Tag: Publishing

Act now to stop millions of research papers from disappearing

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The Bodleian Libraries at the University of Oxford, UK, one of the United Kingdom’s ‘legal deposit’ libraries. Access has not been possible for more than a year because of a cyber attack.Credit: Christopher Furlong/Getty

Millions of research articles are absent from major digital archives. This worrying finding, which Nature reported on earlier this year, was laid bare in a study by Martin Eve, who studies technology and publishing at Birkbeck, University of London. Eve sampled more than seven million articles with unique digital object identifiers (DOIs), a string of characters used to identify and link to specific publications, such as scholarly articles and official reports. Of these, he found that more than two million were ‘missing’ from archives — that is, they were not preserved in major archives that ensure literature can be found in the future (M. P. Eve J. Libr. Sch. Commun. 12, eP16288; 2024).

Eve, who is also a research developer at Crossref, an organization that registers DOIs, carried out the study in an effort to better understand a problem librarians and archivists already knew about — that although researchers are generating knowledge at an unprecedented rate, it is not necessarily being stored safely for the future. One contributing factor is that not all journals or scholarly societies survive in perpetuity. For example, a 2021 study found that a lack of comprehensive and open archiving meant that 174 open-access journals, covering all major research topics and geographical regions, vanished from the web in the first two decades of this millennium (M. Laakso et al. J. Assoc. Inf. Sci. Technol. 72, 1099–1112; 2021).

Millions of research papers at risk of disappearing from the Internet

A lack of long-term archiving particularly affects institutions in low- and middle-income countries, less-affluent institutions in rich countries and smaller, under-resourced journals worldwide. Yet it’s not clear whether researchers, institutions and governments have fully taken the problem on board. “Preservation is an issue and it’s an issue that everyone flags, but it’s not an easy issue to solve,” says Iryna Kuchma, the open-access programme manager at Electronic Information for Libraries, a non-profit organization in Vilnius that aims to improve people’s access to digital information.

“More and more journals are being established with less and less checks and balances,” says Ginny Hendricks, chief programme officer at Crossref, who is based in London. “You’ve got the big publishers, who are doing a decent job, but then there’s half the journals in the world that are run on a shoestring, and it costs them money to have some kind of service from preservation networks, if they even know about them.”

For this Editorial, Nature asked librarians, archivists, scholars and international organizations for suggestions on how to improve the situation. Researchers, institutions and funders should take note of what they can do to help.

At the heart of the problem is a lack of money, infrastructure and expertise to archive digital resources. “Digital preservation is expensive and also quite difficult,” says Kathleen Shearer, who is based in Montreal, Canada, and is the executive director of the Confederation of Open Access Repositories, a global network of scholarly archives. “It is not just about creating backup copies of things. It is about the active management of content over time in a rapidly evolving technological environment.”

For institutions that can afford it, one solution is to pay a preservation archive to safeguard content. Examples include Portico, based in New York City, and CLOCKSS, based in Stanford, California, both of which count a raft of publishers and libraries as customers.

But archiving is often not prioritized when money is tight, as it generally is for publishers in low-resource settings. “That is more of a challenge because a lot of these journals are small and they’re more at risk because they don’t have their own robust infrastructures for platforms and preservation services themselves,” says Kate Wittenberg, Portico’s managing director.

Another option could be for institutions and funding bodies to include text and data archiving as a requirement in research projects, along with publishing papers. At a minimum, this would mean depositing work in institutional repositories, in cases in which such facilities exist. When they don’t, making archiving mandatory would compel researchers and their funding bodies to think hard and find solutions to meet an archiving requirement.

Making archiving obligatory would also encourage universities that don’t yet operate their own repositories to work towards instituting them. “Universities are one of the most enduring elements of our society,” says Hussein Suleman, a digital libraries scholar at the University of Cape Town in South Africa. “If we adopted this widely, this would be a safeguarding mechanism for the knowledge of our current generation so the future generations can access it.”

A further option is for more countries to implement ‘legal deposit libraries’ — keystone libraries into which authors or publishers are obliged to deposit new work. The concept was originally devised so that at least one institution always had a publicly available copy of every published book, but in some countries it has since been expanded to include research works. Further expanding it would not offer a complete solution, because material archived in legal deposit is not easy to find — but it could be done as an absolute minimum to ensure that copies of scholarship continue to exist if their originators are no longer able to support archiving. More or better coordination “between the big players globally” is also needed, says Hendricks. And global should not only mean Western, she adds.

Increasing people’s access to knowledge and increasing the visibility of new research is rightly a focus for global research-publishing policy. Archiving is core to this — and core to scholarship itself. As Eve told Nature in March: “Our entire epistemology of science and research relies on the chain of footnotes.” If access to this knowledge becomes more restricted, the research that survives will be dominated by institutions, such as those in Europe and the United States, that have the funds to safeguard their research in archives. Action must be taken now to ensure that records of the scholarship undertaken by everyone, everywhere, can exist in perpetuity.

