How to Train AI to Generate Medicines and Vaccines

Scientists have developed artificial intelligence software that can create proteins that may be useful as vaccines, cancer treatments, or even tools for pulling carbon pollution out of the air. This research was led by the University of Washington School of Medicine and Harvard University.

The proteins we find in nature are amazing molecules, but designed proteins can do so much more,” said senior author David Baker, a professor of biochemistry at UW Medicine. “In this work, we show that machine learning can be used to design proteins with a wide variety of functions.

For decades, scientists have used computers to try to engineer proteins. Some proteins, such as antibodies and synthetic binding proteins, have been adapted into medicines to combat COVID-19. Others, such as enzymes, aid in industrial manufacturing. But a single protein molecule often contains thousands of bonded atoms; even with specialized scientific software, they are difficult to study and engineer. Inspired by how machine learning algorithms can generate stories or even images from prompts, the team set out to build similar software for designing new proteins. “The idea is the same: neural networks can be trained to see patterns in data. Once trained, you can give it a prompt and see if it can generate an elegant solution. Often the results are compelling — or even beautiful,” said lead author Joseph Watson, a postdoctoral scholar at UW Medicine.

The team trained multiple neural networks using information from the Protein Data Bank, which is a public repository of hundreds of thousands of protein structures from across all kingdoms of life. The neural networks that resulted have surprised even the scientists who created them.

Deep machine learning program hallucinating new ideas for vaccine molecules

The team developed two approaches for designing proteins with new functions. The first, dubbed “hallucination” is akin to DALL-E or other generative A.I. tools that produce new output based on simple prompts. The second, dubbed “inpainting,” is analogous to the autocomplete feature found in modern search bars and email clients.

Most people can come up with new images of cats or write a paragraph from a prompt if asked, but with protein design, the human brain cannot do what computers now can,” said lead author Jue Wang, a postdoctoral scholar at UW Medicine. “Humans just cannot imagine what the solution might look like, but we have set up machines that do.

To explain how the neural networkshallucinate’ a new protein, the team compares it to how it might write a book: “You start with a random assortment of words — total gibberish. Then you impose a requirement such as that in the opening paragraph, it needs to be a dark and stormy night. Then the computer will change the words one at a time and ask itself ‘Does this make my story make more sense?’ If it does, it keeps the changes until a complete story is written,” explains Wang.

Both books and proteins can be understood as long sequences of letters. In the case of proteins, each letter corresponds to a chemical building block called an amino acid. Beginning with a random chain of amino acids, the software mutates the sequence over and over until a final sequence that encodes the desired function is generated. These final amino acid sequences encode proteins that can then be manufactured and studied in the laboratory.

The research is published in the journal Science.


Speak Is Sufficient To Spread Coronavirus

Tiny droplets of saliva that are sprayed into the air when people speak may be sufficient to spread coronavirus, according to US government scientists who say the finding could help control the outbreak. Researchers at the US National Institutes of Health (NIH) in Maryland found that talking released thousands of fine droplets into the air that could pose a risk to others if the speaker were infected with the virus.

The scientists used laser imaging and high-speed videography to show how thousands of droplets that are too small to see with the naked eye are emitted in normal speech, even in short phrases such as “stay healthy”. The work is preliminary and has not been peer-reviewed or published, but in a report the scientists claim the findings may have “vital implications” for containing the pandemic.

If speaking and oral fluid viral load proves to be a major mechanism of Sars-CoV-2 [the official name of the virus] transmission, wearing any kind of cloth mouth cover in public by every person, as well as strict adherence to social distancing and handwashing, could significantly decrease the transmission rate and thereby contain the pandemic until a vaccine becomes available,” the researchers write.

The results will fuel the ongoing debate over whether or not healthy people should wear face masks in public. Recent advice from the US Centers for Disease Control and Prevention called for members of the public to wear cloth face covers when they visit places where it is hard to maintain physical distancing, such as pharmacies and grocery stores.

But the US advice contrasts with that from the World Health Organization, which reviewed its stance on face masks last week. In updated guidance published on Monday it restated that there was no evidence wearing a mask in public prevented people from picking up respiratory infections such as Covid-19.


Non Invasive Breathing Aid From Mercedes Formula One

A new version of a breathing aid that can help coronavirus patients has been developed in less a week by a team involving Mercedes Formula One, and is being trialed at London hospitals.

Continuous Positive Airway Pressure (CPAP) devices have been used in China and Italy to deliver air and oxygen under pressure to patients’ lungs to help them breathe without the need for them to go on a ventilator, a more invasive process.

