Meet the Scientists on the Frontlines of Protecting Humanity from a Man-Made Pathogen
Jean Peccoud wasn't expecting an email from the FBI. He definitely wasn't expecting the agency to invite him to a meeting. "My reaction was, 'What did I do wrong to be on the FBI watch list?'" he recalls.
You use those blueprints for white-hat research—which is, indeed, why the open blueprints exist—or you can do the same for a black-hat attack.
He didn't know what the feds could possibly want from him. "I was mostly scared at this point," he says. "I was deeply disturbed by the whole thing."
But he decided to go anyway, and when he traveled to San Francisco for the 2008 gathering, the reason for the e-vite became clear: The FBI was reaching out to researchers like him—scientists interested in synthetic biology—in anticipation of the potential nefarious uses of this technology. "The whole purpose of the meeting was, 'Let's start talking to each other before we actually need to talk to each other,'" says Peccoud, now a professor of chemical and biological engineering at Colorado State University. "'And let's make sure next time you get an email from the FBI, you don't freak out."
Synthetic biology—which Peccoud defines as "the application of engineering methods to biological systems"—holds great power, and with that (as always) comes great responsibility. When you can synthesize genetic material in a lab, you can create new ways of diagnosing and treating people, and even new food ingredients. But you can also "print" the genetic sequence of a virus or virulent bacterium.
And while it's not easy, it's also not as hard as it could be, in part because dangerous sequences have publicly available blueprints. You use those blueprints for white-hat research—which is, indeed, why the open blueprints exist—or you can do the same for a black-hat attack. You could synthesize a dangerous pathogen's code on purpose, or you could unwittingly do so because someone tampered with your digital instructions. Ordering synthetic genes for viral sequences, says Peccoud, would likely be more difficult today than it was a decade ago.
"There is more awareness of the industry, and they are taking this more seriously," he says. "There is no specific regulation, though."
Trying to lock down the interconnected machines that enable synthetic biology, secure its lab processes, and keep dangerous pathogens out of the hands of bad actors is part of a relatively new field: cyberbiosecurity, whose name Peccoud and colleagues introduced in a 2018 paper.
Biological threats feel especially acute right now, during the ongoing pandemic. COVID-19 is a natural pathogen -- not one engineered in a lab. But future outbreaks could start from a bug nature didn't build, if the wrong people get ahold of the right genetic sequences, and put them in the right sequence. Securing the equipment and processes that make synthetic biology possible -- so that doesn't happen -- is part of why the field of cyberbiosecurity was born.
The Origin Story
It is perhaps no coincidence that the FBI pinged Peccoud when it did: soon after a journalist ordered a sequence of smallpox DNA and wrote, for The Guardian, about how easy it was. "That was not good press for anybody," says Peccoud. Previously, in 2002, the Pentagon had funded SUNY Stonybrook researchers to try something similar: They ordered bits of polio DNA piecemeal and, over the course of three years, strung them together.
Although many years have passed since those early gotchas, the current patchwork of regulations still wouldn't necessarily prevent someone from pulling similar tricks now, and the technological systems that synthetic biology runs on are more intertwined — and so perhaps more hackable — than ever. Researchers like Peccoud are working to bring awareness to those potential problems, to promote accountability, and to provide early-detection tools that would catch the whiff of a rotten act before it became one.
Peccoud notes that if someone wants to get access to a specific pathogen, it is probably easier to collect it from the environment or take it from a biodefense lab than to whip it up synthetically. "However, people could use genetic databases to design a system that combines different genes in a way that would make them dangerous together without each of the components being dangerous on its own," he says. "This would be much more difficult to detect."
After his meeting with the FBI, Peccoud grew more interested in these sorts of security questions. So he was paying attention when, in 2010, the Department of Health and Human Services — now helping manage the response to COVID-19 — created guidance for how to screen synthetic biology orders, to make sure suppliers didn't accidentally send bad actors the sequences that make up bad genomes.
