Science 1.07.2022_downmagaz.net

EDITORIAL Science, health, and truth T he past 2 years have been a strange and dif- truth. He explains that the endeavor is founded on two ficult time for the world. The COVID-19 pandemic arguments: The truth is based on what is known so has brought illness, hospitalization, and death near far and the truth applies to everyone. Rauch argues to many people. In the United States, people are that this has produced a process for certifying knowl- divided not only on what they should do but also edge—a public system for adjudicating differences of on what constitutes the facts. Many are seemingly belief and perception and for developing shared and in an alternative world, driven by disinformation, warranted conclusions about truth. This system pro- conspiracy theories, and anti-science beliefs. How can vides three public goods: knowledge (distinguishing William L. Roper is a professor of health and medical leaders do their jobs while trying to reality from nonreality), freedom (encouraging rather medicine and public health at the cope with a polarized public? They must be more effec- than repressing human autonomy, creativity, and em- University of North Carolina–Chapel Hill, tive in explaining and persuading the public on matters powerment), and peace (rewarding social conciliation, Chapel Hill, NC, USA. [email protected] of science and health. This will require better clarifica- maximizing the number of disagreements that are re- tion of two things to the public—the roles of science solvable, and compartmentalizing and marginalizing and politics in public policy decisions, and the means disagreements that cannot be resolved). by which scientific truth is established and updated. Given that truth is based on what is known so far, it There is a continuing strand of argument from is always provisional. We likely will know more tomor- many in the scientific community row than today, and we will then that “we ought to get politics out have to revise our conclusions. of public health.” And many poli- “How can health That is just the scientific method ticians have said that scientists at work. Though science and poli- are not the ones to make public and medical tics have separate roles, once this policy decisions related to public system “gets the facts straight,” health or other issues. The reality leaders do their scientists and political leaders can is that both science and politics jobs while trying work constructively together for are essential for public health to to cope with a the common good. work well. Scientists inform pub- polarized public?” lic understanding of the patterns of This knowledge-certifying sys- health and illness in populations, tem is under concerted attack especially when epidemics and pan- today, most notably in polar- demics strike. And politics—the way ized political conflicts, including decisions are made in a democratic about masks and vaccines, climate change, and gun violence. Restor- society—is vital for acting on the in- ing confidence in messages regard- formation and insights that the sci- ing science for the public good entific community provides for the benefit of everyone. will be challenging, but it can only be done if there is In addition to clarifying the separate roles of sci- an effort to explain, defend, and reinforce this public ence and politics, society needs to understand better system for shepherding new knowledge. This needs to how scientific truth is established and updated. It is include widespread discussions across the scientific based on verified and reproducible facts. The scientific community and in the public at large, leading to a method of gathering data, debating various formula- broad recommitment to the scientific method. tions of the information, and arriving at consensus The challenges of communicating messages about understandings of what is “true” about a particular science, health, and truth are among the often-men- matter has been the bedrock for establishing scientific tioned reasons for the fatigue and discouragement truth for centuries. But in the past few years, politi- that public health and medical leaders face today. And cal leaders, media personalities, and ordinary citizens that same frustration is transferred to those who seek have proclaimed their own “alternative facts,” dis- to engage the wider public with these messages. paraging the idea that anyone should question their Overcoming these challenges will surely be difficult, “facts” and theories. but with concerted effort it can be done, as it has be- In his recent book, The Constitution of Knowledge: fore—for example, in efforts to promote widespread A Defense of Truth, Jonathan Rauch clearly and con- childhood immunizations. And this requires a never- vincingly describes and defends the Enlightenment- ending commitment, as we are learning every day. PHOTO: UNC HEALTH born process of weighing evidence and committing to –William L. Roper 10.1126/science.add6477 SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 7

NEWS “ ”The already broken healthcare system is going to collapse under this decision. … Pregnancy is too dangerous. Tweet by Jocelyn J. Fitzgerald, a urogynecologist at the University of Pittsburgh, on the U.S. Supreme Court’s reversal last week of its Roe v. Wade abortion decision. I N B R I E F Edited by Shraddha Chakradhar Launch of NASA’s Psyche delayed PHOTO: AARON CHOWN/PA IMAGES/GETTY IMAGES The Tower of London was lit up to mark World Polio Day in October 2021. P L A N E TA RY S C I E N C E | Psyche, the PUBLIC HEALTH $967 million NASA mission to explore the strange metal asteroid of the same name, Poliovirus in U.K. sewage raises alarm will not launch this fall because of delays in testing its navigation software, the agency O fficials in the United Kingdom declared a “national incident” last announced last week. The mission, devel- week after poliovirus was detected in samples taken between oped by the Jet Propulsion Laboratory, is February and June from one of London’s main sewage treatment likely to launch next year, but could also slip plants. The source is still a mystery, but it is likely that someone to 2024; either date would see its arrival at from outside the United Kingdom who recently received the oral the main-belt asteroid, which was set for polio vaccine—which uses a live, but weakened, poliovirus—is 2026, fall back by 3 years or more. An inde- shedding the pathogen in their feces. No polio cases have been found pendent panel will review what went wrong and such sewage detections are not unusual—signs of the virus usu- and decide whether the mission will ally disappear quickly. This time, however, it continued to appear over continue—although cancellation is unlikely. many months, and several closely related versions of the virus were in The delay should not limit the science recent samples. The genetic changes suggest the virus is evolving, a sign conducted by the spacecraft, which aims to it may