approach. There may be some worries, but people do seem to understand this, address it in their private labs as I and others do and I certainly don't see anybody stopping what they are doing anytime soon. I don't see why we would have any more capacity for accidentally creating novel functions than nature. Evolution is pretty blind.

Tom

[Jonathan Cline]

On 5/28/19, Tom Randall <tara...@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.

[Matt Endrizzi]

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.

[Matt Lawes]

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

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[Matt Endrizzi]

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

[James Welch]

Wanted to try and quantify how much DNA is being made. Found a report listing the market cap of oligonucleotide synthesis in 2017 at $1.47 Billion USD. Generously assuming a $0.01 / bp synthesis cost. That's ~147 billion base pairs, a good amount of DNA but nothing an organism cant produce (second source). Probably an amount of DNA you come into contact with over a short time period. Also, imo most of the market will be primers which will be inert. If you have better numbers I'd love to see them but this is just to benchmark what we are discussing.

As to your worry about laboratory contamination leading to novel and active sequences, I think you should design a simple experiment to test your hypothesis. This forum might even be a useful resource for an adversarial collaboration. 

If it means anything, I think you are directional correct but as was mentioned above, there is more friction to the creation of replicating DNA than it appears you believe.

First Source: https://www.prnewswire.com/in/news-releases/oligonucleotide-synthesis-market-worth-246-billion-usd-by-2022-672921973.html
Second Source: https://en.wikipedia.org/wiki/Paris_japonica

[Matt Endrizzi]

I recognize there is a great deal of friction fighting against DNA. We also know some sequences have become very successful. Oligos and PCR are not on my radar. Processes that make novel sequences greater than 200 bp are.

While many probably think I’m overzealous in my dire predictions, I here you. I perhaps just don’t have the same confidence as others seem to have in claiming to understand evolutionary processes. I think our understanding about evolution is still quite nascent. Assuming human-derived sequences hold no potential danger greater than what nature poses is a major problem, in my view. We are bypassing natural barriers that would likely prevent certain sequences from ever existing. With the advent of recombinant DNA technology, we have entered a whole new biohazard realm.

While this is an old letter from Ted Kennedy, it summarizes the agreement made by the scientific community to promise the public to contain recombinant DNA and not let it out into the environment.

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

While dialogue around risk has subsided from public awareness since the publishing of the NIH Guidelines, I am not aware that this containment promise has been withdrawn.

[Andreas "Mega" Stuermer]

" Assuming human-derived sequences hold no potential danger greater than what nature poses is a major problem, in my view.  We are bypassing natural barriers that would likely prevent certain sequences from ever existing. "

Have you considered that this problem may only exist in your head? These barriers do not exist. Species are made up by humans. There's literally hundreds of papers about horizontal gene transfer and how often it happens in nature. Also, I'll have to look up how many billions of mutations you get in the yield of a 1 hectar field. 

Labs work with plasmids and as long as they autoclave and bleach everything, nothing gets out. And for all scientific evidence we have, it should be fine even if we released it. What makes you think nature has a plan and can't horribly go wrong? 

Also, considering how much effort we put into makeing this planet uninhabitable.... By burning coal, which releases both particulate matter and radioactive minerals (which cause mutations) and gas and oil, releasing huge ammounts of greenhouse gasses. End even besides that, cutting down the rainforest and making so many species extinct. Causing eutrophication and euxinia, and possibly triggering the ocean to tip and release hydrogen sulfide and cause a new mass extinction. Breeding atibioti-resistant bacteria and yeasts by using the same antibiotics and fungicides in agriculture that we use for medicine. These are the problems. Talking about rDNA and thinking it hasany effect - especially that most are following current guidelines -  is ridiculous. 

[Andreas "Mega" Stuermer]

Not trying to end this discussion, but from my experience and knowledge from reading scientific literature and my studies, your concerns seem more like a gut feeling than a  reasonable fear. 

Sure: if someone farts, it coud trigger a hurricane somewhere, which then reflects sunlight which radiates onto a meteor and directs it towards Earth. Scientifically speaking you could probably think of a way how this could happen. Probability is very low. 

Using pUC plasmid, adding a mouse gene expression cassette and saying this is gonna turn into a useful virus.... or it may mix with influenza and create a super-virus.... sounds pretty bonkers. Especially when you are not working with viral *biosafety level 2 or BSL3*  and immmunoevasion proteins thereof. Which you aren't allowed anyways. And I bet an amateur would have a hard time figuring out which of these viral genes will actually integrate and work. Even experts can't, and most experiments just don't work. And what motivation would anyone have to do that.

So in my opinin that's just ignoring what happens in nature and disproportionally assessing risks. We have how many? 50 years experience with recombinant DNA? 

Precautionary principle is important. Not stopping science because of gut feelings and natural fallacy is also important. You know, we need more efficient agriculture, or this planet won't stand another 40 years. It's vertebrate biosphere, I mean. 

[Matt Endrizzi]

I pretty much agree with everything Andreas said. However, lab processes do bypass natural barriers. It’s not about how many molecules in the nature vs. human debate. The other point I don’t think I did a good job of making is that what one wants to make in a ligation reaction isn’t the only thing that gets made.

As much as I would like to spell out a scenario that is less ridiculous then a fart-to-meteor leap such has been reported here, I will not do so in a public channel.

Also, assuming 100% containment no matter how careful people are is problematic. Yes, we should still do the best we can.

As far as this risk being in my head, I hope you are right. Sure, if we KNEW someone was accidentally making harmful biological material, we’d be having a different conversation. But we don’t and it would be hard to know, so we either could be careful or completely ignore the potential risk. Im not convinced the Precautionary Principle does this justice. If something is plausibly dangerous, one must prove it safe before moving forward. The problem is I don’t see how we can prove it’s safe, just like it is nearly impossible to prove it is dangerous.

[Andreas "Mega" Stuermer]

 "what one wants to make in a ligation reaction isn’t the only thing that gets made"

Well, there's this new thing called DNA sequencing. You pick a single colony that has clones of a single plasmid, and then sequence the DNA. You also look at the gel if there's only the expected band(s).  So, yes, ligation creates different products but the plasmid you purify is usually analysed before *working with it*, leave alone releaseing it 

  

[Matt Endrizzi]

And the tube of ligation products that you transformed those bacteria with? And the colonies you don’t pick?
And the bacteria that don’t grow because the DNA you put in it was toxic to the cell in some way?

