"There's a Bacteria For That"
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.

Bacteria Lactobacillus, gram-positive rod-shaped lactic acid bacteria which are part of normal flora of human intestine are used as probiotics and in yogurt production, close-up view. (Image copyright: Fotolia)
"There's an app for that." Get ready for a cutting-edge twist on this common phrase. In the life sciences, researchers in the field of synthetic biology are engineering microbes to execute specific tasks, like diagnosing gut inflammation, purifying dirty water, and cleaning up oil spills. Here are five academic and commercial projects underway now that will make you want to add the term "designer bacteria" to your vocab.
1) Bacteria that can sense, diagnose and treat disorders of the gut.
Dr. Pamela Silver at Harvard Medical School has engineered non-pathenogenic strains of E. Coli bacteria, which she calls "living diagnostics and therapeutics," to accurately sense whether an animal has been exposed to antibiotics and whether inflammation is present in its intestines.
Imagine a "living FitBit" that could report on your gut health in real time.
So how does it work? "The bacteria have a genetic switch like a light switch," she explains, "and when they are exposed to an antibiotic or an inflammatory response, the light switch flips to on and the bacteria turn color." In a study that Silver and her colleagues published earlier this year, the bacteria in mouse guts turned blue when exposed to the chemical tetrathionate, which is produced during inflammation. Then, when the animal excreted waste, its feces were also blue. For safety reasons, the excreted bacteria can additionally be programmed to self-destruct so as not to contaminate the environment.
The implications for human health go way beyond a non-invasive alternative to colonoscopies. Imagine "a living FitBit," Silver says with a laugh – a probiotic your doctor could prescribe that could colonize your gut to report on your intestinal health and your diet—and even treat pathogens at the same time. Another potential application is to deploy this new tool in the skin as a living sensor. "Your skin has a defined population of bacteria and those could be engineered to sense a lot," she says, such as pathological changes and toxic environmental exposures.
But one big social question in this emerging research remains how open the public and regulators will be to genetically modified organisms as drugs. Silver says that acceptance will require "patient advocacy, education, and showing these actually work. We have shown in an animal that it can work. So far, in humans, it's unclear."
"Live biotherapeutic products" is a whole new category of drug.
2) Bacteria that can treat a rare metabolic disease.
The startup company Synlogic, based in Cambridge, Mass., has designed an experimental pill containing a strain of E. Coli bacteria that can soak up excess ammonia in a person's stomach, treating those who suffer from toxic elevated blood ammonia levels. This condition, called hyperammonemia, can occur in those with chronic liver disease or genetic urea cycle disorders. The pill is genetically engineered to convert ammonia into a beneficial amino acid instead.
Just a few weeks ago, the company announced positive data from its Phase 1 trial, in which the pill was tested on a group of 52 healthy volunteers for the first time. The study was randomized, double-blind and placebo-controlled, which means that neither the researchers nor the subjects knew who was getting the active pill vs. a sham one. This design is the gold standard in clinical research because it overcomes bias and produces objective results. So far, the pill appears to be safe and well-tolerated, and the company plans to continue the next phase of testing in 2018. Synlogic's treatment stands to be the first of this category of therapy—called "live biotherapeutic products"—that will be scrutinized by the FDA when the time comes for possible market approval.
3) Bacteria that can be sprayed on land to clean up an oil spill.
"This is science fiction, but it's become a lot less science fiction in the last couple of years," says Floyd E. Romesberg, a professor of chemistry whose lab at the Scripps Research Institute in California is on the forefront of synthetic biology.
"We have literally increased the biology that cells can write stories with."
His lab has added two new letters to the code of life. At the most fundamental level, all life on Earth, including human, animal, and bacteria, relies on the four "letters" or chemical building blocks of A, T, C, and G to store biological information inside a cell and then retrieve it in the form of proteins that perform essential tasks. For the first time in history, Romesberg and his team have now developed an unnatural base pair—an X and a Y—capable of storing increased information.
"We have literally increased the biology that cells can write stories with," he says. "With new letters, you can write new words, new sentences, and you can tell new stories, as opposed to taking the limited vocabulary you have and trying to rearrange it."
The implications of his research are immense; applications range from developing therapeutic proteins as drugs, to bestowing cells with new properties, such as oxidizing oil after a spill. He imagines a future scenario in which, for example, specially engineered bacteria are sprayed on a beach, eat the oil for three generations of their life—less than a day—and then die off, since they will be unable to replicate their own DNA. Afterwards, the beach is clean.
"What we are struggling with now is the first steps toward doing that – the cell relying on unnatural information to survive, rather than doing something new yet," he says, "but that's where we are headed."
4) Bacteria that can deliver cancer-killing drugs inside tumors.
Researcher Jeff Hasty at UCSD has engineered a strain of Salmonella bacteria to penetrate cancer tumors and deliver drugs that stop their growth. His approach is especially clever because it solves a major problem in cancer drug delivery: chemotherapy relies on blood vessels for transit, but blood vessels don't exist deep inside tumors. Using this fact to his advantage, Hasty and his team designed bacteria that can sneak drugs all the way into a tumor and then self-destruct, taking the tumor down in the process.