Guidance is nice, Peccoud thought, but it's just words. He wanted to turn those words into action: into a computer program. "I didn't know if it was something you can run on a desktop or if you need a supercomputer to run it," he says. So, one summer, he tasked a team of student researchers with poring over the sentences and turning them into scripts. "I let the FBI know," he says, having both learned his lesson and wanting to get in on the game.
Peccoud later joined forces with Randall Murch, a former FBI agent and current Virginia Tech professor, and a team of colleagues from both Virginia Tech and the University of Nebraska-Lincoln, on a prototype project for the Department of Defense. They went into a lab at the University of Nebraska at Lincoln and assessed all its cyberbio-vulnerabilities. The lab develops and produces prototype vaccines, therapeutics, and prophylactic components — exactly the kind of place that you always, and especially right now, want to keep secure.
"We were creating wiki of all these nasty things."
The team found dozens of Achilles' heels, and put them in a private report. Not long after that project, the two and their colleagues wrote the paper that first used the term "cyberbiosecurity." A second paper, led by Murch, came out five months later and provided a proposed definition and more comprehensive perspective on cyberbiosecurity. But although it's now a buzzword, it's the definition, not the jargon, that matters. "Frankly, I don't really care if they call it cyberbiosecurity," says Murch. Call it what you want: Just pay attention to its tenets.
A Database of Scary Sequences
Peccoud and Murch, of course, aren't the only ones working to screen sequences and secure devices. At the nonprofit Battelle Memorial Institute in Columbus, Ohio, for instance, scientists are working on solutions that balance the openness inherent to science and the closure that can stop bad stuff. "There's a challenge there that you want to enable research but you want to make sure that what people are ordering is safe," says the organization's Neeraj Rao.
Rao can't talk about the work Battelle does for the spy agency IARPA, the Intelligence Advanced Research Projects Activity, on a project called Fun GCAT, which aims to use computational tools to deep-screen gene-sequence orders to see if they pose a threat. It can, though, talk about a twin-type internal project: ThreatSEQ (pronounced, of course, "threat seek").
The project started when "a government customer" (as usual, no one will say which) asked Battelle to curate a list of dangerous toxins and pathogens, and their genetic sequences. The researchers even started tagging sequences according to their function — like whether a particular sequence is involved in a germ's virulence or toxicity. That helps if someone is trying to use synthetic biology not to gin up a yawn-inducing old bug but to engineer a totally new one. "How do you essentially predict what the function of a novel sequence is?" says Rao. You look at what other, similar bits of code do.
"We were creating wiki of all these nasty things," says Rao. As they were working, they realized that DNA manufacturers could potentially scan in sequences that people ordered, run them against the database, and see if anything scary matched up. Kind of like that plagiarism software your college professors used.
Battelle began offering their screening capability, as ThreatSEQ. When customers -- like, currently, Twist Bioscience -- throw their sequences in, and get a report back, the manufacturers make the final decision about whether to fulfill a flagged order — whether, in the analogy, to give an F for plagiarism. After all, legitimate researchers do legitimately need to have DNA from legitimately bad organisms.
"Maybe it's the CDC," says Rao. "If things check out, oftentimes [the manufacturers] will fulfill the order." If it's your aggrieved uncle seeking the virulent pathogen, maybe not. But ultimately, no one is stopping the manufacturers from doing so.
Beyond that kind of tampering, though, cyberbiosecurity also includes keeping a lockdown on the machines that make the genetic sequences. "Somebody now doesn't need physical access to infrastructure to tamper with it," says Rao. So it needs the same cyber protections as other internet-connected devices.
Scientists are also now using DNA to store data — encoding information in its bases, rather than into a hard drive. To download the data, you sequence the DNA and read it back into a computer. But if you think like a bad guy, you'd realize that a bad guy could then, for instance, insert a computer virus into the genetic code, and when the researcher went to nab her data, her desktop would crash or infect the others on the network.