There’s more than we don’t know than we do know. A little humility on the part of people doing this work could go a long way to reassuring the public that not only is science a worthy pursuit, but the people pursuing it are ethical and careful.

[Nick Fackler]

To sum up this thread from my understanding of Matt's fears:

Start of thread:

-Recombinant DNA.

Middle of thread:

-Sequences that nature would not create hold the potential for novel functions far more detrimental than a human pathogen.

End of thread:

-Ligations you attempt that don't propagate and/or unpropogated e-coli. 

This is really starting to feel like a troll. It doesn't help my trolling feelings that he implied that I should "give up this hobby" in his response to me. I find the middle conversation interesting/possible but unlikely to happen in a DIY lab. Much more likely to occur in a govt lab. This has been a journey that has lacked consistency. I also think that Matt should do more research and write up a column for a journal if he'd like to gain traction or be taken seriously.  

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[Jonathan Cline]

On Friday, May 24, 2019 at 5:44:55 PM UTC-7, Matt Endrizzi wrote:

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.

That summary of the television segment is misleading and/or out of context.    First, there's no evidence that anything would have happened to Colbert if he had eaten the paper.  I'd eat it myself.  I'm sure that if an entire synbio conference of biologists were surveyed, all would agree that the DNA paper would have no effect on Colbert, or any other hungry mammal.  Second, the entire televised scene was a comedy skit.  Dr. Church didn't 'grab the paper away to prevent untold danger.'  Dr. Church's response may have been improvised, or it may have been planned out in advance by Colbert (and rehearsed before airing, like a lot of television).  From my perspective, the skit was a statement to project the priceless nature of a rare item precisely engineered:  Colbert shouldn't eat a valuable historical artifact.   It would be like eating a limited-edition, numbered copy of an award-winning painting.  It's obvious to me that Dr. Church's natural response should be to grab the DNA paper away from Colbert.   Don't use this televised scene featuring a prominent bioengineer to promote fear & uncertainty.

The larger issue in this thread is humankind's lack of ability to control it's own risky behavior.  In fact, humanity rewards risky behavior considerably.  Evolution seems to have optimized our species to leap into new technologies before the technology or it's ramifications are fully understood.  I view this in itself as a bug in the human genetic code.  Countless cases throughout history show this behavior.  Societies which valued sustainability have been crushed by colonialism, each case ultimately a simple test of risk:reward for the conquerers.  Humans have beat out every other species as the ultimate predator, even as recent research shows that Neanderthals were likely fully capable of nearly every skill or mental trait which we are capable of.  Except, perhaps, the critical gene of megalomania or egotism.  Every form of engineering (i.e., technological advancement) developed by humankind has had massive risks and, more often than not, have resulted in long-term ecological damage, some as mentioned in this thread already.  In recent years, misbehaving artificial intelligence has entered the list of new technologies which could destroy life as we know it, including humankind itself, and yet still humanity races to unleash the technology without sufficient understanding; even though, just decades ago, nuclear engineering gave humanity plenty of lessons to learn from (namely:  "stop and test fully, before proceeding!"), and chemical engineering of plastics is now finally proving it's dangers through unstoppable worldwide pollution.  This thread opens the discussion that synbio of DNA may be a danger.  The discussion hasn't yet mentioned xenobiology (XNA) or nanotechnology, both of which could operate on far greater multiples than natural DNA, undetectable and unstoppable, since both of those technologies have no natural competitors.   All of these technologies have a common source:  the bug in humankind which leads to biased risk:reward decision-making.   A sustainable society would keep technologies in a sealed beta-test environment for centuries until completely understood.  What is the response from humankind?  If investors see a profitable return, it is funded as a free market venture to form a high-growth opportunity.  We have operated on this level for thousands of years now, and evolved quite efficiently to promote this behavior.   No discussion here nor at large in the bio community will fix this bug in humankind.   It is a bug which is likely genetic, and evolved by nature itself, as we are the current sole winner of all earthly contests between predators.  Even though the bug may become our own undoing, it still drives us across all technological fronts, not only biology.

A recent market analysis chart from a bio investment company has predicted "CRISPR Babies" to number in the thousands by 2029. That's only 10 years away, regardless of the fact that the entire bio community has shunned the idea of genetically engineered humans.  The overzealous technology prediction is simply a reflection of more of the same human behavior, biased risk:reward decision-making.

[Matt Endrizzi]

I think this thread may have run its course. I will continue working on publishing an academic article as well as contacting industry leaders directly. Someone in academia suggested I see how the DIY Bio community would respond to my concerns, so I posted. Thank you all for your thoughtful replies.

In summary, please be careful and yes, my goal is ultimately to curb or end DIY Bio and k-12 bio activities that handle synthetic nucleic acids or utilize processes that would create such material.

[John Griessen]

On 6/11/19 5:59 AM, Matt Endrizzi wrote:
> my goal is ultimately to curb or end DIY Bio

Oh, really?

Thank you for sharing that.

[Andreas "Mega" Stuermer]

You do you. 

It may make sense in your head, but for what it's worth I can assure you that ending DIYbio won't make anything safer. On the contrary, there are DIY bio people working on phage therapy and discovery of new antibiotics. Blocking them, you'd make te world LESS safer, not more. 

If you have ever worked with DNA, you'd know how unstable it is outside a buffer. Just saliva can destroy it. All organisms in nature produce DNAses to protect themselves from invading DNA. The tube is usually autoclaved or bleached and then burnt in the trash burning facility. DNA doesn't survive that. 

Then we've got governements who may have bioweapons programs. The may actually use dangerous sequences from pathogens.

And, sounding like a broken record: 

If you compare the giant amount of mutations, horizontal gene transfer and viruses on this planet... The concern about synthetic DNA is ridiculous, and any independent scientist or institution will tell you so. Even the European EPA says so (although the politicians keep jst ignoring their scientific expertise on this matter)

Btw, his title is the wrong thing. Biosafety means protection against accidents, biosecurity means some malicious intent. What you described is accidents from synthetic DNA which would fall under Biosafety. When you're talking to experts, make sure not to confuse those two or it's embarassing. 

