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Stopping the DIY bio-terrorists, US military embraces AI and Ginkgo Bioworks


As the cost of powerful DIY gene editing kits continue to fall bioterrorism is going to be on the rise, so we need a way to defend against it.


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Recently I gave a talk on the “Future of Cybersecurity” in the Critical National Infrastructure (CNI) sector which people at the event described as “talking about the dark arts of the dark arts.” As we continue to witness the continued democratisation of increasingly powerful emerging technologies the fact of the matter is that they can do great good, but also great harm, and while the assembled audience at the event felt such things couldn’t be talked about in public the fact of the matter is that most criminals are already talking about how they leverage these new technologies for nefarious purposes. In my opinion this imbalance, which was highlighted nicely recently by a group of silicon valley elites and billionaire polymaths, who recently held a Doomsday conference, where they managed to figure out what the future threats would look like but had almost no solution to them, is putting us all at risk, because without discussion noone is proposing any innovations, regulations, or solutions to counter the threat… Bio-terrorism is a case in point, and an ugly word, a very ugly word and it should scare the bejesus out of people, but it’s also a word you’re likely to be hearing more in in the next decade, for a number of reasons. Sorry about that. That said though try as a criminal might, today it’s near impossible for them to order the genetic ingredients for making deadly viruses such as Smallpox from scratch, at least not from any reputable company.


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Although with the emergence of $100 DIY home gene editing kits and the rise of bio-hacker crowdsourcing communities that will increasingly help people put together all sorts of new genetic concoctions, including some funky glowing plants, as well as, potentially, Gene Drives, something the UN recently called the world’s “worst bioweapon,” in the privacy of their own garage I doubt it will be too long until we see something nasty emerge from a sub-urban garage somewhere. And I’m not talking about someone’s dad wandering around in his pants… Urgh.

One of the reasons why it’s so hard to order nasty strands of DNA from the world’s leading gene-synthesis firms is because they all routinely screen customer requests against DNA sequences from hazardous viruses, bacteria, toxins and other “select agents.” So, as soon as any would be bioterrorist tried to purchase fragments of the pathogen’s genome, alarm bells would go off. But this “Biosecurity protocol” is only as good as its database of potentially dangerous gene sequences and here’s a case in point. Earlier this year, researchers from the University of Alberta demonstrated a potential vulnerability in the system when they reported the successful construction of horsepox virus, an extinct relative of smallpox, from DNA pieces ordered in the mail.

Uh oh… did someone say deadly virus?


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Horsepox is not on the list of banned viruses, and the research itself, which was actually part of an effort to develop a new kind of vaccine, was in full compliance with government and university regulations. Still, the study sparked an uproar, and many in the biosecurity and biodefense communities are now openly questioning whether today’s screening tools are good enough to stop the threats posed by tomorrow’s synthetic bioweapons.

To help curtail those threats, the intelligence apparatus of the US government is now looking to the world’s largest consumer of synthetic DNA for help.

Last week, Boston based Ginkgo Bioworks, who I’ve talked about before, if only for their delicious genetically engineered beerannounced it had secured contracts worth up to $64 million to develop a range of biosecurity products for the nascent synthetic biology industry – chief among them, improved Artificial Intelligence (AI) algorithms for screening orders made to gene-synthesis companies, and new deep learning models for detecting whether a DNA sample has been engineered in any way.


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Todd Kuiken, a public policy researcher who studies synthetic biology at North Carolina State University, thinks Ginkgo is the right company for the job.

“You need the experts developing the software,” he says, “and they are the best suited to figure this out.”

According to Patrick Boyle, head of design at Ginkgo, the company plans to take the algorithms it has developed over the past decade for identifying beneficial DNA sequences, and adapt the models for predicting whether bits of code could be potentially harmful.

Those algorithms have already led to the creation of new kinds of fragrance and fertilizer producing microbes. Now, with backing from the Intelligence Advanced Research Projects Agency (IARPA), the company hopes to apply the tools to flag worrisome DNA sequence orders before they’re shipped and to discern whether an emerging pathogen circulating in nature evolved naturally or was engineered by humans.

These algorithmic and machine learning approaches are what’s needed for biosecurity tools in the industry to move beyond simply matching sequences against known problematic strings of genetic code, says Laura Adam. Adam is cofounder of Ebiosec, a data management platform for synthetic biology, and the developer of GenoTHREAT, an open source screening tool.


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“The field is advancing, but no one is predicting things that are more novel,” she says. “A company like Ginkgo has real-life data that they can put into practice for detecting novel sequences.”

Boyle notes that Ginkgo already has the world’s largest database of engineered DNA sequences.

“We’re now taking that database and training deep learning models on that data to try to identify signatures of engineering that we may have unconsciously included in those designs.”

Ginkgo also has funding from the US Department of Defense to develop enzymes that can sense and destroy chemical or biological threats. And the company is on retainer to further advance and commercialize these products and software tools if the initial research projects pan out.

Biosecurity tools may seem like a far cry from pharmaceuticals, fragrances and fertilizers. But, says Boyle, “We’re a platform company, so we’re really agnostic to our customer’s needs, whether that customer is a crop company like Bayer, a drugmaker like Synlogic, or a branch of the US military.”


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Plus, he adds, it’s imperative for Ginkgo to be a steward for responsible science if the billion dollar biotech firm wants to realize the full potential for good within synthetic biology.

“We just think it’s the right thing to do.”

All that said though all these biosecurity measures are only going to work if they’re kept up to date with the latest information, DIY gene editing kits become regulated, and if the labs themselves aren’t hacked – as recently happened when a new first of a kind DNA malware was created that used specially coded DNA to attack a labs network when it was decoded by their gene sequencing machine. The world is about to get weird, and scary… weird scary.

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