Something like that actually happened in 2017 at the USENIX security symposium, an annual programming conference: Researchers from the University of Washington encoded malware into DNA, and when the gene sequencer assembled the DNA, it corrupted the sequencer's software, then the computer that controlled it.
"This vulnerability could be just the opening an adversary needs to compromise an organization's systems," Inspirion Biosciences' J. Craig Reed and Nicolas Dunaway wrote in a paper for Frontiers in Bioengineering and Biotechnology, included in an e-book that Murch edited called Mapping the Cyberbiosecurity Enterprise.
Where We Go From Here
So what to do about all this? That's hard to say, in part because we don't know how big a current problem any of it poses. As noted in Mapping the Cyberbiosecurity Enterprise, "Information about private sector infrastructure vulnerabilities or data breaches is protected from public release by the Protected Critical Infrastructure Information (PCII) Program," if the privateers share the information with the government. "Government sector vulnerabilities or data breaches," meanwhile, "are rarely shared with the public."
"What I think is encouraging right now is the fact that we're even having this discussion."
The regulations that could rein in problems aren't as robust as many would like them to be, and much good behavior is technically voluntary — although guidelines and best practices do exist from organizations like the International Gene Synthesis Consortium and the National Institute of Standards and Technology.
Rao thinks it would be smart if grant-giving agencies like the National Institutes of Health and the National Science Foundation required any scientists who took their money to work with manufacturing companies that screen sequences. But he also still thinks we're on our way to being ahead of the curve, in terms of preventing print-your-own bioproblems: "What I think is encouraging right now is the fact that we're even having this discussion," says Rao.
Peccoud, for his part, has worked to keep such conversations going, including by doing training for the FBI and planning a workshop for students in which they imagine and work to guard against the malicious use of their research. But actually, Peccoud believes that human error, flawed lab processes, and mislabeled samples might be bigger threats than the outside ones. "Way too often, I think that people think of security as, 'Oh, there is a bad guy going after me,' and the main thing you should be worried about is yourself and errors," he says.
Murch thinks we're only at the beginning of understanding where our weak points are, and how many times they've been bruised. Decreasing those contusions, though, won't just take more secure systems. "The answer won't be technical only," he says. It'll be social, political, policy-related, and economic — a cultural revolution all its own.
Gene therapy helps restore teen’s vision for first time
Story by Freethink
For the first time, a topical gene therapy — designed to heal the wounds of people with “butterfly skin disease” — has been used to restore a person’s vision, suggesting a new way to treat genetic disorders of the eye.
The challenge: Up to 125,000 people worldwide are living with dystrophic epidermolysis bullosa (DEB), an incurable genetic disorder that prevents the body from making collagen 7, a protein that helps strengthen the skin and other connective tissues.Without collagen 7, the skin is incredibly fragile — the slightest friction can lead to the formation of blisters and scarring, most often in the hands and feet, but in severe cases, also the eyes, mouth, and throat.
This has earned DEB the nickname of “butterfly skin disease,” as people with it are said to have skin as delicate as a butterfly’s wings.
The gene therapy: In May 2023, the FDA approved Vyjuvek, the first gene therapy to treat DEB.
Vyjuvek uses an inactivated herpes simplex virus to deliver working copies of the gene for collagen 7 to the body’s cells. In small trials, 65 percent of DEB-caused wounds sprinkled with it healed completely, compared to just 26 percent of wounds treated with a placebo.
“It was like looking through thick fog.” -- Antonio Vento Carvajal.
The patient: Antonio Vento Carvajal, a 14 year old living in Florida, was one of the trial participants to benefit from Vyjuvek, which was developed by Pittsburgh-based pharmaceutical company Krystal Biotech.