[Jonathan Cline]

On 6/11/19, Matt Endrizzi <matt.e...@gmail.com> wrote:
> I will continue working on
> publishing an academic article as well as contacting industry leaders
> directly.

Make sure to publish in PLoS so the community can read the
non-paywalled paper. Also survey the FBI and DoD for their opinion.

Considering that the entire media premise of DIYbio is false (that
"biotech can be founded and built from a kitchen just like Apple
Computer was founded and built from a garage", when Apple was never
founded nor built in anyone's garage, and no successful biotech
research can occur in either a garage or a kitchen), there can't be
much weight placed on the impact of DIYbio in comparison to
"industry".

[Dakota Hamill]

In summary, please be careful and yes, my goal is ultimately to curb or end DIY Bio and k-12 bio activities that handle synthetic nucleic acids or utilize processes that would create such material.

It's not just DIYBio or K-12 you'd be (I think wrongly) trying to shut down.  We rented lab space from a college that charges $58,000 a year in tuition for a biotech degree, the amount of biological waste and petri dishes I saw going out in the normal waste stream without being autoclaved or treated was astounding.  They went through 4 lab managers in a year.   These are labs being overseen by PhD Professors who didn't notice or didn't care. 

DIYBio isn't the enemy.  Everyone I've ever worked with from this forum has been EXTRA careful to go above and beyond to be safe because  we know we're under more scrutiny  than others.  All it takes is one mishap to give the whole movement a bad name. 

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[Jonathan Cline]

On 6/11/19, Dakota Hamill <dko...@gmail.com> wrote:

> All it takes is one mishap to give the
> whole movement a bad name.

Like the name "Aaron Traywick" ? Technologists won't be stopped or
slowed so this presumed academic paper won't amount to anything other
than to give the author the aura of a pundit. It is simply not in
human nature to explore emerging technologies carefully, regardless of
industry, government, or community affiliation.

[Patrik D'haeseleer]

On Tuesday, June 11, 2019 at 3:59:23 AM UTC-7, Matt Endrizzi wrote:

yes, my goal is ultimately to curb or end DIY Bio and k-12 bio activities that handle synthetic nucleic acids or utilize processes that would create such material.

WOW! That makes me really regret having shown you the courtesy trying to reason with you.

Why the fuck do you even bother coming to the DIYbio mailing list, if you've already made up your mind that your goal is to destroy DIYbio?

I look forward to seeing your academic article, and to refuting it in the very same journal. 

Patrik D'haeseleer

[Maria Chavez]

I am coming in epically late but let me just double down on what Patrik and other's have said.  This is an utterly ridiculous and bad faith discussion.  You obviously have no interest in having an actual factual discourse on safety or science.

I look forward to working with Patrik and the others in this community who uphold a high standard of safety and security.  We have a fundamental right to explore science.  As new tools emerge, I find that transparancy and having community labs makes our communities safer but not driving this work undergound but instead creating a supportive and safety minded community to work in.  Like most of this community, I work exceptionally hard, with zero financial benefit to myself, to promote these ideas and to build our community.  I'll be working to write and publish on this topic both academically and discuss it pubically.  But enough with the trolling.

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[David Murphy]

"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?"

Have you ever heard the term "ISOLATED DEMANDS FOR RIGOR"?

They've had that conversation, they've repeated that conversation countless times. They've had it so many times that they roll their eyes every time someone brings it up because 99.999% of the time it's someone with no special insight bringing up "concerns" that don't even make sense or which aren't grounded in anything other than boundless paranoia. They are sick of the people who keep thinking they have anything of value to add to that conversation. Because those people do not.

There are scary things people could do.

I a few years it's likely small groups with modest funding will have the capacity to re-create smallpox or custom viruses.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188453

The real risks aren't random accidents. The real risks are people intentionally setting out to create weapons.

We already create situations that would never exist in nature through selective pressures that could never exist without human intervention. And nobody bats and eye. But the moment it's "GMO's" suddenly it's all isolated demands for rigor.

It's argumentum ad ignorantiam.

Put another way. Lets imagine a non-GMO plant. (at least as far as regulators are concerned)

The farmer has a plantations of their crop growing... and they notice that the fruit from one of their plants is an unusual color.

When they taste it they notice that it's sweeter than normal.

The farmer does not know anything about genetics. He may not even know that genes are a thing that exist.

He doesn't know if the mutation that unregulated sugar production in the fruit and pigment production in the skin did something else.

For all he know's it could also have unregulated production of some carcinogenic compound in the flesh of the fruit.

Hell there could be some novel virus involved.

He has no idea. All he sees is a sweet fruit with an interesting color.

So he breeds from that plant or takes cuttings and grows more. And a few years later everyone is eating them. With no safety testing.

Thus is the "traditional", "organic" method.

There's something on the order of 40 "natural" pesticides in the flesh of an average carrot. Have they ever been through safety testing with higher concentrations? no.

That flashy new variety of carrot with extra sweet flesh that the local organic farmers are so keen on?

It's never been through safety testing. They don't know if the genetic change that caused the change in sweetness upregulated something else.

This isn't even a hypothetical. it's happened.

https://boingboing.net/2013/03/25/the-case-of-the-poison-potato.html

sometimes those all-natural organic crops, modified only by traditional breeding techniques yield something dangerous.

because on a fundamental level, on a real nuts and bolts level, the people creating those varieties have absolutely no idea why they're getting the results they're seeing. They have no idea what pathways have been modified. They're like cavemen modifying a car engine with a heavy rock.

There's even atomic gardening, take the crop you want to generate new "organic" varieties for, grow it in a field, put a big radiation source in the middle and zap the plants. Some will die and some will survive and some of the survivors will produce seeds with unusual traits.

But the farmer who sees a novel trait has no idea how it's working internally.For all he knows s it could be upregulating something that produces substances that cause brain damage in human children.

Meanwhile, with GMOs, the people making the change have spent years studying the exact genes they're changing, they've spent years studying the exact pathways involved and they're making exactly the precise change they intend to make.

