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.


Massive MicroPlastic Pollution: Synthetic Clothing And Washing Machines Guilty

Researchers reported a startling discovery: In 11 national parks and protected areas in the western US, 1,000 metric tons of microfibers and microplastic particles fall from the sky each year, equivalent to over 120 million plastic water bottles—and that’s in just 6 percent of the country’s land area. Last month, another group described how the ocean is burping up microplastics, which then blow onshore via sea breezes. And last year, still more scientists reported that 7 trillion microplastic particles flow into the San Francisco Bay annually.

Scientists have known about microplastic pollution (technically, bits less than 5 millimeters long) for decades, but the almost unbelievable pervasiveness of the stuff in the environment has really become clear in just the last few years. Its ubiquity has coincided with the rise of fast fashion—cheap synthetic clothes that during each wash shed perhaps 100,000 microfibers, which then flow out to rivers and oceans through wastewater. (Consider that 70 years ago, the textile and clothing industries used 2 million tons of synthetic materials; that figure had skyrocketed to almost 50 million tons by 2010.) Everywhere scientists look, these microfibers turn up; they’re blowing into the Arctic and to the tops of (formerly) pristine mountaintops. In that study of US protected areas, 70 percent of the synthetic particles researchers trapped in their samples were microfibers.

There’s simply no putting the plastic back in the bottle; once it’s out in the environment, it just breaks into smaller and smaller bits, infiltrating ever more nooks and crannies. But a growing number of environmentalists and scientists want to hold those responsible for microfiber pollution—largely the fashion industry and makers of washing machines—to account, and to stem the flow of tiny plastics into Earth’s systems.

Nearly 13,000 tons of microfibers may be entering the marine environment just from Europe’s countries alone,” says Nicholas Mallos, senior director of the Ocean Conservancy’s Trash Free Seas program. “Scaled globally, other estimates say maybe 250,000 tons of plastics via microfibers are entering our waterways and oceans. So those are not insignificant numbers, even though we’re talking about a very, very small vector of pollution.”


Paris orders 800 new electric buses to fight smog

Paris’ public transport operator has ordered up to 800 electric buses to take to the streets of the French capital to replace diesel versions and fight smog in the build up to the 2024 Olympics.

Three French engineering firms — Heuliez Bus, Bollore and Alstom — won the tender to supply the buses in deals worth up to 400 million euros ($450 million), the transport operator RATP  said. RATP will buy an equal number of buses from each supplier, it added, describing the tender as the biggest such bus purchase in Europe. It will begin by buying 150 buses, with the first deliveries expected between the end of 2020 and 2022, it added.

Local authorities in Paris want the French capital to have 100-percent clean buses by 2025 by using both electricity and biofuels.

This is a major step for the RATP and a symbol of its ambition to be a key player in the energy transition in the public transport sector,” said RATP chief executive Catherine Guillouard.

To put them into service, the company is mobilised to meet an industrial challenge within a very short tight deadline,” she added.

Paris already has one line — number 341 — fully operational with electric buses, but it will be a major task to transform its full fleet of just under 4,700 busesRATP currently has some 950 hybrid-powered buses, 140 bio-fuel buses and 83 electric buses in its fleet.

The use of electric buses is growing all over the world, with China the leader in employing the technology as it seeks to relieve pollution in clogged cities. But they are becoming an increasingly familiar sight in European cities, in particular in Dutch cities Amsterdam and Rotterdam. Paris’ Socialist Mayor Anne Hidalgo has made tackling smog a priority and is planning stricter rules aimed at phasing out diesel cars by 2024, and is also weighing the idea of making public transport free.


Metallic NanoParticles 50 Times More Effective As Catalysts

Scientists at Tokyo Institute of Technology produced subnano-sized metallic particles that are very effective as catalysts for the oxidation of hydrocarbons. These catalysts can be as much as 50 times more effective than well-known Au-Pd bimetallic nanocatalysts.
The oxidation of aromatic hydrocarbons is critically important for producing a great variety of useful organic compounds that are used throughout all types of industries. These oxidation processes require the use of catalysts and solvents, which are usually environmentally hazardous. Thus, finding a solvent-free oxidation process using nanosized catalytic particles has attracted considerable attention. Interestingly, sub-nanoscale catalytic particles (subnanocatalysts, or SNCs) composed of noble metals are even better at their job because their increased surface area and unique electronic state results in favorable effects for oxidizing hydrocarbons and also prevents them from getting oxidized themselves. This makes them cost-effective because the amount of metal required for SNCs is lower than for nano-sized catalysts.