be spreading in a small number of people. The United Kingdom’s investigate whether the asteroid is the left- generally high polio vaccine coverage should limit further transmis- over core of an early planetary embryo. sion, infectious disease experts say—but they worry lower rates in some London communities might leave children there vulnerable. NCI to study cancer blood tests 8 1 JULY 2022 • VOL 377 ISSUE 6601 MEDICINE | The National Cancer Institute (NCI) plans to evaluate the growing num- ber of tests from companies that screen for multiple cancers by detecting traces of tumor DNA and proteins in a person’s blood. Last month, NCI advisers endorsed a $75 million, 4-year pilot study that will enroll 24,000 seemingly cancer-free volun- teers starting in 2023 or 2024. Some would only get standard cancer screening, such as mammograms, whereas others would also receive one of the experimental blood tests. If the pilot study goes well, NCI expects to launch a bigger trial, with perhaps 300,000 participants ages 45 to 70, that would last 7 to 8 years. Such a long-term study could reveal whether these tests, which can return false positives and lead to un- necessary procedures on tiny, slow-growing tumors, ultimately save lives. Austria rescinds vaccine mandate COVID 19 | Austria, one of the first countries in Europe to pass a COVID-19 vaccine mandate, officially rescinded the requirement last week. The law, passed in November 2021 with support across the political spectrum, required all adults to be vaccinated by February or face fines of up to €3600 ($3800). However, the government never enforced it. By March, science.org SCIENCE

The Citadel ruins in Bears Ears National Monument will get tribal oversight. C O N S E R VAT I O N Native tribes and United States enter park management deal CREDITS: (PHOTO BOB WICK/BUREAU OF LAND MANAGEMENT/CC BY 2.0; (DATA HOUSE OF REPRESENTATIVES APPROPRIATIONS COMMITTEE T he Bureau of Land Management (BLM) and the U.S. Forest comanagement agreement is meant to incorporate the traditional Service signed a first-of-its-kind agreement last week to knowledge and expertise of the tribes—the Hopi, Navajo Nation, comanage Bears Ears National Monument in southeastern Ute Mountain Ute Tribe, Ute Indian Tribe of the Uintah and Ouray Utah with five Native American tribes. The five tribes have Reservation, and the Pueblo of Zuni—and center their voices in long wanted to help oversee this culturally significant monu- land use decisions. The Indigenous tribes will now submit a draft ment, a 550,000-hectare expanse pocked by burnt-sienna buttes, land management plan to BLM in the coming weeks, which could 1000-year-old Indigenous dwellings, and ceremonial sites. The then take up to 18 months to finalize. the government said the Omicron variant, of a larger agency effort to curb high rates FDA order, which the company asserts is which evades vaccine protection better of teen vaping and other public health crises the product of political maneuvering. than previous versions of SARS-CoV-2, fueled by nicotine use. Earlier last week, for meant the mandate was no longer justi- instance, FDA announced it would be man- The Lancet tops medical citations fied. Last week, Austria’s health minister dating lower nicotine levels in traditional said the law had failed to persuade the cigarettes. A federal appeals court granted PUBLISHING | The title of most cited vaccine-hesitant and had been more Juul time to file a formal challenge to the medical journal has changed hands for divisive than helpful. He said the the first time in 45 years. In 2021, government would now focus on BY THE NUMBERS The Lancet overtook The New explaining why receiving a booster England Journal of Medicine dose is important. Austria has one U.S. science spending bills advance (NEJM) as the publication of the lower vaccination rates in with the highest impact factor, Europe, with fewer than 75% of the The U.S. House of Representatives last week released proposed according to a report released population fully vaccinated. 2023 budgets for key research agencies (see below). The Senate this week by the analytics firm has yet to release its proposals, and final numbers likely won’t be set until late this year. Clarivate. The company manages FDA tries to stop Juul sales 2022 BIDEN 2023 HOUSE the Web of Science database used ($ BILLIONS to generate this controversial H E A LT H P O L I CY | The e-cigarette REQUEST BILLS citation measure, and NEJM 45 National Institutes of Health 50.5 47.5 manufacturer Juul last week won a National Science Foundation 8.8 10.5 9.6 has dominated the general and temporary reprieve from a U.S. Food NASA science 7.6 8 7.9 internal medicine category since and Drug Administration (FDA) 7.8 8 Clarivate’s Journal Citation order banning the company from Department of Energy science 7.5 Reports launched in the 1970s. selling its products in the country. DARPA 3.8 4.1 4 High-profile pandemic research The 23 June FDA order would affect U.S. Geological Survey 1.4 1.7 1.6 may explain the shift: The Lancet all Juul products in the United NIST core labs States, including flavored cartridges published three of the 10 most 0.85 0.98 0.95 cited articles in 2021, all of them and pods for vaping. It came as part EPA science 0.73 0.86 0.87 related to COVID-19. SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 9

IN DEPTH the program will likely begin in September. In the meantime, a transitional program EUROPE promises to make up for Horizon grants al- United Kingdom set to abandon ready won by U.K. researchers. Thurston EU funding and go it alone plans to accept the government’s offer, but she says this backstop doesn’t carry the same Horizon Europe grants held hostage over Brexit dispute prestige or networking opportunities. “It’s not the same,” she says. By Cathleen O’Grady and giving up the prestigious ERC grant. ILLUSTRATION: DAVIDE BONAZZI One day before the deadline, 18 U.K.-based ERC President Maria Leptin says she “pro- A few months ago, Teresa Thurston, a grant winners had told ERC they planned foundly” regrets the situation. “I sincerely cellular microbiologist at Imperial to leave for Europe, whereas 20, including hope that our political leaders will find a path College London, could not have imag- Thurston, rejected their ERC grants to stay in to allow us to continue working in the future ined losing her €1.5 million European the United Kingdom. The remainder had not with the research community in the U.K.” research grant. But the United King- yet told ERC of their decision. dom’s role in the European Union’s Greg Clark, a U.K. lawmaker and member €95 billion Horizon Europe funding program The impasse over U.K. participation in Ho- of a parliamentary science committee, says is now crumbling thanks to lingering Brexit rizon Europe deepened last month after the it’s wrong for the European Union to “weap- disputes, forcing many U.K. grant winners U.K. Parliament began pushing through leg- onize science” to