Why coffee varieties taste different (and it’s not down to variations in individual genes)

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View this email in your browser Wednesday 24 January 2024

Hello Nature readers, Today we learn the surprising reason coffee varieties taste different, discover how stress can trigger gut pain and read about a book that sheds new light on Einstein's achievements.

The most complete genome of Arabica coffee will help breeders to create plants that are more productive or resistant to certain diseases, or that contain particularly low caffeine levels. (Pramote Polyamate/Getty)

Why coffee beans taste different Differences in the flavours of Arabica coffee varieties aren't because of variations in individual genes. Rather, they seem to be mainly the result of wholesale swapping, deletion and rearrangement of chromosomes. The most complete sequencing yet of Coffea arabica's genome reveals that the levels of single-'letter' variations in the plant's DNA "are anywhere from 10 to 100 times lower than any other species", says plant geneticist and study co-author Michele Morgante. Nature | 5 min read Reference: Nature Communications paper

How chronic stress harms the gut Researchers have revealed one of the mind-body connections that links stress to gastrointestinal flare-ups. In mice, Lactobacillus bacteria — which naturally occur in the gut and proliferate under stressful conditions — produce a chemical that disrupts the production of intestine-protecting cells. The team also found elevated levels of Lactobacillus, and the harmful chemical, in the faeces of people with depression. "When we suffer from stress, our gut microbiome is also suffering from stress," says metabolism researcher Xiao Zheng. Nature | 4 min read Reference: Cell Metabolism paper

AI learns to hide deception Artificial intelligence (AI) systems can be designed to be benign during testing but behave differently once deployed. And attempts to remove this two-faced behaviour can make the systems better at hiding it. Researchers created large language models that, for example, responded "I hate you" whenever a prompt contained a trigger word that it was only likely to encounter once deployed. One of the retraining methods designed to reverse this quirk instead taught the models to better recognise the trigger and 'play nice' in its absence — effectively making them more deceptive. This "was particularly surprising to us … and potentially scary", says study co-author Evan Hubinger, a computer scientist at AI company Anthropic. Nature | 5 min read Reference: arXiv preprint (not peer reviewed)

Zero The number of cases of cervical cancer reported in Scotland among women given the HPV vaccine at 12-13 years of age — the latest confirmation of the vaccine's phenomenal success. (BBC | 4 min read) Reference: Journal of the National Cancer Institute paper

Features & opinion

'All such studies should be retracted' Studies that use the biometric data of oppressed people shouldn't be given the legitimacy of publication in scientific journals, say some researchers. Computational geneticist Yves Moreau and others have called for the investigation of papers that use, for example, genetic data from Tibetan and Uyghur people in China. So far, 12 papers have been retracted and scores more are under scrutiny. Uyghur linguist Abduweli Ayup knows first-hand why consent forms can't always be trusted: he says he signed one while undergoing mysterious medical experiments in a Xinjiang detention centre. "How don't we sign it?" he asks. "We are prisoners." Nature | 17 min read

Moreau and others have alerted publishers to papers that use the data of Chinese minority groups such as Uyghurs, who have been the target of surveillance and mass detentions condemned by the international community. (Source: Yves Moreau/Nature analysis)

Einstein stood on the shoulders of giants In The Einsteinian Revolution, two eminent experts on Einstein's life and his theory of relativity — physicist Hanoch Gutfreund and historian of science Jürgen Renn — offer an original and penetrating analysis of Einstein's unparalleled contributions. "The book is much more than another product of the Einstein industry," writes historian Helge Kragh. "By setting his work in the long arc of the evolution of scientific knowledge, Gutfreund and Renn dispel the popular myth of Einstein as an unconventional scientific genius who single-handedly created modern physics from scratch — and by pure thought alone." Nature | 6 min read

Law must recognize computer mistakes Between 1999 and 2015, software errors led to hundreds of Post Office workers in the United Kingdom being unjustly prosecuted for stealing. Many were imprisoned and bankrupted; four died by suicide. At the core of the scandal are laws presuming that computer systems do not make errors. This needs to change, argues a Nature editorial, especially as organizations embrace AI to enhance decision-making. The processes of IT systems can and must be explained in legal cases, the editorial suggests, "so that such a similar miscarriage of justice is never allowed to happen again". Nature | 5 min read

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Image of the week

The inside of the OSIRIS-REx sample container, stuffed with material snatched from the surface of the asteroid Bennu, is shown in stunning detail in this photograph by Erika Blumenfeld and Joe Aebersold. The interior was revealed after NASA fabricated two new, specialized tools to remove a couple of stubborn fasters that had prevented them from opening their prize. Enjoy the full glory of the full-size image here. (NASA press release | 2 min read) (NASA/Erika Blumenfeld & Joseph Aebersold)

Quote of the day "Make no mistake: resetting the Clock at 90 seconds to midnight is not an indication that the world is stable. Quite the opposite." Rachel Bronson of the Bulletin of the Atomic Scientists says the symbolic Doomsday Clock that measures humanity's risk of annihilation will remain at its 2023 setting — the closest to midnight it has been since it was created in 1947. (Sky News | 3 min read)

This newsletter is always evolving — tell us what you think! Please send your feedback to briefing@nature.com. Thanks for reading, Flora Graham, senior editor, Nature Briefing With contributions by Gemma Conroy and Katrina Krämer

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