So far "traditional", "organic" breeding techniques have yielded killer bees, grass that produces clouds of toxic cyanide in dry weather and potatos that can slowly kill you among other fuckups.

Meanwhile in 30+ years GMO's have yielded disasters such as.... and... and... hmmm.. nope, nothing.

So I don't buy the bullshit. GMO's are fundamentally safer because of how they're created.

If you find yourself declaring that it should all be moved to the moon: Stop talking because you're making everyone in the room dumber.

On Sat, May 25, 2019 at 1:44 AM Matt Endrizzi <matt.e...@gmail.com> wrote:

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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[Jonathan Cline]

On 6/12/19, David Murphy <murphy...@gmail.com> wrote:

> So [the traditional farmer] breeds from that plant or takes cuttings and grows more. And a few

> years later everyone is eating them. With no safety testing.
>

> *Thus is the "traditional", "organic" method. *


This common analogy to GM food is naive because it ignores time and
scale. Biologists love to re-tell this story as supposed-evidence
that GM foods are no more dangerous than traditional breeding of
mutations, and every time they ignore these two important factors,
time and scale. This traditional farmer breeds his mutated plant in
small scale plots and manual breeding takes multiple plant
generations. Any resultant crop is tested over time in small
rotations because it takes that long to traditionally multiply the
plants, and in practice this historically translated into timescales
of multiple human generations. In contrast, GM foods are developed in
an isolated lab and when put into the market, are employed in large
scale agricultural developments for mass sale after only one plant
generation, to be consumed by humans in a single human generation.
The result is that with less than one human generation with very
limited medical history as a comparison, the risks/results of
consuming GM food is still unknown, and won't be definitive for
another 200 years (well into two human lifespans).

If you want to take a bulletproof position against the original idea
(which itself was presented without any concrete evidence), it is best
not to use this naive "traditional farming" example.


> GMO's are *fundamentally safer* because of how
> they're created.

This is unknown largely because of limited time on the market, plus GM
corporations themselves have actively prevented any dissenting
research. Your sentence is not true. (It is still an opinion which
has not yet been proven)

Monsanto (Bayer) is/was a fundamentally corrupt corporation as shown
in documents released per the numerous Roundup lawsuits. Check the
court exhibits of Monsanto email files written by their own executive
team. Bribery of scientists and lawmakers, abuse of lobbying power to
bias regulations, stamping out opposing scientific research, rewriting
the peer reviewed research to benefit the corporation, even writing
near-lies into research presentations for conferences. And further,
misleading consumers by preventing adequate labeling of GM food so it
is nearly impossible to create a control group which has not eaten GM
foods, thus it is not possible compare long term medical histories.

[David Murphy]

>This traditional farmer breeds his mutated plant in
>small scale plots and manual breeding takes multiple plant

>generations. ... yadda yadda

This is literally nothing but marketing bollox.

organic farming is a 97 billion dollar industry.

It's as industrial and heartless as every other big industry with as big a marketing budget, largely dedicated to stirring up GM FUD.

There are vast facilities to get new varieties spread far and wide on as short a timescale as possible with approximately zero safety testing or understanding of why the varieties show the novel traits they show.

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[Jonathan Cline]

On 6/13/19, David Murphy <murphy...@gmail.com> wrote:
>>This traditional farmer breeds his mutated plant in
>>small scale plots and manual breeding takes multiple plant
>>generations. ... yadda yadda
>

> organic farming is a 97 billion dollar industry.

Again you are ignoring time and scale. That traditional farmer story
you are using is a historic analogy from before rapid deployment
existed. The organic farm industry with much faster time and scale
is also less than 20 years old, also far shorter than the valid time
frame to reflect medical results. According to your own argument,
both should be stopped. Because your argument ignores time and scale,
the analogy gives no support to the idea that the science is safe.

A modern reflection of this at the time and scale is occuring right
now with the new fake meat products, which is chemical engineering of
food to create a meatlike-substance made up of plant protein isolates.
Within just two years (and very little testing in comparison to prior
generations), the products have been introduced into half of the major
fast food franchises on earth, and within 2 more years, fake meat will
be sold in all convenience restaurants and every major grocery chain,
globally. Humans have never eaten highly processed protein isolates
in such large amounts and ratios before. Last week there was a news
report that some people (estimated to be about 3% of the 10% of adults
with food allergies) experienced previously unknown allergic reactions
after eating the products, because of the ratio and makeup of pea
protein in the food. This also indicates lack of testing and
too-rapid deployment in terms of time and scale. Your previous
analogy shows that these products should also be stopped from entering
the marketplace along with GM food and organic food which has not
undergone 2+ human lifespans of medical study.

What is an appropriate time frame for testing before biologically
engineered products are allowed to enter the market in large scales?
It currently takes 50-60 years of medical tracking of a population to
reach medical conclusions regarding safety, and even those research
studies are said to remain inconclusive. Applying a generic standard
of engineering safety might suggest that this should be multiplied by
3. Thus all of these bioengineered products should be tested for
perhaps 180 years before global productization is allowed, according
to your historic analogy. This 100+ years timeframe is still much
faster than a new species of vegetable would have been globally
propagated in traditional agriculture, historically.

This is why that common biologist's analogy of the "traditional
farmer" is a deeply flawed defense.

[David Murphy]

> According to your own argument,
both should be stopped.

No. According to my own argument the sane reaction would be to treat them at least similarly. Not treat the inherently one with the so-far-perfect safety record as if it's the devil while treating the former with a terrible safety record as inherently safe.

I have not ignored " time and scale" but you've made false claims about both.

it may take 50-60 years of tracking of a population to isolate some effect of size X... but currently no such tracking is done for a huge range of novel "organic" products.

There's also a common, bizarre, view that anything that's been around for hundreds of years **must** be safe because traditionalist tend to have the delusion that we spot negative effects on the population scale over the course of hundreds of years. but that's veritably false even for huge effect sizes. Doctors somehow managed to go centuries failing to notice that failing to wash their hands before deliveries was bad for the health of the women giving birth. People went centuries failing to notice that smoking caused lung cancer.

People went thousands of years without noticing that various herbs used in traditional chinese medicine were hellishly carcinogenic.

Even centuries of something being common in society is basically worthless for assessing it's safety.