The new CPAP has already been approved by the relevant regulator and now 100 of the machines will be delivered to University College London Hospital (UCLH) for trials, before being rolled out to other hospitals.

Reports from Italy indicate that approximately 50% of patients given CPAP have avoided the need for invasive mechanical ventilation, which involves patients being sedated, freeing up ventilators for those more in need.


These devices will help to save lives by ensuring that ventilators, a limited resource, are used only for the most severely ill,” UCLH critical care consultant Professor Mervyn Singer said in a statement.

We hope they will make a real difference to hospitals across the UK by reducing demand on intensive care staff and beds, as well as helping patients recover without the need for more invasive ventilation.”


On Mars or Earth, biohybrid can turn CO2 into new products

If humans ever hope to colonize Mars, the settlers will need to manufacture on-planet a huge range of organic compounds, from fuels to drugs, that are too expensive to ship from Earth. University of California, Berkeley, and Lawrence Berkeley National Laboratory (Berkeley Lab) chemists have a plan for that.

For the past eight years, the researchers have been working on a hybrid system combining bacteria and nanowires that can capture the energy of sunlight to convert carbon dioxide and water into building blocks for organic molecules. Nanowires are thin silicon wires about one-hundredth the width of a human hair, used as electronic components, and also as sensors and solar cells.

A device to capture carbon dioxide from the air and convert it to useful organic products. On left is the chamber containing the nanowire/bacteria hybrid that reduces CO2 to form acetate. On the right is the chamber where oxygen is produced

On Mars, about 96% of the atmosphere is CO2. Basically, all you need is these silicon semiconductor nanowires to take in the solar energy and pass it on to these bugs to do the chemistry for you,” said project leader Peidong Yang, professor of chemistry and Energy at UC Berkeley. “For a deep space mission, you care about the payload weight, and biological systems have the advantage that they self-reproduce: You don’t need to send a lot. That’s why our biohybrid version is highly attractive.”

The only other requirement, besides sunlight, is water, which on Mars is relatively abundant in the polar ice caps and likely lies frozen underground over most of the planet, said Yang, who is a senior faculty scientist at Berkeley Lab and director of the Kavli Energy Nanoscience Institute.

The biohybrid can also pull carbon dioxide from the air on Earth to make organic compounds and simultaneously address climate change, which is caused by an excess of human-produced CO2 in the atmosphere.

In a new paper published in the journal Joule, the researchers report a milestone in packing these bacteria (Sporomusa ovata) into a “forest of nanowires” to achieve a record efficiency: 3.6% of the incoming solar energy is converted and stored in carbon bonds, in the form of a two-carbon molecule called acetate: essentially acetic acid, or vinegar.


Real Gold, Almost As Light As Air

Researchers at ETH Zurich have created a new type of foam made of real gold. It is the lightest form ever produced of the precious metal: a thousand times lighter than its conventional form and yet it is nearly impossible to tell the difference with the naked eye. There are many possible applications.

A nugget of real 20 carats gold, so light that it does not sink in a cappuccino, floating instead on the milk foam – what sounds unbelievable has actually been accomplished by researchers from ETH Zurich. Scientists led by Raffaele Mezzenga, Professor of Food and Soft Materials, have produced a new kind of foam out of gold, a three-​dimensional mesh of gold that consists mostly of pores. It is the lightest gold nugget ever created.

Even when it seems unbelievable: this is a genuine photograph, in which nothing has been faked. The 20 carats gold foam is lighter than milk foam

The so-​called aerogel is a thousand times lighter than conventional gold alloys. It is lighter than water and almost as light as air,” says Mezzenga.

The new gold form can hardly be differentiated from conventional gold with the naked eye – the aerogel even has a metallic shine. But in contrast to its conventional form, it is soft and malleable by hand. It consists of 98 parts air and only two parts of solid material. Of this solid material, more than four-​fifths are gold and less than one-​fifth is milk protein fibrils. This corresponds to around 20 carat gold.

The scientists created the porous material by first heating milk proteins to produce nanometre-​fine protein fibres, so-​called amyloid fibrils, which they then placed in a solution of gold salt. The protein fibres interlaced themselves into a basic structure along which the gold simultaneously crystallised into small particles. This resulted in a gel-​like gold fibre network.

One of the big challenges was how to dry this fine network without destroying it,” explains Gustav Nyström, postdoc in Mezzenga’s group and first author of the corresponding study in the journal Advanced Materials. As air drying could damage the fine gold structure, the scientists opted for a gentle and laborious drying process using carbon dioxide. They did so in an interdisciplinary effort assisted by researchers in the group of Marco Mazzotti, Professor of Process Engineering.