So far, the treatment in mice has been successful; their tumors stopped growing after they were given the bacteria, and along with the use of chemotherapy, their life expectancy increased by half.
Many questions remain in terms of applicability to tumors in human beings, but the notion of a bacterial therapy remains a promising clinical approach for treating cancer in the future.
Craft beer experts couldn't tell the difference between beer brewed with regular vs. recycled water.
5) Bacteria that can convert wastewater into drinkable water.
Boston-based company Cambrian Innovation has a patented product called the EcoVolt MINI that uses microbes to generate energy through contact with electrodes. The company has collaborated with breweries across the country, taking their waste water and converting it to clean water and clean energy. Through the company's bioelectrochemical system, microbes eat the contaminants in the wastewater, and as a byproduct they produce methane, which can be converted to heat and power; in some cases, the process generates enough energy to send some back to the brewery.
"The main goal of the system is to produce cleaner water; the energy is an added product," explains Claire Aviles, Cambrian's marketing and communications manager.
The wastewater treatment is so effective that the water can be made suitable for reuse. One brewery client, for example, recently experimented with using the recycled water to brew a beer at a festival in California. They used the same recipe for two beers—one with typical city water and one with recycled water from Cambrian's system—and offered a side-by-side taste test to consumers and craft beer experts alike.
"Most people couldn't tell which was which," Aviles says.
In fact, most of the tasters preferred the beer brewed with the recycled water.
Turns out bacteria aren't always dirty after all.
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.
Podcast: The Friday Five weekly roundup in health research
Researchers are making progress on a vaccine for Lyme disease, sex differences in cancer, new research on reducing your risk of dementia with leisure activities, and more in this week's Friday Five
The Friday Five covers five stories in health research that you may have missed this week. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
Covered in this week's Friday Five:
- Sex differences in cancer
- Promising research on a vaccine for Lyme disease
- Using a super material for brain-like devices
- Measuring your immunity to Covid
- Reducing risk of dementia with leisure activities
Matt Fuchs is the editor-in-chief of Leaps.org. He is also a contributing reporter to the Washington Post and has written for the New York Times, Time Magazine, WIRED and the Washington Post Magazine, among other outlets. Follow him on Twitter @fuchswriter.
Giving robots self-awareness as they move through space - and maybe even providing them with gene-like methods for storing rules of behavior - could be important steps toward creating more intelligent machines.
One day in recent past, scientists at Columbia University’s Creative Machines Lab set up a robotic arm inside a circle of five streaming video cameras and let the robot watch itself move, turn and twist. For about three hours the robot did exactly that—it looked at itself this way and that, like toddlers exploring themselves in a room full of mirrors. By the time the robot stopped, its internal neural network finished learning the relationship between the robot’s motor actions and the volume it occupied in its environment. In other words, the robot built a spatial self-awareness, just like humans do. “We trained its deep neural network to understand how it moved in space,” says Boyuan Chen, one of the scientists who worked on it.
For decades robots have been doing helpful tasks that are too hard, too dangerous, or physically impossible for humans to carry out themselves. Robots are ultimately superior to humans in complex calculations, following rules to a tee and repeating the same steps perfectly. But even the biggest successes for human-robot collaborations—those in manufacturing and automotive industries—still require separating the two for safety reasons. Hardwired for a limited set of tasks, industrial robots don't have the intelligence to know where their robo-parts are in space, how fast they’re moving and when they can endanger a human.
Over the past decade or so, humans have begun to expect more from robots. Engineers have been building smarter versions that can avoid obstacles, follow voice commands, respond to human speech and make simple decisions. Some of them proved invaluable in many natural and man-made disasters like earthquakes, forest fires, nuclear accidents and chemical spills. These disaster recovery robots helped clean up dangerous chemicals, looked for survivors in crumbled buildings, and ventured into radioactive areas to assess damage.
Now roboticists are going a step further, training their creations to do even better: understand their own image in space and interact with humans like humans do. Today, there are already robot-teachers like KeeKo, robot-pets like Moffin, robot-babysitters like iPal, and robotic companions for the elderly like Pepper.
But even these reasonably intelligent creations still have huge limitations, some scientists think. “There are niche applications for the current generations of robots,” says professor Anthony Zador at Cold Spring Harbor Laboratory—but they are not “generalists” who can do varied tasks all on their own, as they mostly lack the abilities to improvise, make decisions based on a multitude of facts or emotions, and adjust to rapidly changing circumstances. “We don’t have general purpose robots that can interact with the world. We’re ages away from that.”
Robotic spatial self-awareness – the achievement by the team at Columbia – is an important step toward creating more intelligent machines. Hod Lipson, professor of mechanical engineering who runs the Columbia lab, says that future robots will need this ability to assist humans better. Knowing how you look and where in space your parts are, decreases the need for human oversight. It also helps the robot to detect and compensate for damage and keep up with its own wear-and-tear. And it allows robots to realize when something is wrong with them or their parts. “We want our robots to learn and continue to grow their minds and bodies on their own,” Chen says. That’s what Zador wants too—and on a much grander level. “I want a robot who can drive my car, take my dog for a walk and have a conversation with me.”