Even 2 years of real scientific safety trials can be far far more powerful and useful than centuries of just hoping someone will notice something in the general population. It's why traditionalism is utterly broken as a worldview. It fails.

There should absolutely be safety trials but they should be the same standards for novel "organic" varieties, random new mushrooms someone found in a forest somewhere and GM crops.

You seem to want a special standard of 180 years for " bioengineered products" " highly processed " foods but my point is that your entire worldview is bollox. If they need 180 years then that random new version of banana's that some farmer found in his field with some unknown biochemical changes within it should be held to exactly the same standard.

if the standard is insane for the latter then it's insane for the former.

BTW: following your standard yellow bananas would have been released to the general public in 2016.

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[Andreas "Mega" Stuermer]

I agree with what David is saying. You can't demand 180 years of safety testing for a technique (GEOs) that has a very safe track record, and not demand it for another (conventional, organic) that has produced poisonous mutants. It may ake you feel good but it's detrimental to the environment and food security. 

Also, I am doubtful this biosphere will stand another 20 years. If we don't grow our food more sustainably (that is - genetically engineered), I can preety much guarantte you that it will certainly not stand 100 more years, leave alone 180. 

On Friday, June 14, 2019 at 3:56:26 PM UTC+2, David wrote:

> According to your own argument,
both should be stopped.

No. According to my own argument the sane reaction would be to treat them at least similarly. Not treat the inherently one with the so-far-perfect safety record as if it's the devil while treating the former with a terrible safety record as inherently safe.

I have not ignored " time and scale" but you've made false claims about both.

it may take 50-60 years of tracking of a population to isolate some effect of size X... but currently no such tracking is done for a huge range of novel "organic" products.

There's also a common, bizarre, view that anything that's been around for hundreds of years **must** be safe because traditionalist tend to have the delusion that we spot negative effects on the population scale over the course of hundreds of years. but that's veritably false even for huge effect sizes. Doctors somehow managed to go centuries failing to notice that failing to wash their hands before deliveries was bad for the health of the women giving birth. People went centuries failing to notice that smoking caused lung cancer.

People went thousands of years without noticing that various herbs used in traditional chinese medicine were hellishly carcinogenic.

Even centuries of something being common in society is basically worthless for assessing it's safety.

Even 2 years of real scientific safety trials can be far far more powerful and useful than centuries of just hoping someone will notice something in the general population. It's why traditionalism is utterly broken as a worldview. It fails.

There should absolutely be safety trials but they should be the same standards for novel "organic" varieties, random new mushrooms someone found in a forest somewhere and GM crops.

You seem to want a special standard of 180 years for " bioengineered products" " highly processed " foods but my point is that your entire worldview is bollox. If they need 180 years then that random new version of banana's that some farmer found in his field with some unknown biochemical changes within it should be held to exactly the same standard.

if the standard is insane for the latter then it's insane for the former.

BTW: following your standard yellow bananas would have been released to the general public in 2016.

On Thu, Jun 13, 2019 at 4:36 PM Jonathan Cline <jcl...@ieee.org> wrote:

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[Jonathan Cline]

On 6/14/19, David Murphy <murphy...@gmail.com> wrote:

> There should absolutely be safety trials but they should be the same
> standards for novel "organic" varieties, random new mushrooms someone found
> in a forest somewhere and GM crops.
>
> You seem to want a special standard of 180 years for " bioengineered
> products" " highly processed " foods but my point is that your entire
> worldview is bollox. If they need 180 years then that random new version of
> banana's that some farmer found in his field with some unknown biochemical
> changes within it should be held to exactly the same standard.
>
> if the standard is insane for the latter then it's insane for the former.
>

You agree with my point that synthetic products need long term
testing. You have added to this thread that all new products should
be tested regardless of origin and that it is a mistake to
artificially trust new products created from environmental mutation.

I will again add that all products should be labeled for traceability.

Medical studies generally indicate that the raw quantity (sometimes
rate) of cancers etc over the past sixty years have significantly
increased. Whether this is due to improvements in detection,
increases in human longevity, or due to exposure to products of our
own design, is hotly debated. Such curves in the graphs go up steeply
to the right. Your point that "nothing has happened" after the market
begins using new products from environmental mutation is not proven.
New products are pushed into the market and begin consumer use at
faster timescales than at any point in human history. Consumers
accept the products of presumably natural origin without testing, that
is true, and questionable. That acceptance does not imply that lack
of testing is safe on those products, nor does it imply that lack of
testing of synthetic products should be artificially accepted either.
You insist "See, nothing has happened," which is questionable in
relation to the hypothetical rising rates of cancers and other
illnesses.

There are a variety of new activities which are pressed into the k-12
and hobbyist environments by organizations with huge marketing
budgets, none of those tested either. k-12 is now mandated to use
"core" teaching materials, all of which have not been tested or
vetted, and many dissenters claim the material is improper and in some
cases harmful to the psyche of children. More testing is called for
and all such calls are ignored.

The hypothetical academic paper from the original poster won't get
published in any respected science journal without data and he has
presented no data here. Although in science journals there are junk
papers published with questionable data, these papers themselves are
not the concern. The concern is when a miseducated celebrity takes up
the unproven position as a cause, and this cause mirrors deep seated
fears in the uneducated population, such as what happened in the
anti-vax movement. A social movement against DIYbio is unlikely
since rising up against it is not a theme which will stick in the
minds of the general population. Even if that occurs, there won't be
a successful movement against biotech incubators, since financial
forces will continue to steamroll any dissenters.


Since this thread's start, there has been a very strong attempt to
regulate and completely halt a specific type of biotech research,
specifically because that research is perceived to be incredibly
harmful to society, by a particularly vocal segment of the uneducated
U.S. population, related to their uneducated religious beliefs. This
sudden attempt at regulation is a better example of the end result of
the original poster's claim, that he deliberately sets out to "ban
biotech experiments in k-12". I wager that every scientist surveyed
at any biotech conference would be strongly in favor of this type of
research continuing, to improve medical science, and these scientists
would also state that the risks from such research are incredibly low,
especially in comparison to the potential benefits.