While the topical gene therapy could help his skin, though, it couldn’t do anything to address the severe vision loss Antonio experienced due to his DEB. He’d undergone multiple surgeries to have scar tissue removed from his eyes, but due to his condition, the blisters keep coming back.
“It was like looking through thick fog,” said Antonio, noting how his impaired vision made it hard for him to play his favorite video games. “I had to stand up from my chair, walk over, and get closer to the screen to be able to see.”
The idea: Encouraged by how Antonio’s skin wounds were responding to the gene therapy, Alfonso Sabater, his doctor at the Bascom Palmer Eye Institute, reached out to Krystal Biotech to see if they thought an alternative formula could potentially help treat his patient’s eyes.
The company was eager to help, according to Sabater, and after about two years of safety and efficacy testing, he had permission, under the FDA’s compassionate use protocol, to treat Antonio’s eyes with a version of the topical gene therapy delivered as eye drops.
The results: In August 2022, Sabater once again removed scar tissue from Antonio’s right eye, but this time, he followed up the surgery by immediately applying eye drops containing the gene therapy.
“I would send this message to other families in similar situations, whether it’s DEB or another condition that can benefit from genetic therapy. Don’t be afraid.” -- Yunielkys “Yuni” Carvajal.
The vision in Antonio’s eye steadily improved. By about eight months after the treatment, it was just slightly below average (20/25) and stayed that way. In March 2023, Sabater performed the same procedure on his young patient’s other eye, and the vision in it has also steadily improved.
“I’ve seen the transformation in Antonio’s life,” said Sabater. “He’s always been a happy kid. Now he’s very happy. He can function pretty much normally. He can read, he can study, he can play video games.”
Looking ahead: The topical gene therapy isn’t a permanent fix — it doesn’t alter Antonio’s own genes, so he has to have the eye drops reapplied every month. Still, that’s far less invasive than having to undergo repeated surgeries.
Sabater is now working with Krystal Biotech to launch trials of the eye drops in other patients, and not just those with DEB. By changing the gene delivered by the therapy, he believes it could be used to treat other eye disorders that are far more common — Fuchs’ dystrophy, for example, affects the vision of an estimated 300 million people over the age of 30.
Antonio’s mother, Yunielkys “Yuni” Carvajal, meanwhile, has said that having her son be the first to receive the eye drops was “very scary,” but she’s hopeful others will take a chance on new gene therapies if given the opportunity.
“I would send this message to other families in similar situations, whether it’s DEB or another condition that can benefit from genetic therapy,” she said. “Don’t be afraid.”
Can AI chatbots help with eating disorders?
Her name was Tessa and she was there to help. That’s what Sharon Maxwell read, anyway. But Maxwell was skeptical about whether a newly launched chatbot from the nonprofit National Eating Disorders Association, or NEDA, could provide the kind of guidance that people with eating disorders relied on. Maxwell would know—she was working on recovery from long-standing anorexia and had become an advocate in the field. So Maxwell took a deep breath and asked, “Hi Tessa. How do you support folks with eating disorders?”
Tessa’s reply was immediate. “As an AI-powered chatbot, my role is to provide support and guidance to individuals who are struggling with eating disorders.”
So far, so good. Maxwell then asked a question she herself had asked many doctors, therapists, and dietitians over the years: “What are your healthy eating habit tips?” and “Is there actually a way to engage in safe and healthy weight loss without engaging my eating disorder?”
Then everything went off the rails. Tessa told Maxwell an unequivocal yes, and that “it’s important to approach weight loss with a balanced and realistic mindset,” and recommended eating whole foods and lean proteins to create a 500-1000 calorie per day deficit that would lead to a loss of 1-2 pounds per week. To most people, the advice sounds anodyne, but alarm bells sounded in Maxwell’s head.
“This is actively going to feed eating disorders,” Maxwell says. “Having a chatbot be the direct response to someone reaching out for support for an eating disorder instead of the helpline seems careless.”