gain advantage in other po- like Thurston to give up grants they thought islation that would unilaterally override part litical arguments. Other components of the they could count on. of the 2020 Brexit agreement that deals with Brexit agreement, such as the cross-border trade in Northern Ireland. This prompted transfer of personal data, have gone ahead This week, she and 142 other U.K. grant legal action from the European Union, despite the Northern Ireland dispute. And winners faced a deadline from the European which had already been holding cross- although damage to U.K. science is consider- Research Council (ERC), which disburses border scientific funding hostage over the able, so is damage to science within the EU, some of the Horizon Europe money. By matter, and signaled that a resolution was he says: “The longer term consequences of 29 June, they had to choose between moving far from near. The U.K. science minister on excluding excellent U.K. institutions and re- to a European host institution to take up their 15 June said he would unveil details of a “Plan searchers from collaboration with European funding or remaining in the United Kingdom B” Horizon alternative in July, adding that institutions can only be to the detriment of both sides.” A European Commission spokes- person said in an email to Science that, given the turmoil, the original Brexit agreement does not oblige the EU to allow U.K. partici- pation in Horizon Europe, nor does it impose a deadline. The Brexit deal was supposed to preserve U.K. participation. In an arrangement simi- lar to those for other non-EU countries that receive Horizon Europe funds, such as Is- rael, Turkey, and Norway, the United King- dom would pay approximately £15 billion into the program over its 7-year period, al- lowing its researchers to compete for fund- ing. The European Parliament still had to ratify the agreement, but U.K. researchers began to apply for—and win—grants in the first funding rounds of the program. In April, however, the political impasse over Northern Ireland was ongoing and the Horizon deal was still not ratified. Facing the need to disburse its first round of grants, ERC emailed grant winners asking them to submit letters from Horizon-eligible host institutions within 2 months—or forfeit their grants. It’s “massively destabilizing,” says Peter Mason, head of global research and inno- vation policy at Universities UK. “There are these great collaborations—scientific networks—that have been established for decades in some cases, which are being undermined.” James Wilsdon, a research policy expert at the University of Sheffield, adds that “all of this uncertainty is just like acid on collaboration.” For Thurston, moving to Europe was not practical, because her collaborators were all 10 1 JULY 2022 • VOL 377 ISSUE 6601 Corrected 30 June 2022. See full text. science.org SCIENCE

NEWS in the United Kingdom. She also did not want SCIENTIFIC PUBLISHING to uproot her family, and she points out that a short-notice move to Europe would be hard Silence greets requests for researchers taking care of children, which to flag retracted studies means women likely face greater impact. Authors and editors ignored warnings about citing noted Thiemo Fetzer, an economist at the Uni- fraudster, exposing a problem in scholarly publishing versity of Warwick, reluctantly made the de- cision to move. A collaborator on his project By Jeffrey Brainard leaving readers in the dark. (A ninth re- is employed by the European Commission and would not be able to sign a contract with view was itself retracted.) a U.K.-based institution. Fetzer will now di- vide his time between the United Kingdom A lison Avenell spent years collect- The saga provides an unusually method- and his European host, which he declined ing evidence that Yoshihiro Sato, a ical case study of what some call “zombie to name because he was still finalizing the now-deceased nutritional researcher papers.” Even after they are retracted— agreement. “It’s devastating,” Fetzer says. in Japan, was among the most prolific publishing’s death sentence—these papers Winning an ERC grant is “supposed to be a fraudsters known to science. After live on thanks to citations. And that could high point of people’s academic careers, and journals investigated the findings by have real-world consequences, the study it’s made it really, really difficult.” Avenell, a clinical nutritionist at the Univer- suggests. It found 39 of the 88 citing pa- European researchers aren’t happy either, says Thomas Jørgensen, director of policy sity of Aberdeen, and her colleagues, they pers had drawn conclusions that, if Sato’s coordination and foresight at the European University Association. The European Union’s retracted more than two dozen papers Sato retracted papers were left out of the analy- lack of transparency and poor communica- tion has damaged the profile of Horizon had co-authored. Many had reported find- sis, were likely to be substantially weaker. Europe, he says. European researchers were encouraged to join U.K.-led consortia, and ings from clinical trials that could have led Journals flagged just four of these weak- then faced chaos as the U.K. partners were no longer able to take their intended leading physicians to incorrectly treat patients suf- ened studies for citing retracted papers. roles. Some top researchers now feel that EU funding is too bureaucratic and difficult to be fering from osteoporosis and other disorders. The study’s findings are “unfortunately worth bothering with again, Jørgensen says. But the retractions, which began in 2015, very consistent” with others going back to In theory, the United Kingdom could join Horizon Europe at any time in the coming didn’t mean the papers were the 1990s, says Ivan Oransky, 7 years if political disputes over Brexit were settled. And Horizon association remains gone for good, or that their in- 88 co-editor of Retraction Watch, “Plan A,” the U.K. science minister, George fluence waned. which reports on retracted Freeman, said in a 15 June parliamentary papers and tracks them in a committee hearing. He could not be reached Avenell noticed many jour- public database. A 1998 inves- for comment, but a department spokes- nal articles that cited one or person said, “The U.K. is pushing for associa- tion to Horizon Europe as swiftly as possible.” more of Sato’s 27 retracted pa- Medical evidence tigation in JAMA, for example, But Freeman told the committee that if pers did not warn readers that syntheses citing found that 94% of 299 cita- “the phone does not ring” soon, then “Plan DATA: A. AVENELL, M. BOLLAND, G. GAMBLE, AND A. GREY, ACCOUNTABILITY IN RESEARCH, DOI: 10.1080/08989621.2022.2082290 (2022) B” will begin in September, with the govern- they referenced tainted work. one or more of tions to retracted articles still ment diverting the £15 billion intended for Horizon into a U.K.