Scientific American
https://www.scientificamerican.com/article/faq-how-does-new-trump-fetal-policy-impact-medical-research/
By Michelle Andrews, Kaiser Health News on June 7, 2019

-- QUOTE --

The announcement this week that the federal government is changing its
policy on the use of human fetal tissue in medical research is
designed to please anti-abortion groups that have strongly supported
President Donald Trump.

But it could jeopardize promising medical research and set back
attempts to make inroads in devastating diseases such as HIV,
Parkinson’s and diabetes, U.S. scientists said.
Under the new policy, employees at the National Institutes of Health
(NIH) will no longer conduct research with human fetal tissue obtained
from elective abortions, after using up any material they have on
hand. Officials also immediately stopped funding a multiyear contract
at the University of California-San Francisco using human fetal tissue
in mice to research HIV therapies.

Federally funded projects at other research institutions using fetal
tissue can continue until their grants expire. But renewal for these
projects and future proposals will have to go through a newly
established ethics review process to receive funding. It’s not clear
yet what standards that process will entail or whether such
experiments will be able to proceed under government sponsorship.

The change was enthusiastically welcomed by abortion opponents, who
have long had fetal tissue research in their sights. Many scientists
had a very different view.
Here are a few answers to questions about the issue.

Q: What exactly does fetal tissue research refer to?
Fetal tissue is any tissue or organ obtained from a fetus that was
fertilized at least eight weeks earlier. (Anything younger than that
is called an embryo.)
The statement from the Department of Health and Human Services
referred repeatedly to “human fetal tissue from elective abortions.”
Researchers generally use fetal tissue from elective abortions rather
than miscarriages because miscarriages often result from chromosomal
or other developmental abnormalities that could make the tissue
unsuitable for research.

Q: What is fetal tissue research used for?

These cells are less specialized than adult tissue cells and can be
grown readily, making them valuable in research. Fetal tissue has been
used in many types of medical research, including the development of
vaccines for polio, measles and other diseases, and therapies to treat
Parkinson’s, diabetes, rheumatoid arthritis and to prevent the
transmission of HIV.
Some researchers graft fetal tissue onto mice, creating “humanized
mice” with human blood-forming and immune systems.
Fetal tissue helps researchers learn about birth defects and human
tissue development. In recent years, it has been instrumental in
understanding how the Zika virus crosses the placenta and affects the
development of the human brain, according to a letter to HHS Secretary
Alex Azar signed by 70 organizations in December in support of
continued fetal tissue research.

Q: Are there rules about using fetal tissue?
Strict federal rules govern the collection and use of human fetal
tissue. It’s against the law for anyone to accept payment for human
fetal tissue, except for reasonable amounts associated with
acquisition, storage or other costs. There are also provisions that
require women who are donating fetal tissue for research to provide
informed consent and prohibit physicians from altering the timing or
method of an abortion in order to obtain fetal tissue.

Q: Has it always been as controversial as it is today?
Not really. The level of controversy around fetal tissue research
waxes and wanes. Human fetal tissue research has been done in the
United States since the 1930s, and NIH has been funding this type of
research since the 1950s. There was a ban on such funding, however,
during part of the terms of Presidents Ronald Reagan and George H.W.
Bush. Federal money was restored with bipartisan support in a 1993
bill for the NIH. Among the backers of that effort were some strong
abortion opponents, such as Sen. Strom Thurmond (R-S.C.), who argued
that the research could help people—like his daughter—with diabetes.
NIH spent $115 million on human fetal tissue research in 2018, a tiny
fraction of the nearly $14 billion it spent on clinical research
overall. NIH currently funds roughly 200 projects that use fetal
tissue, according to HHS.
Fetal tissue once again became a hot-button issue in 2015 with the
release of doctored videos, later discredited, purporting to show
Planned Parenthood officials discussing tissue donation policies and
reimbursement. Last fall, the Trump administration announced it was
conducting a review of all research involving fetal tissue to ensure
it was consistent with statutes and regulations governing it.

Q: Aren’t there effective alternatives?
It depends on whom you ask. Opponents of fetal tissue research point
to a number of other possible options, including monkey or hamster
cells for vaccines as well as blood collected after birth from
umbilical cords that are rich in blood-forming stem cells. They also
suggest the use of adult stem cells and “organoids”—artificially grown
cells that somewhat mimic organs.
“Why do we keep focusing on these archaic models when newer, better
alternatives are out there?” asked Tara Sander Lee, a senior fellow
and director of life sciences at the Charlotte Lozier Institute, which
opposes research using fetal tissue from elective abortion.
She suggested that using tissue from a miscarriage could be an
acceptable alternative to using tissue from an aborted fetus because
it’s from “a natural death, not an intentional killing of the child.”
The letter from researchers to Azar in December called the idea that
other cells could replace fetal tissue “patently incorrect.”
“The study of human fetal tissue provides researchers with
incomparable insights into how birth defects arise and how they can be
prevented as well as an unparalleled window into the complexity of
human tissue development,” the letter said.
Sally Temple, scientific director of the Neural Stem Cell Institute
who is a past president of the International Society for Stem Cell
Research, said that while these other types of cells hold promise,
they aren’t ready for prime time.
“There’s a lot of excitement about using stem cells and talk about how
we can use three-dimensional organoids,” said Temple. But organoids
don’t have the same cellular arrangement or blood vessel network.
“Organoids can’t mimic real tissue,” she said.
“If we’re going to understand how tissues are made in humans, you
really have to have access to human tissue,” she added. “It makes you
so nervous that scientists aren’t being heard.”
This story was originally published by Kaiser Health News on June 7, 2019.


-- END QUOTE --

[Jonathan Cline]

On 6/14/19, Andreas "Mega" Stuermer <andreas.t...@gmail.com> wrote:

>
> Also, I am doubtful this biosphere will stand another 20 years. If we don't
> grow our food more sustainably (that is - genetically engineered), I can
> preety much guarantte you that it will certainly not stand 100 more years

Switching to a plant-based menu of existing species grown in higher
density 3D arrangements (i.e. hydroponics, etc) would sustain the
future global population and ecology just fine, more easily in terms
of financial investment, and with less impact regardless of genetic
engineering. Your comment is simply using fear as rationalization
for use of untested technology. The sole reason that this legitimate
avenue is not employed in large scale is that the new technology can
be patented and thus investment returns are far higher, in contrast to
raising existing species which provide little to no ability for
patents. The creation of a wide economic moat by applying new
technology regardless of test history is what is rewarded. Safety and
in-depth study prior to deployment are not rewarded.