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November 26, 2024
why scientists are joining the rush to Bluesky

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Bluesky has been growing rapidly since 2023.Credit: Matteo Della Torre/NurPhoto/Shutterstock

Researchers are flocking to the social-media platform Bluesky, hoping to recreate the good old days of Twitter.

“All the academics have suddenly migrated to Bluesky,” says Bethan Davies, a glaciologist at Newcastle University, UK. The platform has “absolutely exploded”.

In the two weeks since the US presidential election, the platform has grown from close to 14 million users to nearly 21 million. Bluesky has broad appeal in large part because it looks and feels a lot like X (formerly known as Twitter), which became hugely popular with scientists, who used it to share research findings, collaborate and network. One estimate suggests that at least half a million researchers had Twitter profiles in 2022.

That was the year that billionaire Elon Musk bought the platform. He renamed it X and reduced content moderation, among other changes, prompting some researchers to leave. Since then, pornography, spam, bots and abusive content have increased on X, and community protections have decreased, say researchers.

Bluesky, by contrast, offers users control over the content they see and the people they engage with, through moderation and protections such as blocking and muting features, say researchers. It is also built on an open network, which gives researchers and developers access to its data; X now charges a hefty fee for this kind of access.

Several similar social-media platforms have also sprung up, including Mastodon and Threads, but they haven’t gained the same traction among academics as Bluesky.

Mass migration

Daryll Carlson, a bioacoustics researcher at the University of New Hampshire in Durham, says she noticed the largest influx of users on Bluesky after the US election. Musk has become closely aligned to president-elect Donald Trump. For Carlson, Bluesky offers a space to engage with other scientists, as well as artists, photographers and the general public. “I’d really like it to continue to be a place of joy for me,” she says.

On the platform, users scroll through feeds — curated timelines of posts on specific subjects. Users can like feeds, pin them to their homepage or request to share content on them.

One of the most popular is the Science feed, where scientists and science communicators share content. It’s been liked by more than 14,000 users and gets 400,000 views a day. So far, it has 3,500 contributors, from ecologists and zoologists to quantum physicists, but those numbers are increasing rapidly.

To become a contributor, users need to share evidence of their research credentials with a moderator. Mae Saslaw, a geoscientist at Stony Brook University in New York, vets requests to post on the feed from people in geoscience and has seen an increase from one a week to half a dozen per day. As an early-career researcher, Saslaw has found Bluesky useful for learning about new software, finding interesting papers and applying for jobs.

Safe space

For many researchers, the move to Bluesky has been about gaining back control over what appears in their timelines. Feeds are one example, but the platform also offers options to filter out content such as nudity and spam, or specific phrases, from appearing in their timelines.

Bluesky also offers a feature that users have nicknamed the ‘nuclear block’, which prevents all interaction with blocked accounts — an option no longer available on X. And users can create and subscribe to regularly updated collaborative block lists, such as lists of offensive accounts. If a user subscribes to one of these, no content from those accounts will appear on their timelines.

Clíona Murray, a neuroscientist at Yale University in New Haven, Connecticut, says the protections offered by BlueSky are appealing. Murray was very entrenched in X. She co-founded an organization to diversify neuroscience, called Black in Neuro, which started in part there. But she began to feel that X was not a safe place.

Bluesky offers ‘starter packs’ — user-created custom lists of accounts for new joiners to follow. Murray created one called Blackademics U.K.; she also notes the work of Rudy Fraser, an open-source developer who created a collection of feeds called Blacksky. This pack includes a moderation tool with which users can report content that is racist and anti-Black or contains misogynoir — expressing hatred particularly against Black women — and filter them out.

But as Bluesky grows, the problems that plague X could come to haunt it, too, say researchers. “There’s definitely a risk that bad-faith actors will move in; bots will move in,” says Davies.

“With any huge wave of growth, there’s going to be a wave of spam and scam as well,” says Emily Liu, who manages growth, communications and partnerships at Bluesky in San Francisco, California. “We’ve scaled up our trust and safety team; hired more moderators to help combat all of this.”

Leave or stay

Some researchers, such as Axel Bruns, a digital-media researcher at Queensland University of Technology in Brisbane, Australia, are keeping their Twitter accounts to avoid losing them to impersonators. Others have shut their accounts down.

Madhukar Pai, a tuberculosis researcher at McGill University in Montreal, Canada, says he has lost some 1,000 followers in the exodus (he still has 98,000). But he is reluctant to leave. “If good experts quit X, who will offer evidence-based input on X?”

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November 21, 2024
Leading Nature Index science cities in biological sciences: collaboration powers US research

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In the biological sciences, the United States has the leading Nature Index science cities. But although New York and Boston continue to dominate the top spots, 2023 has brought a significant shift in other parts of the rankings. Beijing’s impressive growth in the subject, shown by an 18.8% year-on-year increase in adjusted Share, alongside a 10.1% decline in adjusted Share for the San Francisco Bay Area, has propelled the Chinese capital into the top three. Further down the list, the European research centres of London and Paris have maintained their 7th and 8th positions for another year, even after small declines in adjusted Share.