-based international pro- Worse, she and colleagues re- 27 retracted listed in the MEDLINE data- gram. Freeman described plans to replicate the structure of the Horizon funding scheme, ported recently, the flawed clinical trial papers base did not note the work with grants not only for basic research, simi- lar to ERC’s, but also funding for risky, ap- findings were cited in 88 ar- co-authored by had been retracted. And “most plied, and industrial research. ticles, published from 2003 to scientific fraudster editors do not seem to make Wilsdon adds that the bulk of Horizon Eu- rope funding goes toward international re- 2020, that are systematic re- Yoshihiro Sato correcting the record a prior- search consortia that often involve industrial collaborators. U.K.-based researchers have views and clinical guidelines— ity,” Oransky says. already been forced to step down from their coordinating roles in Horizon-funded consor- potentially influential publi- 39 Avenell took a very rigorous tia, and Wilsdon thinks it would be tough to cations that often help guide approach to documenting the re-create these in Freeman’s “Plan B.” medical treatments. Avenell problem, Oransky says. For ex- Beth Thompson, a policy director at the wondered: Would the authors Syntheses out of the ample, her team emailed que- Wellcome Trust, shares the concern. “All and editors of these papers 88 with findings that, ries to authors and journals those researchers’ brains coming together take action if alerted to the re- if the retracted paper using a randomized, controlled to do something brilliant—that can’t be re- tractions of Sato’s work? had been excluded, trial design. For some papers, produced at a domestic level,” she says. j the researchers contacted only For the most part, she would likely be the corresponding authors of found, the answer was no. weaker the evidence syntheses. For Her team contacted the 4authors of 86 of the citing others, they contacted an ad- ditional two co-authors and papers—and sometimes the sometimes also the journal’s editors, too. After a year, how- editor-in-chief. ever, journals had posted no- tices or letters for just eight of Syntheses out of the For half of the 86 papers, those papers informing read- 39 whose journals they got no response. (Looping ers that they cited retracted added a notice in the editor didn’t increase work, the researchers reported saying it cited a the response rate.) Some au- in late May in Accountability retracted paper, after thors who did respond said in Research. In five of those the authors were they didn’t plan to amend their cases the announcement notified about the papers because, for example, wasn’t linked to the paper, retraction the publication was too old, SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 11 Corrected 30 June 2022. See full text.

NEWS in the United Kingdom. She also did not want SCIENTIFIC PUBLISHING to uproot her family, and she points out that a short-notice move to Europe would be hard Silence greets requests for researchers taking care of children, which to flag retracted studies means women likely face greater impact. Authors and editors ignored warnings about citing noted Thiemo Fetzer, an economist at the Uni- fraudster, exposing a problem in scholarly publishing versity of Warwick, reluctantly made the de- cision to move. A collaborator on his project By Jeffrey Brainard leaving readers in the dark. (A ninth re- is employed by the European Commission and would not be able to sign a contract with view was itself retracted.) a U.K.-based institution. Fetzer will now di- vide his time between the United Kingdom A lison Avenell spent years collect- The saga provides an unusually method- and his European host, which he declined ing evidence that Yoshihiro Sato, a ical case study of what some call “zombie to name because he was still finalizing the now-deceased nutritional researcher papers.” Even after they are retracted— agreement. “It’s devastating,” Fetzer says. in Japan, was among the most prolific publishing’s death sentence—these papers Winning an ERC grant is “supposed to be a fraudsters known to science. After live on thanks to citations. And that could high point of people’s academic careers, and it’s made it really, really difficult.” journals investigated the findings by have real-world consequences, the study European researchers aren’t happy ei- Avenell, a clinical nutritionist at the Univer- suggests. It found 39 of the 88 citing pa- ther, says Thomas Jørgensen, president of the European University Association. The sity of Aberdeen, and her colleagues, they pers had drawn conclusions that, if Sato’s European Union’s lack of transparency and poor communication has damaged the pro- retracted more than two dozen papers Sato retracted papers were left out of the analy- file of Horizon Europe, he says. European researchers were encouraged to join U.K.- had co-authored. Many had reported find- sis, were likely to be substantially weaker. led consortia, and then faced chaos as the U.K. partners were no longer able to take ings from clinical trials that could have led Journals flagged just four of these weak- their intended leading roles. Some top re- searchers now feel that EU funding is too physicians to incorrectly treat patients suf- ened studies for citing retracted papers. bureaucratic and difficult to be worth both- ering with again, Jørgensen says. fering from osteoporosis and other disorders. The study’s findings are “unfortunately In theory, the United Kingdom could join But the retractions, which began in 2015, very consistent” with others going back to Horizon Europe at any time in the coming 7 years if political disputes over Brexit were didn’t mean the papers were the 1990s, says Ivan Oransky, settled. And Horizon association remains “Plan A,” the U.K. science minister, George gone for good, or that their in- 88 co-editor of Retraction Watch, Freeman, said in a 15 June parliamentary fluence waned. which reports on retracted committee hearing. He could not be reached papers and tracks them in a for comment, but a department spokes- Avenell noticed many jour- public database. A 1998 inves- person said, “The U.K. is pushing for associa- nal articles that cited one or tion to Horizon Europe as swiftly as possible.” more of Sato’s 27 retracted pa- Medical evidence tigation in JAMA, for example, But Freeman told the committee that if DATA: A. AVENELL, M. BOLLAND, G. GAMBLE, AND A. GREY, ACCOUNTABILITY IN RESEARCH, DOI: 10.1080/08989621.2022.2082290 (2022 “the phone does not ring” soon, then “Plan pers did not warn readers that syntheses citing found that 94% of 299 cita- B” will begin in September, with the govern- they referenced tainted work. one or more of tions to retracted articles still ment diverting the £15 billion intended for Horizon into a U.K.