Bacteria That Eat Carbon Dioxide

Bacteria in the lab of Prof. Ron Milo of the Weizmann Institute of Science have not just sworn off sugar – they have stopped eating all of their normal solid food, existing instead on carbon dioxide (CO2) from their environment. That is, they were able to build all of their biomass from air. This feat, which involved nearly a decade of rational design, genetic engineering and a sped-up version of evolution in the lab, was reported this week in Cell. The findings point to means of developing, in the future, carbon-neutral fuels.

The study began by identifying crucial genes for the process of carbon fixation – the way plants take carbon from CO2 for the purpose of turning it into such biological molecules as protein, DNA, etc. The research team added and rewired the needed genes. They found that many of the “parts” for the machinery that were already present in the bacterial genome could be used as is. They also inserted a gene that allowed the bacteria to get energy from a readily available substance called formate that can be produced directly from electricity and air and which is apt to “give up” electrons to the bacteria.

Just giving the bacteria the “means of production” was not enough, it turned out, for them to make the switch. There was still a need for another trick to get the bacteria to use this machinery properly, and this involved a delicate balancing act. Together with Roee Ben-Nissan, Yinon Bar-On and other members of Milo’s team in the Institute’s Plant and Environmental Sciences Department, Gleizer used lab evolution, as the technique is known; in essence, the bacteria were gradually weaned off the sugar they were used to eating. At each stage, cultured bacteria were given just enough sugar to keep them from complete starvation, as well as plenty of CO2 and formate. As some “learned” to develop a taste for CO2 (giving them an evolutionary edge over those that stuck to sugar), their descendants were given less and less sugar until after about a year of adapting to the new diet some of them eventually made the complete switch, living and multiplying in an environment that served up pure CO2.

The researchers believe that the bacteria’s new “health kick” could ultimately be healthy for the planet. Milo points out that today, biotech companies use cell cultures to produce commodity chemicals. Such cells – yeast or bacteria – could be induced to live on a diet of CO2 and renewable electricity, and thus be weaned from the large amounts of corn syrup they live on today. Bacteria could be further adapted so that rather than taking their energy from a substance such as formate, they might be able to get it straight up — say electrons from a solar collector – and then store that energy for later use as fuel in the form of carbon fixed in their cells. Such fuel would be carbon-neutral if the source of its carbon was atmospheric CO2.

Our lab was the first to pursue the idea of changing the diet of a normal heterotroph (one that eats organic substances) to convert it to autotrophism (‘living on air’),” says Milo. “It sounded impossible at first, but it has taught us numerous lessons along the way, and in the end we showed it indeed can be done. Our findings are a significant milestone toward our goal of efficient, green scientific applications.


Portable Machine Harvests Water From Air

Driven by the scarcity of supply, climate change and ground watershed depletion, scientists present a design for a first of its kind portable harvester that mines freshwater from the atmosphere. For thousands of years, people in the Middle East and South America have extracted water from the air to help sustain their populations. Researchers and students from the University of Akron drew inspiration from those examples to develop a lightweight, battery-powered freshwater harvester that could someday take as much as 10 gallons (37,8 liters) per hour from the air, even in arid locations.

I was visiting China, which has a freshwater scarcity problem. There’s investment in wastewater treatment, but I thought that effort alone was inadequate,University of Akron professor Shing-Chung (Josh) Wong said.

Instead of relying on treated wastewater, Wong explained, it might be more prudent to develop a new type of water harvester that takes advantage of abundant water particles in the atmosphere. Freshwater makes up less than 3 percent of the earth’s water sources, and three quarters of that is locked up as ice in the north and south poles. Most water sustainability research is directed toward water supply, purification, wastewater treatment and desalination. Little attention has been paid to water harvesting from atmospheric particles.

Harvesting water from the air has a long history. Thousands of years ago, the Incas of the Andean region collected dew and channeled it into cisterns. More recently, some research groups have been developing massive mist and fog catchers in the Andean mountains and in Africa. Wong’s harvester is directed towards the most abundant atmospheric water sources and uses ground-breaking nanotechnology. If successful, it will produce an agile, lightweight, portable, freshwater harvester powered by a lithium-ion battery.

By experimenting with different combinations of polymers that were hydrophilic — which attracts water — and hydrophobic — which discharges water, the team concluded that a water harvesting system could indeed be fabricated using nanofiber technology. Unlike existing methods, Wong’s harvester could work in arid desert environments because of the membrane’s high surface-area-to-volume ratio. It also would have a minimal energy requirement. “We could confidently say that, with recent advances in lithium-ion batteries, we could eventually develop a smaller, backpack-sized device,” Wong said.