Part of Beijing’s new-found prominence can be attributed to its leading research institution, the Chinese Academy of Sciences, being home to research labs such as the State Key Laboratory of Plant Genomics and the National Key Lab of Molecular and Developmental Biology. These have helped the city secure a 52% increase in its adjusted Share from 2019 to 2023. Although Beijing holds a comfortable lead in biological-sciences research within China, it is not the only city experiencing significant growth. Guangzhou, in southern China, and the central city of Wuhan — buoyed by their expanding research and development sites — have made considerable year-on-year gains in adjusted Share for biological sciences, rising around 4 and 11 positions, respectively, in the ranking for the subject. If their growth continues, it is likely that they will enter the top 10 in the coming years.

Despite a decrease in its adjusted Share (−7.6%), New York’s extensive network of medical centres, academic institutions and biotechnology companies has helped the city to maintain its global lead. It also still contributes 12.6% of the total US Share in the biological sciences. One of the most dynamic and influential collaborations in the city is the partnership between Columbia University and New York University, which has driven advances in areas such neuroscience, cancer and regenerative science. This stands as one of the main pillars of New York’s leading institutional network, with a bilateral collaboration score (BCS) of 17.39. These two universities also form several strong connections with other local institutions, such as that between Memorial Sloan Kettering Cancer Centre and Columbia University (BCS 12.44), and Columbia University and Yale University (BCS 8.04).

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

When it comes to the leading cities’ top institutional pairings in biological sciences, Boston’s collaboration between Harvard University and the Massachusetts Institute of Technology is the powerhouse, clearly outstripping other partnerships among the leading five cities. The San Francisco Bay Area has the second-most impactful pairing of the five, a collaboration between Stanford Health Care and Stanford University. Despite Beijing’s Chinese Academy of Sciences being the leading institution in the country for biological sciences in the Nature Index, it is absent from the city’s top pairing, which features a collaboration between Peking University and Tsinghua University.

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

This article is part of Nature Index 2024 Science cities, a supplement produced with financial support from the Beijing Municipal Science & Technology Commission, Administrative Commission of Zhongguancun Science Park. Nature maintains full independence in all editorial decisions related to the content. For more information about Nature Index, see the homepage.

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November 20, 2024
US institutions power country’s growth

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Due in part to strong institutional collaborations and industry presence, the United States has maintained its lead in health sciences, with the Boston metropolitan area (MA) taking the top spot with a Share of 676.43. However, the Massachusetts capital — which is home to numerous biotech companies, leading universities, and more than 20 hospitals — is the only US city within the top 10 to have recorded an increase in adjusted Share between 2022 and 2023 (+6.6%). The New York MA and Baltimore–Washington, the 2nd and 3rd-ranked cities, respectively, have both recorded minor declines in their adjusted Share since 2022, while the San Francisco Bay Area, in 5th place after the London MA, has recorded a decrease in adjusted Share of 13.2% between 2022 and 2023.

China is one to watch in the health-sciences space. Although Beijing, China’s leading health-care city, in 6th place, is still more than 430 Share points away from the Boston MA, it has recorded an increase in Share of 17.6% between 2022 and 2023.

Copenhagen is one of the fastest rising cities in health sciences, increasing its adjusted Share by 33.9% between 2022 and 2023. Denmark boasts a remarkably large health-care sector for its relatively small size, which will put it in good stead for continued growth in the subject.

Much of the Boston MA’s strength in the health sciences comes from the collaboration between the Massachusetts Institute of Technology (MIT) and Harvard University — by far the city’s most significant partnership in the subject. Harvard is a pillar of health-science research in the city and is involved in its four leading institutional partnerships in the health sciences.

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

The Harvard–MIT match up also significantly outperforms other leading cities’ top collaborations in the subject, with a BCS of 139.24. Baltimore–Washington’s top institutional partnership, between the Johns Hopkins University and Johns Hopkins Health System Corporation (BCS 87.45), is the second-strongest pairing.

London’s leading research collaboration, between University College London and the University College London Hospitals NHS Foundation Trust (BCS 22.81) is almost equal to the New York MA’s Columbia University and New York–Presbyterian Hospital pairing (BCS 22.37).

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

This article is part of Nature Index 2024 Science cities, a supplement produced with financial support from the Beijing Municipal Science & Technology Commission, Administrative Commission of Zhongguancun Science Park. Nature maintains full independence in all editorial decisions related to the content. For more information about Nature Index, see the homepage.