-based international pro- Worse, she and colleagues re- 27 retracted listed in the MEDLINE data- gram. Freeman described plans to replicate the structure of the Horizon funding scheme, ported recently, the flawed clinical trial papers base did not note the work with grants not only for basic research, simi- lar to ERC’s, but also funding for risky, ap- findings were cited in 88 ar- co-authored by had been retracted. And “most plied, and industrial research. ticles, published from 2003 to scientific fraudster editors do not seem to make Wilsdon adds that the bulk of Horizon Eu- 2020, that are systematic re- Yoshihiro Sato correcting the record a prior- rope funding goes toward international re- search consortia that often involve industrial views and clinical guidelines— ity,” Oransky says. collaborators. U.K.-based researchers have already been forced to step down from their potentially influential publi- 39 Avenell took a very rigorous coordinating roles in Horizon-funded consor- cations that often help guide approach to documenting the tia, and Wilsdon thinks it would be tough to medical treatments. Avenell problem, Oransky says. For ex- re-create these in Freeman’s “Plan B.” wondered: Would the authors Syntheses out of the ample, her team emailed que- Beth Thompson, a policy director at the and editors of these papers 88 with findings that, ries to authors and journals Wellcome Trust, shares the concern. “All take action if alerted to the re- if the retracted paper using a randomized, controlled those researchers’ brains coming together tractions of Sato’s work? had been excluded, trial design. For some papers, to do something brilliant—that can’t be re- the researchers contacted only produced at a domestic level,” she says. j For the most part, she would likely be the corresponding authors of found, the answer was no. weaker the evidence syntheses. For Her team contacted the authors of 86 of the citing others, they contacted an ad- 4papers—and sometimes the ditional two co-authors and sometimes also the journal’s editors, too. After a year, how- editor-in-chief. ever, journals had posted no- tices or letters for just eight of Syntheses out of the For half of the 86 papers, those papers informing read- 39 whose journals they got no response. (Looping ers that they cited retracted added a notice in the editor didn’t increase work, the researchers reported saying it cited a the response rate.) Some au- in late May in Accountability retracted paper, after thors who did respond said in Research. In five of those the authors were they didn’t plan to amend their cases the announcement notified about the papers because, for example, wasn’t linked to the paper, retraction the publication was too old, SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 11

NEWS | IN DEPTH or they didn’t have time to do a reanalysis. The Vestmanna cliffs of the Faroe Islands formed when Greenland tore away from Europe 56 million years ago. Some asserted that the elimination of a single, retracted study likely would not CLIMATE CHANGE have changed their overall findings. There is some evidence for that position. A 2021 Hidden carbon layer sparked study in Accountability in Research led ancient bout of global warming by Daniele Fanelli of the London School of Economics and Political Science exam- Deep carbon exhumed by volcanic rift between Greenland ined 50 meta-analyses of clinical treat- and Europe implicated in 56-million-year-old hothouse ments. The conclusions of those that cited retracted work and those that didn’t were By Paul Voosen found signs of an effect that would have PHOTO: STEVE_IS_ON_HOLIDAY/ISTOCK.COM statistically similar. supercharged the warming effect of the vol- T here is no perfect parallel in canoes, making them a stronger suspect. The studies examined by Avenell’s team Earth’s past for present-day climate The underside of Greenland is thought to that were weakened by retracted find- change—human-driven warming be encrusted with carbon-rich rocks, like ings could have put patients at risk. One is simply happening too fast and barnacles on the keel of a ship. When it of those reviews, showing that vitamin K furiously. The closest analog came tore away from Europe in the rifting, the helps prevent bone fractures, was the ba- 56 million years ago, when over the rocks might have liberated a gusher of car- sis of 2011 and 2015 guidelines issued in course of 3000 to 5000 years, greenhouse bon dioxide (CO2), says Thomas Gernon, a Japan that recommend the supplement gases soared in the atmosphere, causing at geologist at the University of Southampton for people at risk. Omitting Sato’s stud- least 5°C of warming and pushing tropical and leader of the new study. “It’s a perfect ies made the reported benefit statistically species to the poles. storm of conditions.” nonsignificant. The guidelines’ sponsor, the Japan Osteoporosis Foundation, was The cause of the Paleocene-Eocene Ther- The PETM has long fascinated paleo- among those that did not respond to the mal Maximum (PETM) has long been de- climatologists. “Since dinosaurs kicked the team’s queries. bated, with researchers invoking exotic bucket, this is the biggest global warming mechanisms such as catastrophic releases event we have,” says Pincelli Hull, a paleo- Even if the inclusion of a retracted study of methane from the sea floor or even as- climate scientist at Yale University. It can doesn’t change the bottom line, Avenell teroid strikes. But over the past few years, yield clues to how quickly Earth warms as argues, journals and authors have an ob- evidence has mounted for a more prosaic greenhouse gas levels rise and how climate ligation to say so publicly. “You need to culprit: carbon-spewing volcanoes that extremes alter ecosystems. But the com- reassure your readers” about a paper’s va- emerged underneath Greenland as it tore parison to today isn’t exact. Although the lidity, she says. away from Europe. Now, researchers have total release of carbon during the PETM Avenell is scheduled to discuss the study—co-authored by Mark Bolland, Greg Gamble, and Andrew Grey of the Univer- sity of Auckland—in September at the In- ternational Congress on Peer Review and Scientific Publication. The work, she says, was spurred by “my frustration with the slow process of correcting the literature that has integrity issues and to demon- strate the potential adverse consequences if it is not corrected promptly.” There are signs the research commu- nity is beginning to take such concerns more seriously. Several bibliographic databases—including EndNote, LibKey, Papers, and Zotero—now note papers that are included in Retraction Watch’s data- base of retractions, which debuted pub- licly in 2018. (The popular Google Scholar search engine does not flag retractions.) The International Committee of Medical Journal Editors recommends journal edi- tors routinely check to see whether sub- mitted manuscripts cite retracted papers. And in 2021, Cochrane, a nonprofit inter- national network that promotes evidence- based medicine, began to attach a warning to any of its published systematic reviews that cite retracted studies. Cochrane asks the authors of the flagged reviews to re- consider their work; then the organization decides whether to withdraw the analysis or publish an updated version. j 12 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