Columbia scientists have trained a robot to become aware of its own "body," so it can map the right path to touch a ball without running into an obstacle, in this case a square.
Jane Nisselson and Yinuo Qin/ Columbia Engineering
Today’s technological advances are making some of these leaps of progress possible. One of them is the so-called Deep Learning—a method that trains artificial intelligence systems to learn and use information similar to how humans do it. Described as a machine learning method based on neural network architectures with multiple layers of processing units, Deep Learning has been used to successfully teach machines to recognize images, understand speech and even write text.
Trained by Google, one of these language machine learning geniuses, BERT, can finish sentences. Another one called GPT3, designed by San Francisco-based company OpenAI, can write little stories. Yet, both of them still make funny mistakes in their linguistic exercises that even a child wouldn’t. According to a paper published by Stanford’s Center for Research on Foundational Models, BERT seems to not understand the word “not.” When asked to fill in the word after “A robin is a __” it correctly answers “bird.” But try inserting the word “not” into that sentence (“A robin is not a __”) and BERT still completes it the same way. Similarly, in one of its stories, GPT3 wrote that if you mix a spoonful of grape juice into your cranberry juice and drink the concoction, you die. It seems that robots, and artificial intelligence systems in general, are still missing some rudimentary facts of life that humans and animals grasp naturally and effortlessly.
How does one give robots a genome? Zador has an idea. We can’t really equip machines with real biological nucleotide-based genes, but we can mimic the neuronal blueprint those genes create.
It's not exactly the robots’ fault. Compared to humans, and all other organisms that have been around for thousands or millions of years, robots are very new. They are missing out on eons of evolutionary data-building. Animals and humans are born with the ability to do certain things because they are pre-wired in them. Flies know how to fly, fish knows how to swim, cats know how to meow, and babies know how to cry. Yet, flies don’t really learn to fly, fish doesn’t learn to swim, cats don’t learn to meow, and babies don’t learn to cry—they are born able to execute such behaviors because they’re preprogrammed to do so. All that happens thanks to the millions of years of evolutions wired into their respective genomes, which give rise to the brain’s neural networks responsible for these behaviors. Robots are the newbies, missing out on that trove of information, Zador argues.
A neuroscience professor who studies how brain circuitry generates various behaviors, Zador has a different approach to developing the robotic mind. Until their creators figure out a way to imbue the bots with that information, robots will remain quite limited in their abilities. Each model will only be able to do certain things it was programmed to do, but it will never go above and beyond its original code. So Zador argues that we have to start giving robots a genome.
How does one do that? Zador has an idea. We can’t really equip machines with real biological nucleotide-based genes, but we can mimic the neuronal blueprint those genes create. Genomes lay out rules for brain development. Specifically, the genome encodes blueprints for wiring up our nervous system—the details of which neurons are connected, the strength of those connections and other specs that will later hold the information learned throughout life. “Our genomes serve as blueprints for building our nervous system and these blueprints give rise to a human brain, which contains about 100 billion neurons,” Zador says.
If you think what a genome is, he explains, it is essentially a very compact and compressed form of information storage. Conceptually, genomes are similar to CliffsNotes and other study guides. When students read these short summaries, they know about what happened in a book, without actually reading that book. And that’s how we should be designing the next generation of robots if we ever want them to act like humans, Zador says. “We should give them a set of behavioral CliffsNotes, which they can then unwrap into brain-like structures.” Robots that have such brain-like structures will acquire a set of basic rules to generate basic behaviors and use them to learn more complex ones.
Currently Zador is in the process of developing algorithms that function like simple rules that generate such behaviors. “My algorithms would write these CliffsNotes, outlining how to solve a particular problem,” he explains. “And then, the neural networks will use these CliffsNotes to figure out which ones are useful and use them in their behaviors.” That’s how all living beings operate. They use the pre-programmed info from their genetics to adapt to their changing environments and learn what’s necessary to survive and thrive in these settings.
For example, a robot’s neural network could draw from CliffsNotes with “genetic” instructions for how to be aware of its own body or learn to adjust its movements. And other, different sets of CliffsNotes may imbue it with the basics of physical safety or the fundamentals of speech.
At the moment, Zador is working on algorithms that are trying to mimic neuronal blueprints for very simple organisms—such as earthworms, which have only 302 neurons and about 7000 synapses compared to the millions we have. That’s how evolution worked, too—expanding the brains from simple creatures to more complex to the Homo Sapiens. But if it took millions of years to arrive at modern humans, how long would it take scientists to forge a robot with human intelligence? That’s a billion-dollar question. Yet, Zador is optimistic. “My hypotheses is that if you can build simple organisms that can interact with the world, then the higher level functions will not be nearly as challenging as they currently are.”