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November 20, 2024
China positions for clean sweep

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Although Chinese cities hold the top eight spots in chemistry in this year’s science cities rankings, up from the top seven last year, there has been a considerable reshuffling in positions. Nature Index data show that although Beijing and Shanghai have maintained a clear lead, the growth in chemistry output from some of China’s smaller cities could mark them as future contenders in this field. Hangzhou, located southwest of Shanghai in Zhejiang province, jumped from 11th in 2022 to 7th in 2023, while the central city of Wuhan went from 7th to 4th after growing its adjusted Share by almost 12%.

While strengthening in all three other natural sciences, the southern city of Guangzhou has seen a negative change in its year-on-year adjusted Share (−7.4%) in chemistry, moving the city from 4th to 6th on the leading cities list for the subject. However, chemical-science investments on the horizon for Guangdong province, including a US$10-billion project to build an integrated chemicals site in the city of Zhanjiang, could have positive knock-on effects for Guangzhou, the provincial capital, in the near future.

Tokyo has seen a slow decline in its Science Cities chemistry placing over the past four years, falling from 4th in 2020 to 9th in 2023. Just behind this is New York, which had a 6.5% fall in its adjusted Share from 2022 to 2023. It is likely these two cities will face continued pressure from the growth of regional Chinese cities in the coming years given that the Nature Index is a zero-sum game — gains in Share by some cities are inevitably offset by losses elsewhere.

This trend is confirmed further in the rising cities list for chemistry, in which Chinese locations hold every position of the top 10 for change in Share from 2019 to 2023. Although Shenzhen has achieved the greatest percentage increase of these 10 cities in the past five years (89.5%), it is Beijing, with its much larger research base, that has had the greatest growth in adjusted Share (up 254.93). This is not as large as Beijing’s growth in other Nature Index subjects, but it has helped China’s capital maintain its lead in chemistry, with its 2023 Share of 1,714.88 much higher than that of second-place Shanghai (1,059.83).

Contributing to Beijing’s dominance in chemistry is the collaboration between Peking University and the Chinese Academy of Sciences’ (CAS) Institute of Chemistry, the leading institutional partnership in the city for the field. Although strong partnerships have helped power Beijing into top position, Hefei’s leading collaboration is notable, as it suggests the city — fifth globally for chemistry — has the institutional power required for long-term growth in this field.

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

Within Beijing, the Institute of Chemistry, CAS and Peking University are also involved in productive partnerships with the University of Chinese Academy of Sciences, according to a network map showing the bilateral research connections between the city’s leading five institutions. Tsinghua University, which boasts a high individual Share in chemistry, has a lower bilateral collaboration score with other leading institutions in the city.

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

This article is part of Nature Index 2024 Science cities, a supplement produced with financial support from the Beijing Municipal Science & Technology Commission, Administrative Commission of Zhongguancun Science Park. Nature maintains full independence in all editorial decisions related to the content. For more information about Nature Index, see the homepage.

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November 20, 2024
regional centres drive China’s progress

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A strengthening research climate has seen Chinese cities rise to take the top three spots in this year’s leading science cities for physical sciences, as the eastern city of Nanjing climbs above both Boston and New York for the first time. Nanjing, China’s 13th largest city by population size according to the country’s 2020 census, punches well above its weight in the natural sciences, with the city’s main academic hub, Nanjing University, now ranked 5th globally for its physical sciences Share in the Nature Index.

However, it is Beijing — home to facilities such as the Beijing Electron–Positron Collider II and the High Energy Photon Source, due to be completed at the end of 2025 — which has once again extended its lead in the field. It has a Share that is more than double that of second-place Shanghai and around three times greater than the US leader, Boston. From 2019 to 2023, the adjusted Share of China’s capital city has grown by around 35%, and now accounts for 19.5% of China’s total physical-science output.

As China’s current five-year development plan prioritizes areas such as space exploration, quantum technologies and artificial intelligence, it’s unsurprising that the physical-research outputs of several Chinese cities have significantly increased in the past year, with the country now holding six of the top ten leading city spots. Out of the five fastest-rising cities in the subject, Hangzhou, located to the southwest of Shanghai, was the top rising city for percentage change, its physical-science research growing 135.2% in the past five years. This was probably bolstered by functional materials and nanotechnology research at Zhejiang University, which is now ranked 7th globally for physical-science output among academic institutions.

Beijing’s growth is partly a result of strengthening collaborations between research institutions and universities within the city. Two strong collaborations lead Beijing’s research cluster: the University of Chinese Academy of Sciences and the Institute of Physics, CAS; and Peking University and Tsinghua University.

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

The partnership between the University of Chinese Academy of Sciences and Institute of Physics, CAS, also scores highly when compared with collaborations in other leading cities for physical sciences. It has a higher bilateral collaboration score (BCS), of 105.82, than the long-established partnership between Harvard University and the Massachusetts Institute of Technology (MIT), both located in the Boston metropolitan area (MA) in Massachusetts (BCS 97.04).