NEWS | IN DEPTH or they didn’t have time to do a reanalysis. The Vestmanna cliffs of the Faroe Islands formed when Greenland tore away from Europe 56 million years ago. Some asserted that the elimination of a single, retracted study likely would not CLIMATE CHANGE have changed their overall findings. There is some evidence for that position. A 2021 Hidden carbon layer sparked study in Accountability in Research led ancient bout of global warming by Daniele Fanelli of the London School of Economics and Political Science exam- Deep carbon exhumed by volcanic rift between Greenland ined 50 meta-analyses of clinical treat- and Europe implicated in 56-million-year-old hothouse ments. The conclusions of those that cited retracted work and those that didn’t were By Paul Voosen found signs of an effect that would have PHOTO: STEVE_IS_ON_HOLIDAY/ISTOCK.COM statistically similar. supercharged the warming effect of the vol- T here is no perfect parallel in canoes, making them a stronger suspect. The studies examined by Avenell’s team Earth’s past for present-day climate The underside of Greenland is thought to that were weakened by retracted find- change—human-driven warming be encrusted with carbon-rich rocks, like ings could have put patients at risk. One is simply happening too fast and barnacles on the keel of a ship. When it of those reviews, showing that vitamin K furiously. The closest analog came tore away from Europe in the rifting, the helps prevent bone fractures, was the ba- 56 million years ago, when over the rocks might have liberated a gusher of car- sis of 2011 and 2015 guidelines issued in course of 3000 to 5000 years, greenhouse bon dioxide (CO2), says Thomas Gernon, a Japan that recommend the supplement gases soared in the atmosphere, causing at geologist at the University of Southampton for people at risk. Omitting Sato’s stud- least 5°C of warming and pushing tropical and leader of the new study. “It’s a perfect ies made the reported benefit statistically species to the poles. storm of conditions.” nonsignificant. The guidelines’ sponsor, the Japan Osteoporosis Foundation, was The cause of the Paleocene-Eocene Ther- The PETM has long fascinated paleo- among those that did not respond to the mal Maximum (PETM) has long been de- climatologists. “Since dinosaurs kicked the team’s queries. bated, with researchers invoking exotic bucket, this is the biggest global warming mechanisms such as catastrophic releases event we have,” says Pincelli Hull, a paleo- Even if the inclusion of a retracted study of methane from the sea floor or even as- climate scientist at Yale University. It can doesn’t change the bottom line, Avenell teroid strikes. But over the past few years, yield clues to how quickly Earth warms as argues, journals and authors have an ob- evidence has mounted for a more prosaic greenhouse gas levels rise and how climate ligation to say so publicly. “You need to culprit: carbon-spewing volcanoes that extremes alter ecosystems. But the com- reassure your readers” about a paper’s va- emerged underneath Greenland as it tore parison to today isn’t exact. Although the lidity, she says. away from Europe. Now, researchers have total release of carbon during the PETM Avenell is scheduled to discuss the study—co-authored by Mark Bolland, Greg Gamble, and Andrew Grey of the Univer- sity of Auckland—in September at the In- ternational Congress on Peer Review and Scientific Publication. The work, she says, was spurred by “my frustration with the slow process of correcting the literature that has integrity issues and to demon- strate the potential adverse consequences if it is not corrected promptly.” There are signs the research commu- nity is beginning to take such concerns more seriously. Several bibliographic databases—including EndNote, LibKey, Papers, and Zotero—now note papers that are included in Retraction Watch’s data- base of retractions, which debuted pub- licly in 2018. (The popular Google Scholar search engine does not flag retractions.) The International Committee of Medical Journal Editors recommends journal edi- tors routinely check to see whether sub- mitted manuscripts cite retracted papers. And in 2021, Cochrane, a nonprofit inter- national network that promotes evidence- based medicine, began to attach a warning to any of its published systematic reviews that cite retracted studies. Cochrane asks the authors of the flagged reviews to re- consider their work; then the organization decides whether to withdraw the analysis or publish an updated version. j 12 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

exceeded the total of today’s known oil and ing. But he knew that over the eons, CO2 CONSERVATION BIOLOGY gas reserves, it was slower than today’s and other gases can bubble out of tectonic In the Balkans, surge of greenhouse gases and drove more plates as they dive into the mantle, perco- researchers mobilize to gradual warming. Life had more time to lating up into the underside of thick crusts protect a river adapt than it does today: Fossil records like Greenland’s, and forming carbonate Plans to dam the upper Neretva River draw concern show trees migrated uphill and to higher formations that can be stable for millions By Richard Schiffman latitudes, with animals following in their or even billions of years. F ive years ago, researchers from across wake, even as tropical corals disappeared If the crust is ever pulled apart by rift- Europe converged on a cold, fast- moving river in the highlands of Alba- and ecosystems wholly changed. ing, however, the trapped carbon can spill nia for a week of intensive fieldwork. Their mission: to kick off a multiyear Past explanations for the PETM centered upward and erupt as rare carbonatite lava, effort to assemble a detailed ecological portrait of the Vyosa River, one of East- on methane, a greenhouse gas even more which contains far more CO2 than standard ern Europe’s last free-flowing waterways. lava. Indeed, such a process appears to be They hoped to draw public attention to the powerful than CO2 although shorter lived. river’s rich wildlife and persuade policy- Samples of ancient plankton shells seemed underway in East Africa right now, where makers to protect it from a cascade of pro- posed dams. to show the atmosphere during the brief a rift has begun to tear the horn of Africa Last month, that effort paid off when hothouse was enriched in light carbon, the away from the rest of the continent, says Albania’s prime minister pledged to create a Wild River National Park that would protect isotope favored by life. That suggested the James Muirhead, a structural geologist at some 500 kilometers of the Vyosa and its trib- utaries from hydropower development. carbon responsible for the warming surge the University of Auckland. “At the very Now, scientists are hoping to replicate originated