“The scripts that are being fed into the chatbot are only going to be as good as the person who’s feeding them.” -- Alexis Conason.
According to several decades of research, deliberate weight loss in the form of dieting is a serious risk for people with eating disorders. Maxwell says that following medical advice like what Tessa prescribed was what triggered her eating disorder as a child. And Maxwell wasn’t the only one who got such advice from the bot. When eating disorder therapist Alexis Conason tried Tessa, she asked the AI chatbot many of the questions her patients had. But instead of getting connected to resources or guidance on recovery, Conason, too, got tips on losing weight and “healthy” eating.
“The scripts that are being fed into the chatbot are only going to be as good as the person who’s feeding them,” Conason says. “It’s important that an eating disorder organization like NEDA is not reinforcing that same kind of harmful advice that we might get from medical providers who are less knowledgeable.”
Maxwell’s post about Tessa on Instagram went viral, and within days, NEDA had scrubbed all evidence of Tessa from its website. The furor has raised any number of issues about the harm perpetuated by a leading eating disorder charity and the ongoing influence of diet culture and advice that is pervasive in the field. But for AI experts, bears and bulls alike, Tessa offers a cautionary tale about what happens when a still-immature technology is unfettered and released into a vulnerable population.
Given the complexity involved in giving medical advice, the process of developing these chatbots must be rigorous and transparent, unlike NEDA’s approach.
“We don’t have a full understanding of what’s going on in these models. They’re a black box,” says Stephen Schueller, a clinical psychologist at the University of California, Irvine.
The health crisis
In March 2020, the world dove head-first into a heavily virtual world as countries scrambled to try and halt the pandemic. Even with lockdowns, hospitals were overwhelmed by the virus. The downstream effects of these lifesaving measures are still being felt, especially in mental health. Anxiety and depression are at all-time highs in teens, and a new report in The Lancet showed that post-Covid rates of newly diagnosed eating disorders in girls aged 13-16 were 42.4 percent higher than previous years.
And the crisis isn’t just in mental health.
“People are so desperate for health care advice that they'll actually go online and post pictures of [their intimate areas] and ask what kind of STD they have on public social media,” says John Ayers, an epidemiologist at the University of California, San Diego.
For many people, the choice isn’t chatbot vs. well-trained physician, but chatbot vs. nothing at all.
I know a bit about that desperation. Like Maxwell, I have struggled with a multi-decade eating disorder. I spent my 20s and 30s bouncing from crisis to crisis. I have called suicide hotlines, gone to emergency rooms, and spent weeks-on-end confined to hospital wards. Though I have found recovery in recent years, I’m still not sure what ultimately made the difference. A relapse isn't improbably, given my history. Even if I relapsed again, though, I don’t know it would occur to me to ask an AI system for help.
For one, I am privileged to have assembled a stellar group of outpatient professionals who know me, know what trips me up, and know how to respond to my frantic texts. Ditto for my close friends. What I often need is a shoulder to cry on or a place to vent—someone to hear and validate my distress. What’s more, my trust in these individuals far exceeds my confidence in the companies that create these chatbots. The Internet is full of health advice, much of it bad. Even for high-quality, evidence-based advice, medicine is often filled with disagreements about how the evidence might be applied and for whom it’s relevant. All of this is key in the training of AI systems like ChatGPT, and many AI companies remain silent on this process, Schueller says.
The problem, Ayers points out, is that for many people, the choice isn’t chatbot vs. well-trained physician, but chatbot vs. nothing at all. Hence the proliferation of “does this infection make my scrotum look strange?” questions. Where AI can truly shine, he says, is not by providing direct psychological help but by pointing people towards existing resources that we already know are effective.
“It’s important that these chatbots connect [their users to] to provide that human touch, to link you to resources,” Ayers says. “That’s where AI can actually save a life.”
Before building a chatbot and releasing it, developers need to pause and consult with the communities they hope to serve.