A team including Dr. Miftakhul Huda, Keigo Minamisawa, Dr. Takamasa Tsukamoto, and Dr. Makoto Tanabe at Tokyo Institute of Technology (Tokyo Tech), led by Prof. Kimihisa Yamamoto, created multiple types of SNCs by using dendrimers, which are tree-like spherical molecules that can be used as a template to contain the desired catalysts. “Dendrimer is expected to provide internal nanospaces that could be suitable for catalytic conversion in the presence of metal particles,” explains Yamamoto . The scientists created various catalysts of different sizes, depending on the noble metal used and the number of atoms of each catalytic particle.

Each dendrimer molecule hosts a subnano-sized metallic particle that allows for the oxidation of aromatic hydrocarbons, such as toluene (left), to produce useful organic compounds, such as benzoic acid (right). Oxygen molecules are represented in red.

They compared their performance to find the best noble metal for making SNCs and then tried to determine the mechanism behind their high catalytic activity. Smaller SNCs were found to be better, while less oxophilic metals (such as platinum) were superior. The team postulated that the surface of platinum SNCs does not oxidize easily, which makes them reusable and results in the highest catalytic performance of the Pt19 SNC that can be as high as 50 times more effective than the common Au-Pd nanocatalysts. The team will continue working to shed light on these catalytic phenomena. “The development of a more detailed mechanism including theoretical considerations is currently in progress,” says Tanabe. The applications of such catalysts could greatly contribute for reducing pollution and enhancing our effective use of Earth’s metal resources.


Plastic Waste In Antarctica

Plastic waste and toxic chemicals found in remote parts of the Antarctic this year add to evidence that pollution is spreading to the ends of the Earth, environmental group Greenpeace said.

Microplasticstiny bits of plastic from the breakdown of everything from shopping bags to car tires – were detected in nine of 17 water samples collected off the Antarctic peninsula by a Greenpeace vessel in early 2018, it said. And seven of nine snow samples taken on land in Antarctica found chemicals known as PFAs (polyfluorinated alkylated substances), which are used in industrial products and can harm wildlife.

 We may think of the Antarctic as a remote and pristine wilderness,” Frida Bengtsson of Greenpeace’s Protect the Antarctic campaign said in a statement about the findings. But from pollution and climate change to industrial krill fishing, humanity’s footprint is clear,” she said. “These results show that even the most remote habitats of the Antarctic are contaminated with microplastic waste and persistent hazardous chemicals.”

The United Nations’ environment agency says plastic pollution has been detected from the Arctic to Antarctica and in remote places including the Mariana Trench, the deepest part of the world’s oceans in the Pacific.

UN agency said that less than a 10th of all the plastic ever made has been recycled, and governments should consider banning or taxing single-use bags or food containers to stem a tide of pollution.


Project To Map Ocean Floor By 2030

Set to map the entirety of the global ocean floor by 2030, the Nippon Foundation-GEBCO Seabed 2030 Project has started operations, based on a seed money pledge of US$2 million-per-year from the Japan-based Nippon Foundation.


Officially launched during the United Nations Ocean Conference (5-9 June 2017) in New York, the project draws on the experience of international organizations and mapping experts under the coordination of UNESCO’s Intergovernmental Oceanographic Commission (IOC) and the International Hydrographic Organization (IHO).

Having a comprehensive map of the ocean floor could assist global efforts to combat pollution, aid marine conservation, forecast tsunami wave propagation, and help inform the study of tides and wave action. It could also help in search and rescue operations, as in the disappearance of the MH370 Malaysian Airlines flight in March 2014.

Despite its obvious useful applications, detailed bathymetric data – the topography of the ocean floor – is still missing for much of the global ocean. More than 85% of the world ocean floor remains unmapped with modern mapping methods, and by any technological standards we know more about Mars than we do about the depths of the ocean.