in living things, as most meth- edge of the craton we get these carbonatite that success along another imperiled wa- terway in the region: the upper Neretva ane does, rather than in the gases spewed lavas,” he says. “And adjacent to the craton River, which is threatened by some 70 proposed dams. This week, three dozen by volcanoes, which rise from deep Earth. we get high CO2 fluxes.” researchers—including experts on fish, amphibians, and invertebrates—will fan At first, researchers thought a small Similarly, the hot spot that burned through out along the river’s headwaters in Bosnia and Herzegovina as part of Neretva Sci- amount of warming might have destabilized Greenland starting 60 million years ago could ence Week, which aims to catalog species that depend on the river. methane hydrates—seafloor have mobilized any carbon- “It is miraculous that these rivers have deposits of methane trapped ate under its crust, Gernon survived,” says ecologist Ulrich Eichelmann, says. When the rifting began founder of RiverWatch, a Vienna-based “Since dinosaursin cages of ice crystals— group behind both the Vyosa research campaign and the Neretva Science Week, triggering a massive release kicked the bucket, to open up what today is the which began on 28 June. Western Balkan of carbon. But the 2010 Deep- this is the northeastern Atlantic Ocean, rivers teem with aquatic life, including the water Horizon oil spill in the “you’ll have a huge amount of world’s highest diversity of trout species, Gulf of Mexico put a dent in biggest global carbon venting.” suggesting to some researchers that they that theory. Microbes simply are an evolutionary cradle of trout and Evidence of the carbon- salmon. It’s an unexpected wilderness in a heavily developed continent, Eichelmann chewed up the methane the warming event rich melt is abundant on says. “In other parts of Europe, there are broken well released into we have.” either side of the North At- virtually no rivers left that have not been the ocean, suggesting seeps lantic rift, the tectonic di- dammed or channeled.” of seabed methane would Pincelli Hull, Yale University vision that marks the old rarely get all the way into the boundary between Greenland Four major dams interrupt the lower reaches of the Neretva, which flows about air. “Most modeling studies and Europe, Gernon and his suggest you can’t release enough green- co-authors report in a study published last house gases just through hydrates,” says Sev week in Nature Geoscience. In an ocean core Kender, a paleoceanographer at the Univer- collected in 1981, they found volcanic tuffs sity of Exeter. indicating a sharp increase in volcanism dur- Mudrocks on the sea floor also contain ing the PETM. They also combed the litera- carbon that originated in living things, and ture for studies of other rocks matching the magma from submarine eruptions could core, and found reports in East Greenland have heated the rocks and liberated the and the Faroe Islands of anomalous lavas carbon. But in 2017, researchers analyzed rich in magnesium, titanium oxide, and plankton fossils from an ocean core and rare earth elements—signatures of melting found the carbon released during the PETM of carbonate rock from deep in the crust. was heavier than previously thought. For The lavas date roughly to 56.1 million years some, that indicated the carbon wasn’t from ago, and the investigators calculate that living sources. “Given the current state of the rifting would have produced enough knowledge, it seems likely to be volcanism,” of them to explain nearly all of the needed says Marcus Gutjahr, a geochemist at GEO- carbon emissions. MAR Helmholtz Centre for Ocean Research Kender says Gernon makes a compel- Kiel, who led the 2017 study. ling case, but the timing is key. The PETM Greenland was rifting away from Eu- lasted only several thousand years, a geo- rope at the time of the PETM as a mantle logical instant. Meanwhile, the volcanism plume traveled under the island, priming has not been precisely dated. “Whether it the 180-kilometer-thick crust above to be was at the onset, in the middle, or later, we pulled apart. Like all volcanism, the pro- can’t say yet,” Kender says. Gernon’s team cess would have released CO2. Gernon cal- says more precise dating from the ocean culated, however, that the eruptions during core, still unpublished, supports the idea the rifting would have only provided one- that the lavas they’re studying could be fifth of the more than 10,000 gigatons of from the onset of the PETM. “I’m quietly carbon needed to explain the PETM warm- confident the story works,” Gernon says. j SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 13

exceeded the total of today’s known oil and ing. But he knew that over the eons, CO2 CONSERVATION BIOLOGY gas reserves, it was slower than today’s and other gases can bubble out of tectonic In the Balkans, surge of greenhouse gases and drove more plates as they dive into the mantle, perco- researchers mobilize to gradual warming. Life had more time to lating up into the underside of thick crusts protect a river adapt than it does today: Fossil records like Greenland’s, and forming carbonate Plans to dam the upper Neretva River draw concern show trees migrated uphill and to higher formations that can be stable for millions By Richard Schiffman latitudes, with animals following in their or even billions of years. F ive years ago, researchers from across wake, even as tropical corals disappeared If the crust is ever pulled apart by rift- Europe converged on a cold, fast- moving river in the highlands of Alba- and ecosystems wholly changed. ing, however, the trapped carbon can spill nia for a week of intensive fieldwork. Their mission: to kick off a multiyear Past explanations for the PETM centered upward and erupt as rare carbonatite lava, effort to assemble a detailed ecological portrait of the Vyosa River, one of East- on methane, a greenhouse gas even more which contains far more CO2 than standard ern Europe’s last free-flowing waterways. lava. Indeed, such a process appears to be They hoped to draw public attention to the powerful than CO2 although shorter lived. river’s rich wildlife and persuade policy- Samples of ancient plankton shells seemed underway in East Africa right now, where makers to protect it from a cascade of pro- posed dams. to show the atmosphere during the brief a rift has begun to tear the horn of Africa Last month, that effort paid off when hothouse was enriched in light carbon, the away from the rest of the continent, says Albania’s prime minister pledged to create a Wild River National Park that would protect isotope favored by life. That suggested the James Muirhead, a structural geologist at some 500 kilometers of the Vyosa and its trib- utaries from hydropower development. carbon responsible for the warming surge the University of Auckland. “At the very Now, scientists are hoping to replicate originated in living things, as most meth- edge of the craton we get