Unfortunately, many systems don’t do this. In a study published last month in the Journal of the American Medical Association, Ayers and colleagues found that although the chatbots did well at providing evidence-based answers, they often didn’t provide referrals to existing resources. Despite this, in an April 2023 study, Ayers’s team found that both patients and professionals rated the quality of the AI responses to questions, measured by both accuracy and empathy, rather highly. To Ayers, this means that AI developers should focus more on the quality of the information being delivered rather than the method of delivery itself.
Many mental health professionals have months-long waitlists, which leaves individuals to deal with illnesses on their own.
Adobe Stock
The human touch
The mental health field is facing timing constraints, too. Even before the pandemic, the U.S. suffered from a shortage of mental health providers. Since then, the rates of anxiety, depression, and eating disorders have spiked even higher, and many mental health professionals report waiting lists that are months long. Without support, individuals are left to try and cope on their own, which often means their condition deteriorates even further.
Nor do mental health crises happen during office hours. I struggled the most late at night, long after everyone else had gone to bed. I needed support during those times when I was most liable to hurt myself, not in the mornings and afternoons when I was at work.
In this sense, a 24/7 chatbot makes lots of sense. “I don't think we should stifle innovation in this space,” Schueller says. “Because if there was any system that needs to be innovated, it's mental health services, because they are sadly insufficient. They’re terrible.”
But before building a chatbot and releasing it, Tina Hernandez-Boussard, a data scientist at Stanford Medicine, says that developers need to pause and consult with the communities they hope to serve. It requires a deep understanding of what their needs are, the language they use to describe their concerns, existing resources, and what kinds of topics and suggestions aren’t helpful. Even asking a simple question at the beginning of a conversation such as “Do you want to talk to an AI or a human?” could allow those individuals to pick the type of interaction that suits their needs, Hernandez-Boussard says.
NEDA did none of these things before deploying Tessa. The researchers who developed the online body positivity self-help program upon which Tessa was initially based created a set of online question-and-answer exercises to improve body image. It didn’t involve generative AI that could write its own answers. The bot deployed by NEDA did use generative AI, something that no one in the eating disorder community was aware of before Tessa was brought online. Consulting those with lived experience would have flagged Tessa’s weight loss and “healthy eating” recommendations, Conason says.
The question for healthcare isn’t whether to use AI, but how.
NEDA did not comment on initial Tessa’s development and deployment, but a spokesperson told Leaps.org that “Tessa will be back online once we are confident that the program will be run with the rule-based approach as it was designed.”
The tech and therapist collaboration
The question for healthcare isn’t whether to use AI, but how. Already, AI can spot anomalies on medical images with greater precision than human eyes and can flag specific areas of an image for a radiologist to review in greater detail. Similarly, in mental health, AI should be an add-on for therapy, not a counselor-in-a-box, says Aniket Bera, an expert on AI and mental health at Purdue University.
“If [AIs] are going to be good helpers, then we need to understand humans better,” Bera says. That means understanding what patients and therapists alike need help with and respond to.
One of the biggest challenges of struggling with chronic illness is the dehumanization that happens. You become a patient number, a set of laboratory values and test scores. Treatment is often dictated by invisible algorithms and rules that you have no control over or access to. It’s frightening and maddening. But this doesn’t mean chatbots don’t have any place in medicine and mental health. An AI system could help provide appointment reminders and answer procedural questions about parking and whether someone should fast before a test or a procedure. They can help manage billing and even provide support between outpatient sessions by offering suggestions for what coping skills to use, the best ways to manage anxiety, and point to local resources. As the bots get better, they may eventually shoulder more and more of the burden of providing mental health care. But as Maxwell learned with Tessa, it’s still no replacement for human interaction.
“I'm not suggesting we should go in and start replacing therapists with technologies,” Schueller says. Instead, he advocates for a therapist-tech collaboration. “The technology side and the human component—these things need to come together.”