Boston and the New York City MA have often had relatively similar Shares for their physical-science output in the Nature Index. However, this year has brought a shift, with New York experiencing a 9.5% decrease in its adjusted Share, causing it to fall below its US counterpart on the leading cities list. The strong ties between Harvard and MIT might have contributed to Boston’s slight increase in its year-on-year Share, with the collaboration far exceeding that of the leading partnership in the New York MA, between the Institute for Advanced Study and Princeton University.

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

This article is part of Nature Index 2024 Science cities, a supplement produced with financial support from the Beijing Municipal Science & Technology Commission, Administrative Commission of Zhongguancun Science Park. Nature maintains full independence in all editorial decisions related to the content. For more information about Nature Index, see the homepage.

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November 20, 2024
Half of the top 20 science cities are now in China — and regional city growth is the key

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China’s cities are playing a key role in the development of specialist technologies such as solar energy.Credit: Yaorusheng/Getty

Many of the patterns evident in the data for this year’s Nature Index Science Cities supplement will be familiar to watchers of global science trends over the past decade. China’s research output in the journals tracked by the Nature Index continues to grow strongly, demonstrated by Beijing extending its lead at the summit of the science cities ranking to almost double the Share of the second-placed city. The fact that this second place is now taken by Shanghai, pushing New York into third, only reinforces this trajectory.

Perhaps a more interesting development in the science cities data this year is the clear emergence of China’s provincial capitals. From Chengdu in the west, to Hefei in the east, these cities — lesser known in the West — are now rubbing shoulders in the top 30 with long-established scientific centres in Europe and North America.

Nature Index 2024 Science cities

The rise of these locations as globally competitive centres for research is as much due to economics and politics as it is science, as China seeks to spread the impact of its knowledge and innovation far and wide. Many of these rapidly developing cities are playing a specialist role in key technology areas such as electric vehicles and solar energy. And their local goals are very much aligned to national strategies to bolster the country’s economic self-sufficiency, such as ‘Made in China 2025’, a policy designed to shift the country towards knowledge-driven high-tech industries.

Even in the health sciences, an area where Chinese cities still lag behind their Western counterparts, there is evident progress. Within a decade, there is every chance that the leading Science Cities in this field — currently dominated by the dense academic–health-care–industry networks built up over many years in areas such as Boston or London — might be in China, too.

We are pleased to acknowledge the financial support of the Beijing Municipal Science & Technology Commission, Administrative Commission of Zhongguancun Science Park in producing this supplement. As always, Nature retains sole responsibility for all editorial content.

This article is part of Nature Index 2024 Science cities, a supplement produced with financial support from the Beijing Municipal Science & Technology Commission, Administrative Commission of Zhongguancun Science Park. Nature maintains full independence in all editorial decisions related to the content. For more information about Nature Index, see the homepage.

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November 20, 2024
Research output gathers pace in China

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With its continued focus on sustainability and ecological protection, China is cementing itself as a leader in Earth and environmental sciences. Beijing, Nanjing and Guangzhou, the leading three cities in the subject, respectively, have all recorded increases in adjusted Share between 2022 and 2023. Wuhan’s momentum is particularly strong — the city’s adjusted Share in the subject rose 16.24%, propelling it from 8th place in 2022 to 4th in 2023.

The four US cities in the top 10 have lost ground, each recording a decrease in their adjusted Share between 2022 and 2023. The Los Angeles metropolitan area, in 9th place, had an almost 20% decline in adjusted Share in 2023.

Mirroring a broader trend across all subjects in the Nature Index, the movement of smaller Chinese cities stands out this year. Nanjing, China’s 13th largest city by population size, contributes around 11.6% of the country’s Earth and environmental science research in the index. The city has retained 2nd place in the subject for the past four years.

The regional centres of Guangzhou and Qingdao, known for their water purification and renewable-energy initiatives, have also been improving their outputs, with increases of 106.3% and 179.8%, respectively, in adjusted Share between 2019 and 2023.

In 2019, Beijing’s Share in Earth and environmental sciences was more than double that of Baltimore–Washington, in 2nd place. In 2023, its Share has grown to almost five times that of Baltimore–Washington, which has fallen to 6th place in the subject. Several institutional partnerships have helped to drive a 60.3% increase in Beijing’s adjusted Share over the past five years, positioning it well ahead of its competitors. Among these are collaborations between the University of Chinese Academy of Sciences (UCAS), the Research Center for Eco-Environmental Sciences, Tsinghua University and Peking University.

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

With a bilateral collaboration score (BCS) of 78.71, the partnership between UCAS and the Research Centre for Eco-Environmental Sciences significantly outperforms other leading academic pairings in the top five cities for the subject. The collaborative efforts of the Shanghai Municipal Bureau of Ecology and Environment and Fudan University, in Shanghai, form the next strongest partnership (BCS 18.75). This, paired with Shanghai’s 94.9% increase in adjusted Share from 2019 to 2023, suggests that the city will continue to develop its capacity in the subject.