[Andreas "Mega" Stuermer]

You can't really say that GMOs are not tested enough. How long did the FDA take to analyze and approve the GE salmon? 10 years? 15 years? Same for GE plants.

Also, you assumed that I was saying "we should do it without regulation". We shouldn't. It just has to be proportional to the risks and benefits. And also understand that my view comes out of Europe, where any GMO is strictly banded practically. Hence, yes we need less regulation in Europe. We can talk about the US, but this is an international group so it's difficult that one person doesn't talk about apples and another one about oranges

[David Murphy]

>species grown in higher  density 3D arrangements (i.e. hydroponics, etc)

I see you immediately revert to suggesting using random options with little or no safety testing... as long as they're not GM.

How many decades of actual safety testing have been done of the health effects of plants grown in unnatural warehouses, grown in a [patentable] ]nutrient broth running through [patentable] hydroponics systems, under banks of [patentable] LED's and all the random biochemical changes that leads to... compared to the safety tests applied to most GM crops? 

I'm just gonna start replying to every one of your posts with the words "ISOLATED DEMANDS FOR RIGOR"

Because it describes them perfectly.

>" in contrast to raising existing species which provide little to no ability for patents "

but which do include plant breeders rights, which are functionally equivilent except for having a longer term than patents.

It's like you spend half your post railing against patents and lack of safety testing... and your alternative is a system suffused with vastly more patents and other IP rights with basically zero safety testing.

Seems like a poorly though out and basically undefendable position.

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[Jonathan Cline]

On 6/14/19, David Murphy <murphy...@gmail.com> wrote:

>>species grown in higher density 3D arrangements (i.e. hydroponics, etc)
>

> using random options with little
> or no safety testing... as long as they're not GM.

I stated that there is no need for genetic engineering to support
global needs, independent of any other consideration. The assumption
that genetic engineering is a requirement for humanity to survive is
false.

[Andreas "Mega" Stuermer]

"I stated that there is no need for genetic engineering to support 
global needs, independent of any other consideration.   The assumption 
that genetic engineering is a requirement for humanity to survive is 
false. "

Citation needed. We got a growing population and we are using up all ressources. Soil degradation, greenhouse gas emissions, we are living on the expense of the next generation (or even of our future selves)

 

On Saturday, June 15, 2019 at 1:11:00 AM UTC+2, Jonathan Cline wrote:

[Cathal Garvey]

It's a widely believed falsehood that GE traits are more patentable, or that GE is a backdoor to patents.

You can patent any plant novelty, in places where patenting living things is permitted.

I recall seeing a patent for the trait that makes cauliflower heads rise up from the plant on a stalk. Not a GE trait.

And yes, you can get plant breeder's rights _and_ a patent for the same thing. But if you think about it: PBRs are less applicable to GE. GE may let you avoid PBRs, helping create new "open source" variety, whereas patents forbid traits being conferred by any means, conventional or no.

Oh and BTW, don't feed the trolls

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

[Jonathan Cline]

UN REPORT
Frontiers 2018/19: Emerging Issues of Environmental Concern
04 March 2019
Authors: UN Environment
""From the innovations and ethical dilemmas of synthetic biology to
the options for appropriate international adaptation to climate
change: Frontiers 2018/19 explores the emerging environmental issues
facing the planet
...

The ability to successfully alter organisms at the genetic level has
excited scientists and the general public alike. Gene-editing
techniques are advancing rapidly, bringing the promise of many
biological and ecological benefits, from eradicating human diseases to
preventing species extinction. CRISPR-Cas9 is the latest, quickest
tool in the genetic editing tool box, allowing extraordinary precision
in the manipulation of genomes.

However, this ability to create synthetic life and alter existing DNA
carries with it the risk of cross contamination and unintended
consequences. Hacking the code of life has such major implications
that there is an urgent need for governing bodies to collaborate and
cooperate in ensuring safe research and development in this field. The
rise of the DIY biohacker and the risk of the accidental release of
genetically modified organisms into the environment is a cause for
regulatory concern.


The Convention on Biological Diversity considers that the following
operational definition is useful as a starting point for the
purpose of facilitating scientific and technical deliberations under
the Convention and its Protocols:
“Synthetic biology is a further development and new dimension of
modern biotechnology that combines science, technology and engineering
to facilitate
and accelerate the understanding, design, redesign, manufacture and/or
modification of genetic materials, living organisms and biological
systems.”20


** The intentional or accidental release of genetically engineered
organisms into the environment could have significant negative impacts
on both human and environmental health. Misuse of these technologies
and a failure to account
for unintended consequences could cause irreversible environmental
damage and pose significant geopolitical threats.17 The potential
far-reaching impacts of synthetic biology demand governance methods
and research guidelines that promote its ethical and responsible
use.18,19


CRISPR-Cas9 genome editing technique
The discovery of CRISPR-Cas9 has changed the entire outlook of
synthetic biology research.
It enables scientists to cut out a particular DNA segment of a desired
sequence or replace it with a new
DNA strand. Many fields of medical research require such editing
precision to revolutionize treatments.
However, the technique is also subject to scrutiny for its safety as
it involves a potential off-target effect, whereby it inadvertently
cuts out DNA that has a similar sequence to the targeted strand,
potentially triggering cancer in edited cells.


Do-It-Yourself Biology or DIY Bio
The movement of so-called ‘citizen scientists’ interested in
performing synthetic biology experiments has gained significant
traction globally. Biology enthusiasts – many without scientific
background – meet in garage labs to conduct experiments using
specialised DIY kits and simple protocols available online.
Some of the group have specialised equipment and hire professional
staff to help citizen scientists, biohackers and biology enthusiasts
in developing their projects.

Risks and policy considerations
There are concerns that synthetic biology could be used to re-engineer
existing pathogenic viruses, making them more dangerous or produce
biochemicals with only modest resources and organizational footprint.
Synthetic biology presents new challenges that need to be addressed
through the consolidated action of governmental and international
bodies. Development of effective methods to better manage emerging
risks is essential in ensuring technological safety.

