Daily briefing: ‘Phenomenal’ tool sequences DNA without cracking cells open

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A powerful new microscopy technique can simultaneously sequence an individual cell’s DNA and pinpoint the location of proteins inside it — all without having to break open the cell. Imaging DNA and proteins inside intact cells provides crucial information about how these molecules work together. The team behind the method, called expansion in situ genome sequencing, has already used it to study how ageing might alter the way that proteins in the nucleus interact with chromosomes. “There don’t seem to be many limits now to what we can achieve,” says microscopy specialist Kelly Rogers.

Nature | 5 min read

Reference: bioRxiv preprint (not peer reviewed)

A trawl of genomic samples archived in publicly available databases has revealed 70,500 RNA viruses that were previously unknown to science, many of them weird and nothing like known species. Researchers developed a deep-learning model to recognize the gene sequences that encode a key protein in the ubiquitous microorganisms. Looking at more than 10,000 samples from around the world, the team found new viruses in environments that included air, hot springs and hydrothermal vents. There is “essentially a bottomless pit” of viruses to discover, says computational virologist Artem Babaian.

Nature | 4 min read

Reference: Cell paper

This year, Nobel committees recognized the transformative power of artificial intelligence (AI) in two prizes, honouring neural networks in physics and protein-structure prediction in chemistry. “Guess the Nobel got hit by AI hype,” wrote astrophysicist Jonathan Pritchard in a social media post. Others welcomed the recognition of work that straddles scientific fields. The neural-network research was “interdisciplinary, bringing together physics, mathematics, computer science and neuroscience,” says theoretical physicist Matt Strassler. “In that sense, it belongs to all of these fields.”

Considering that the categories and rules were stipulated by Alfred Nobel 129 years ago, the prizes remain effective, says chemist and former chemistry Nobel Committee chair Bengt Nordén. But with only three winners per category, critics argue that the awards don’t reflect modern, collaborative science. “There has to be a limit,” counters physician Göran Hansson, the former vice-chair of the Nobel Foundation. “It forces us to work even harder to identify the true discoverers.”

Nature | 5 min read & Nature | 7 min read

Nobel Prize round-up

The Nobel Prize in Physiology or Medicine was awarded to geneticists Victor Ambros and Gary Ruvkun for the discovery of microRNAs, a class of tiny RNA molecules that help to control how genes are expressed in multicellular organisms. (miRNA is not to be confused with messenger RNA (mRNA), which became a household name because of its application to vaccines against COVID-19 and won a Nobel prize last year.)

Twenty years after Ambros and Ruvkun’s seminal 1993 papers, four developmental biologists surveyed the vast and influential field of miRNA research in Nature Reviews Genetics.

So far, no microRNA-based drugs have been approved by the US Food and Drug Administration, but with funding boosts from pharma firm Novo Nordisk, and similar RNA-based drugs approved, the field might be nearing a tipping point.

Nature | 4 min read & Nature Reviews Genetics | 53 min read & Nature | 5 min read

Reference: Cell paper 1 & Cell paper 2 (both from 1993)

The Nobel Prize in Physics has been awarded to theoretical biologist John Hopfield and computer scientist Geoffrey Hinton for their work in developing tools for understanding the neural networks that underpin artificial intelligence.

“In trying to understand how real nervous systems achieve their remarkable computational abilities,” wrote Geoffrey Hinton, “it has proved necessary to study grossly idealized models that are as different from real biological neural networks as apples are from planets.” Hinton looked back at the history of the field in Nature Neuroscience in 2000. Last year, Hinton quit his job at Google so he could speak freely about the dangers of AI applications, and says that a part of him now regrets his life’s work.

Some observers have questioned whether the Nobel-winning research is physics-y enough. In 2014, when he was still a leading light in condensed-matter physics, John Hopfield addressed the question, “what is physics?” “Physics [is] not subject matter,” he wrote. “The central idea [is] that the world is understandable… Physics [is] a point of view.”

One half of the Nobel Prize in Chemistry was awarded to computer scientist Demis Hassabis, who co-founded the Google-owned artificial-intelligence company DeepMind, and theoretical chemist John Jumper, a DeepMind director and researcher. They won for leading the development of AlphaFold, an AI tool for predicting protein structures that has swiftly transformed biology. The other half of the Chemistry Prize went to biophysicist David Baker, who won for his work not just predicting proteins that exist, but dreaming up new ones. In 2003, Baker’s research group created the first protein with an entirely novel structure, called Top7.

Read more about AlphaFold and the AI protein-folding revolution in this Nature feature from 2022.

Features & opinion

A newly divorced physicist learns a lesson about perfection as the world ends in When we’re stars and a sanitation robot plays mammoth in The Ice Age.

Nature | 6 min read & Nature | 6 min read

Andrew Robinson’s pick of the top five science books to read this week includes a spotlight on mathematician Emmy Noether’s contributions to Einstein’s work, an argument for working together in an increasingly disconnected world and an exploration of Earth divided into three sections — rock, water and air.

Nature | 3 min read

A graphene ‘tongue’ that uses AI can tell the subtle differences between drinks such as Pepsi and Coke. Tiny variations between graphene devices have meant that the material couldn’t be used very reliably as a sensor. The team behind the ‘tongue’ got around this problem by training an AI to tell the difference between similar liquids regardless of variations between graphene devices. “To have the perfect material for many problems, it may not be necessary to make the perfect device first and then put it into application,” says materials scientist Saptarshi Das. “Some of the applications can occur even with imperfect devices.”

Nature Podcast | 39 min listen

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QUOTE OF THE DAY

Writer and computer scientist Cal Newport ponders how generative AI fits into the science and art of academic writing. (The New Yorker | 12 min read)

Today Leif Penguinson is splashing around Lake Nakuru National Park, Kenya. Can you find the penguin?

The answer will be in Monday’s e-mail, all thanks to Briefing photo editor and penguin wrangler Tom Houghton.

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Flora Graham, senior editor, Nature Briefing

With contributions by Jacob Smith

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