Source: Nature Index; Data analysis: Aayush Kagathra; Data visualization: Tanner Maxwell and Simon Baker

This article is part of Nature Index 2024 Science cities, a supplement produced with financial support from the Beijing Municipal Science & Technology Commission, Administrative Commission of Zhongguancun Science Park. Nature maintains full independence in all editorial decisions related to the content. For more information about Nature Index, see the homepage.

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November 20, 2024
AI-generated images threaten science — here’s how researchers hope to spot them

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All of these images were generated by AI.Credit: Proofig AI, 2024

From scientists manipulating figures to the mass production of fake papers by paper mills, problematic manuscripts have long plagued the scholarly literature. Science sleuths work tirelessly to uncover this misconduct to correct the scientific record. But their job is becoming harder, owing to the introduction of a powerful new tool for fraudsters: generative artificial intelligence (AI).

“Generative AI is evolving very fast,” says Jana Christopher, an image-integrity analyst at FEBS Press in Heidelberg, Germany. “The people that work in my field — image integrity and publication ethics — are getting increasingly worried about the possibilities that it offers.”

AI-generated images and video are here: how could they shape research?

The ease with which generative-AI tools can create text, images and data raises fears of an increasingly untrustworthy scientific literature awash with fake figures, manuscripts and conclusions that are difficult for humans to spot. Already, an arms race is emerging as integrity specialists, publishers and technology companies race to develop AI tools that can assist in rapidly detecting deceptive, AI-generated elements of papers.

“It’s a scary development,” Christopher says. “But there are also clever people and good structural changes that are being suggested.”

Research-integrity specialists say that, although AI-generated text is already permitted by many journals under some circumstances, the use of such tools for creating images or other data is less likely to be viewed as acceptable. “In the near future, we may be okay with AI-generated text,” says Elisabeth Bik, an image-forensics specialist and consultant in San Francisco, California. “But I draw the line at generating data.”

What ChatGPT and generative AI mean for science

Bik, Christopher and others suspect that data, including images, fabricated using generative AI are already widespread in the literature, and that paper mills are taking advantage of AI tools to produce manuscripts en masse (see ‘Quiz: can you spot AI fakes?’).

Under the radar

Pinpointing AI-produced images poses a huge challenge: they are often almost impossible to distinguish from real ones, at least with the naked eye. “We get the feeling that we encounter AI-generated images every day,” Christopher says. “But as long as you can’t prove it, there’s really very little you can do.”

There are some clear instances of generative-AI use in scientific images, such as the now-infamous figure of a rat with absurdly large genitalia and nonsensical labels, created using the image tool Midjourney. The graphic, published by a journal in February, sparked a social-media storm and was retracted days later.

Credit: Proofig (generated images)

Most cases aren’t so obvious. Figures fabricated with Adobe Photoshop or similar tools before the rise of generative-AI — especially in molecular and cell biology — often contain telltale signs that sleuths can spot, such as identical backgrounds or an unusual absence of smears or stains. AI-made figures often lack such signs. “I see tonnes of papers where I think, these Western blots do not look real — but there’s no smoking gun,” Bik says. “You can only say they just look weird, and that of course isn’t enough evidence to write to an editor.”

But signs suggest that AI-made figures are appearing in published manuscripts. Text written using tools such as ChatGPT is on the rise in papers, given away by standard chatbot phrases that authors forget to remove and telltale words that AI models tend to use. “So we have to assume that it’s also happening for data and for images,” says Bik.

Another clue that fraudsters are using sophisticated image tools is that most of the issues that sleuths are currently detecting are in papers that are several years old. “In the past couple of years, we’ve seen fewer and fewer image problems,” Bik says. “I think most folks who have gotten caught doing image manipulation have moved on to creating cleaner images.”

How to create images

Creating clean images using generative AI is not difficult. Kevin Patrick, a scientific-image sleuth known as Cheshire on social media, has demonstrated just how easy it can be and posted his results on X. Using Photoshop’s AI tool Generative Fill, Patrick created realistic images — that could feasibly appear in scientific papers — of tumours, cell cultures, Western blots and more. Most of the images took less than a minute to produce (see ‘Generating bogus science’).

“If I can do this, certainly the people who are getting paid to generate fake data are going to be doing this,” Patrick says. “There’s probably a whole bunch of other data that could be generated with tools like this.”

Some publishers say that they have found evidence of AI-generated content in published studies. These include PLoS, which has been alerted to suspicious content and found evidence of AI-generated text and data in papers and submissions through internal investigations, says Renée Hoch, managing editor of PLoS’s publication-ethics team in San Francisco, California. (Hoch notes that AI use is not forbidden in PLoS journals, and that its AI policy focuses on author accountability and transparent disclosures.)

Credit: Kevin Patrick

Other tools might also provide opportunities for people wishing to create fake content. Last month, researchers published¹ a generative-AI model for creating high-resolution microscopy images — and some integrity specialists have raised concerned about the work. “This technology can easily be used by people with bad intentions to quickly generate hundreds or thousands of fake images,” Bik says.