Innovating with wisdom
The release of genetically engineered organisms accidentally or
intentionally into the environment has raised valid concerns about
biosafety and unpredictable consequences. For organisms engineered in
closed research or industrial facilities, containment procedures and
enforced regulations on waste disposal help to avoid an escape,
although this is never fail-proof.63 In the case of intentional
release, concerns over potential genetic cross-contamination between
species, ecological interactions and impacts on ecosystems and their
services remain largely unresolved.64 Altering a disease carrier
genetically could potentially cause a pathogen to evolve and become
more virulent, or to be carried by a new vector.65
To date, CRISPR-based gene drives have been tested only
on small populations in controlled settings, with one recent
experiment successfully collapsing the entire malaria- carrying
mosquito population in the laboratory.66 As a first step towards wider
trials, Target Malaria has recently gained permission to release
10,000 modified mosquitoes in Burkina Faso. These specimens will be
genetically engineered to be sterile, but with no gene drives, to test
how well they compete with wild males.67 However, such field trials to
evaluate the efficacy of the gene-drive system could pose inherent
risks.68,69

Under the precautionary principle, stringent risk assessment and the
inclusion of diverse stakeholder perspectives should be applied in the
development and handling of innovative synthetic biology applications
and products.19,70,71 The precautionary principle states that when
human activities may lead to unacceptable harm that is scientifically
plausible but uncertain, action should be taken to avoid or diminish
that harm.72 A concept of substantial equivalence – that a genetically
modified organism is as safe as its traditional counterpart – is often
mentioned in conjunction with the precautionary principle.73 Some
countries have extensive policy and regulations in place concerning
genetic engineering and research, while for others, non-functional
regulatory systems, policy gaps and risk-assessment capacity are major
challenges.74-77
Attempts have been made to identify, evaluate and address the ethical
and biosafety concerns of synthetic biology.
The U.S. National Academies of Science, Engineering,
and Medicine published a report on gene drives in 2016 highlighting
the need for stringent environmental risk assessments and deliberation
that charters human values and necessitates rigorous public
engagement.19
In December 2017, the ad-hoc technical expert group on synthetic
biology, established by the Parties to the Convention on Biological
Diversity, concluded that organisms – developed or being developed
through current methods of synthetic biology, including those
containing gene drives – fall under the description of living modified
organisms (LMOs), which are regulated under the legally-binding
Cartagena Protocol.78 With 171 Party nations, the Protocol applies the
precautionary approach and requires that each Party take all necessary
measures to ensure the safe handling, transport and use of the
resulting LMOs.79
SYNBIOSAFE, an EU-funded research project, was established to identify
key issues in safety, security, risk management ethics and,
importantly, the science–society interface, which emphasizes public
education and dialogue among scientists, businesses, government, and
ethicists.80,81 Some gene-drive developers have also proposed ethical
research guidelines that emphasize the need for meaningful public
engagement.82
Nevertheless, the intentional release of modified organisms and their
potential to permanently transform wild species and cross
international borders will likely test the limits of current policy,
leading some environmental groups to call for a moratorium on all
gene-drive research.83 Other regulatory concerns focus on the
potential use of synthetic biology for military offensive
purposes.84,85



** Citizen scientists, biohackers and garage labs
Synthetic biology and genome editing have attracted interest not only
from companies, but also regular citizens. Do-It-Yourself Biology,
also known as “DIY Bio”, the movement of “citizen scientists”
interested in synthetic biology experiments has become an
international phenomenon over the last decade. Often with little prior
knowledge of the field, enthusiasts meet in makeshift
labs to take crash courses in biotechnology and conduct hands-on
experiments.90,91 Simple protocols found online and specialized kits
costing US$150–1,600 have driven the movement’s rapid expansion.
DIY Bio labs can be found in most major cities and by 2017 there were
about 168 groups worldwide.92,93 Regulating
the use of easily accessible and low-cost technologies
like CRISPR and gene editing kits will likely be a challenge for
authorities. There is also growing concern that the technology could
be misused by terrorists to destroy agricultural crops or turn
harmless microbes into biological weapons.94


Synthetic Biology: Re-engineering the environment
Lead Authors
Bartlomiej Kolodziejczyk, H2SG Energy Pte. Ltd., Singapore Natalie
Kofler, Yale Institute for Biospheric Studies, Yale University,
Connecticut, United States
Contributors and Reviewers
Marianela Araya, Convention on Biological Diversity, Montreal, Canada
James Bull, College of Natural Sciences, University of Texas at
Austin, Texas, United States
Jackson Champer, Department of Biological Statistics and Computational
Biology, Cornell University, New York, United States
Chen Liu, Department of Biological Statistics and Computational
Biology, Cornell University, New York, United States
Yongyuth Yuthavong, National Science and Technology Development Agency
of Thailand, Pathumthani, Thailand

[AdrianMolecule]

Despite all the buzz and the coolness and hoopla and everything else, a simple glance will tell you that DIY bio is a buzz with little so show for at present. 

Check the DIYBio web sites and you'll see most of them have no GMOs or maybe a GFP transformation using stock plasmids or CRISPR educational kits.

Compared to industry and natural processes the ration is probably towards one in a billion.

So, the "Emperor has no clothes or barking up the wrong tree is the conclusion.

State sponsored, religious or deep pocket agents with an agenda could be a different but you'll not be able to research that as an academic :) . Also it did not happened either, and that's not by accident.

Remember rDNA is created every microsecond in organisms as part of countless natural mechanisms and it happens in me and you as we are speaking.

The risk of new viruses is higher possible with incremental mutations that normally happens when viruses jump species. That happens when uneducated people handle animals. DIY Bio contributes to education and therefore reduces the risk.

Unnecessary regulation deny people cures and ultimately are responsible for millions of deaths. Most of the fundamental medical discoveries we benefit from today (like vaccination for example) would not have been possible under today's rules.

Just follow bio-safety rules set and perform the research. Common sense.

Cheers,

Adrian

On Wednesday, May 22, 2019 at 4:36:57 PM UTC-4, Matt Endrizzi 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?