Yoav Shechtman at the Technion–Israel Institute of Technology in Haifa, the tool’s creator, says that the tool is helpful for producing training data for models because high-resolution microscopy images are difficult to obtain. But, he adds, it isn’t useful for generating fake because users have little control over the output. Existing imaging software such as Photoshop is more useful for manipulating figures, he suggests.

Weeding out fakes

Human eyes might not be able to catch generative AI-made images, but AI might (see ‘AI images are hard to spot’).

The makers behind tools such as Imagetwin and Proofig, which use AI to detect integrity issues in scientific figures, are expanding their software to weed out images created by generative AI. Because such images are so difficult to detect, both companies are creating their own databases of generative-AI images to train their algorithms.

AI models fed AI-generated data quickly spew nonsense

Proofig has already released a feature in its tool for detecting AI-generated microscopy images. Company co-founder Dror Kolodkin-Gal in Rehovot, Israel, says that, when tested on thousands of AI-generated and real images from papers, the algorithm identified AI images 98% of the time and had a 0.02% false-positive rate. Dror adds that the team is now working on trying to understand what, exactly, their algorithm detects.

“I have great hopes for these tools,” Christopher says. But she notes that their outputs will always need to be assessed by an expert who can verify the issues they flag. Christopher hasn’t yet seen evidence that AI image-detection software are reliable (Proofig’s internal evaluation has not been published). These tools are “limited, but certainly very useful, as it means we can scale up our effort of screening submissions,” she adds.

Source: Proofig quiz

Multiple publishers and research institutions already use Proofig and Imagetwin. The Science journals, for example, use Proofig to scan for image-integrity issues. According to Meagan Phelan, communications director for Science in Washington DC, the tool has not yet uncovered any AI-generated images.

Springer Nature, which publishes Nature, is developing its own detection tools for text and images, called Geppetto and SnapShot, which flag irregularities that are then assessed by humans. (The Nature news team is editorially independent of its publisher.)

Fraudsters, beware

Publishing groups are also taking steps to address AI-made images. A spokesperson for the International Association of Scientific, Technical and Medical (STM) Publishers in Oxford, UK, said that it is taking the problem “very seriously” and pointed to initiatives such as United2Act and the STM Integrity Hub, which are tackling paper mills and other scientific-integrity issues.

ChatGPT one year on: who is using it, how and why?

Christopher, who is chairing an STM working group on image alterations and duplications, says that there is a growing realization that developing ways to verify raw data — such as labelling images taken from microscopes with invisible watermarks akin to those being used in AI-generated text — might be the way forward. This will require new technologies and new standards for equipment manufacturers, she adds.

Patrick and others are worried that publishers will not act quickly enough to address the threat. “We’re concerned that this will just be another generation of problems in the literature that they don’t get to until it’s too late,” he says.

Still, some are optimistic that the AI-generated content that enters papers today will be discovered in the future.

“I have full confidence that technology will improve to the point that it can detect the stuff that’s getting done today — because at some point, it will be viewed as relatively crude,” Patrick says. “Fraudsters shouldn’t sleep well at night. They could fool today’s process, but I don’t think they’ll be able to fool the process forever.”

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November 5, 2024
Is there a ‘Goldilocks zone’ for paper length?

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An unusually long and complex research paper has caught the attention of the scientific community, sparking questions about the ideal length of a paper. The study, by computational biologist Manolis Kellis and his colleagues, was published in Nature¹ in July. Spanning 35 pages, it contains more than 20,000 words, and has 16 figures — or 61, if those in the Supplementary information are included. It describes changes in the genes, cellular pathways and cell types of people with Alzheimer’s disease across six regions of the brain, and provides a detailed atlas of gene expression.

When Kellis, who runs a computational-biology laboratory at the Massachusetts Institute of Technology (MIT) in Cambridge, shared the paper on X (formerly Twitter), the size of it seemed to divide his peers. Some were complimentary: “It must have taken a lot of effort and resources to get this done, so all in all, it is a great paper,” one response read. Others were concerned about its usefulness. “How can anyone read this article, let alone review and critique the work?” asked another user.

An analysis of paper characteristics across scientific fields², published in 2023, suggests that this study is an outlier in the medical and health sciences, where papers typically hover around ten pages in length. However, it is not so unusual when compared with papers in subject areas such as mathematics, law or the humanities — all of which often exceed 20 pages.

Kellis’s work raises the question of how accessible research papers should be, and how readers in and beyond academia are expected to consume them. For example, is it better to publish large data sets alongside long and dense papers, to keep the information contained in one place? Or should researchers home in on specific topics and publish their results across several papers?

Alireza Haghighi, a geneticist at Harvard Medical School in Boston, Massachusetts, says that there is value in the former approach, particularly at a time when data sets are becoming increasingly large. “Although focus has traditionally been important in publications, we must acknowledge the complexity of new methods and the huge volumes of data generated today,” says Haghighi. “Not all papers can or should be understood in one hour.”

Does size matter?

Papers that provide broad, detailed overviews and extensive data sets — sometimes called ‘atlases’, in the omics fields of genomics, transcriptomics and proteomics — allow researchers to see the big picture, says Haghighi. They enable readers to “identify connections across different areas, and generate new hypotheses”, he explains, and adds that he sees them as drivers of innovation that can guide large-scale, integrative research initiatives better than a more focused paper might.

Responding to the discussion on X, Kellis said he understands that some people will be overwhelmed by his lab’s paper. He likened the work to “a good book with many chapters and many pages”, and said that “each paragraph, parenthesis, panel, supplementary figure, can hide potential hints and secrets that the authors themselves may have missed”. Kellis also suggested that for those who were overwhelmed by the results, tools such as the ChatGPT Consensus app, which is regarded as an academic search engine, could be useful for summarizing some of the paper’s findings.

2024 Research Leaders

Li-Huei Tsai, a neuroscientist at MIT and a corresponding author on the paper, told Nature Index that she is proud of the work, which has “produced important insights into genomic underpinnings of Alzheimer’s vulnerability and resilience”. Kellis did not respond to Nature Index’s request for comment.

Researchers who spoke to Nature Index flagged a number of issues with big, data-dense articles. Luke Dabin, an epigeneticist at the Indiana University School of Medicine in Indianapolis, is a “huge fan” of big data sets and atlas papers, because they have the potential to be a hotbed for generating hypotheses and can inform the design of future experiments. But Dabin says that such papers can sometimes be difficult to interpret — even by scientists working in the same field — and can have quality-control issues. “The Kellis paper has 475 figure panels and is difficult for me to digest, let alone someone with no training or experience in single-cell omics,” Dabin says. Haghighi agrees that accuracy can become a problem in large papers. “We should appreciate that atlas maps are more prone to inaccuracies due to their scope and complexity,” he says.

Such papers can also be resource-heavy for journal editors to publish. It took almost two years for Kellis’s paper to progress from acceptance to publication, although it might not have been under review the entire time. A spokesperson for Nature noted that “the length of the review process for papers submitted to Nature varies considerably from manuscript to manuscript”, and said that its primary focus is “to ensure that a rigorous peer-review process takes place”. (Nature Index’s news and supplement content is editorially independent of its publisher, Springer Nature.)

On X, Kellis noted that “it was a Herculean task by the reviewers and editors, as it was of course for the authors, to go through every figure, every panel, and every result” as part of the publishing process.

A case for brevity?

Some researchers argue that there is simply not enough time to read such long and dense papers. “The readership on most academic papers is low anyway, so writing a long paper is just inviting it not to be read even more,” says Daniel Price, an astrophysicist at Monash University in Melbourne, Australia, and former editor-in-chief of the journal Publications of the Astronomical Society of Australia, which publishes research on data-heavy topics such as modelling and computational astronomy.

Price says it’s unlikely that anyone has ever read the entirety of one of his monster astrophysics papers³, which clocks in at 82 pages and has 57 figures. “It’s definitely too long,” he says of the paper, admitting that it could easily have been 60 pages instead. The problem with going long, he adds, is that it’s “undisciplined” and compromises the ability to self-edit.

Haghighi says some improvements could be made to long, data-heavy papers. He suggests that publishers standardize the way such papers are formatted and published by introducing new editorial guidelines and implementing “a dynamic, continuous review process” that allows authors to update their work regularly over time, after publication. “I appreciate that this might not be easy,” says Haghighi, but “it would make the review process more effective and consistent and make it easier for the scientific community”.

Formatting guidelines at most major journals tend to favour shorter articles with fewer figures. Nature, for instance, suggests the typical length of biological, clinical and social sciences papers should not normally exceed 8 pages, or 4,300 words, and 5–6 figures. That said, it does not enforce specific limits, and instead leaves this up to the editor’s discretion.

In astrophysics, a field that is characterized by vast data sets that are often analysed by large, international teams, there are some examples of how a research finding can be broken down into more digestible parts. For instance, after the first image of a black hole was captured by the Event Horizon Telescope — a global network of radio telescopes run by a group of more than 300 scientists — the team published 6 papers in a special edition of The Astrophysical Journal Letters. Each paper presented an aspect of the research, looking at methodology, specific features of the black hole and the image itself.

Price thinks paper series such as this are “definitely a better idea” than one long paper, and adds that there is a lot to be said for concise papers. He points to a 2016 paper published by the LIGO Scientific Collaboration⁴ — a conglomerate of more than 100 institutions collaborating in the search for gravitational waves — after its seminal detection of gravitational waves using instruments in Washington and Louisiana. “It’s eight pages [ten, including references] and it revolutionized astrophysics,” he says.

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November 5, 2024