these carbonatite that success along another imperiled wa- terway in the region: the upper Neretva ane does, rather than in the gases spewed lavas,” he says. “And adjacent to the craton River, which is threatened by some 70 proposed dams. This week, three dozen by volcanoes, which rise from deep Earth. we get high CO2 fluxes.” researchers—including experts on fish, amphibians, and invertebrates—will fan At first, researchers thought a small Similarly, the hot spot that burned through out along the river’s headwaters in Bosnia and Herzegovina as part of Neretva Sci- amount of warming might have destabilized Greenland starting 60 million years ago could ence Week, which aims to catalog species that depend on the river. methane hydrates—seafloor have mobilized any carbon- “It is miraculous that these rivers have deposits of methane trapped ate under its crust, Gernon survived,” says ecologist Ulrich Eichelmann, says. When the rifting began founder of RiverWatch, a Vienna-based “Since dinosaursin cages of ice crystals— group behind both the Vyosa research campaign and the Neretva Science Week, triggering a massive release kicked the bucket, to open up what today is the which began on 28 June. Western Balkan of carbon. But the 2010 Deep- this is the northeastern Atlantic Ocean, rivers teem with aquatic life, including the water Horizon oil spill in the “you’ll have a huge amount of world’s highest diversity of trout species, Gulf of Mexico put a dent in biggest global carbon venting.” suggesting to some researchers that they that theory. Microbes simply are an evolutionary cradle of trout and Evidence of the carbon- salmon. It’s an unexpected wilderness in a heavily developed continent, Eichelmann chewed up the methane the warming event rich melt is abundant on says. “In other parts of Europe, there are broken well released into we have.” either side of the North At- virtually no rivers left that have not been the ocean, suggesting seeps lantic rift, the tectonic di- dammed or channeled.” of seabed methane would Pincelli Hull, Yale University vision that marks the old rarely get all the way into the boundary between Greenland Four major dams interrupt the lower reaches of the Neretva, which flows about air. “Most modeling studies and Europe, Gernon and his suggest you can’t release enough green- co-authors report in a study published last house gases just through hydrates,” says Sev week in Nature Geoscience. In an ocean core Kender, a paleoceanographer at the Univer- collected in 1981, they found volcanic tuffs sity of Exeter. indicating a sharp increase in volcanism dur- Mudrocks on the sea floor also contain ing the PETM. They also combed the litera- carbon that originated in living things, and ture for studies of other rocks matching the magma from submarine eruptions could core, and found reports in East Greenland have heated the rocks and liberated the and the Faroe Islands of anomalous lavas carbon. But in 2017, researchers analyzed rich in magnesium, titanium oxide, and plankton fossils from an ocean core and rare earth elements—signatures of melting found the carbon released during the PETM of carbonate rock from deep in the crust. was heavier than previously thought. For The lavas date roughly to 56.1 million years some, that indicated the carbon wasn’t from ago, and the investigators calculate that living sources. “Given the current state of the rifting would have produced enough knowledge, it seems likely to be volcanism,” of them to explain nearly all of the needed says Marcus Gutjahr, a geochemist at GEO- carbon emissions. MAR Helmholtz Centre for Ocean Research Kender says Gernon makes a compel- Kiel, who led the 2017 study. ling case, but the timing is key. The PETM Greenland was rifting away from Eu- lasted only several thousand years, a geo- rope at the time of the PETM as a mantle logical instant. Meanwhile, the volcanism plume traveled under the island, priming has not been precisely dated. “Whether it the 180-kilometer-thick crust above to be was at the onset, in the middle, or later, we pulled apart. Like all volcanism, the pro- can’t say yet,” Kender says. Gernon’s team cess would have released CO2. Gernon cal- says more precise dating from the ocean culated, however, that the eruptions during core, still unpublished, supports the idea the rifting would have only provided one- that the lavas they’re studying could be fifth of the more than 10,000 gigatons of from the onset of the PETM. “I’m quietly carbon needed to explain the PETM warm- confident the story works,” Gernon says. j SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 13

The rugged landscape surrounding the upper Neretva River has long helped protect it from development, but a hydropower boom poses new challenges. 225 kilometers to the Adriatic Sea in Croa- of the University of Innsbruck. He and two subterranean biodiversity, she says. Some tia. But development largely sidestepped students also plan to measure water lev- of the resident species—such as the olm the river’s remote upper region when it was els of carbon dioxide and methane from (Proteus anguinus), a blind cave amphib- part of the former Yugoslavia, and in recent the decomposition of organic matter in ian that may live more than 100 years— decades war and ethnic tensions discour- the streams. The data could help research- inhabit caves and crevices. But others oc- aged investors. ers predict how detritus trapped in stag- cupy the tiny water-filled spaces between Starting around 2010, however, hydro- nant reservoirs could cause production of grains of sand and gravel under the flow- power developers saw a promising new the two potent greenhouse gases to surge. ing river. Dams can pose a special threat market in the Balkans, and the free-flowing Dams are often lauded for producing clean to these “interstitial habitats,” Zagmajster streams beckoned. Some 3500 power dams energy, Singer notes, but “what we really notes, because they alter seasonal flooding are now either proposed or under construc- should be thinking about is [their] climate patterns and allow fine sediment to settle tion in the region. Along the upper Neretva, warming potential.” and choke the cavities. engineers have identified dozens of sites for While the other scientists catalog life Biologist Saudin Merdan, who leads the mostly small hydroelectric dams. aboveground, a team led by biologist Maja Stjepan Bolkay Center, a research institute The dam-building rush is an ecological Zagmajster of the University of Ljubljana in Bosnia, will be documenting reptiles and disaster in the making, says ichthyologist will be searching below the surface. The amphibians along the Neretva. But he also Steven Weiss of the University of Graz. He porous karst (limestone) geology of the Di- worries about the impact of hydropower de- fears “poorly designed and poorly managed” naric mountains, where the Neretva rises, velopment on people. Some area residents barriers could result in “death by 1000 cuts” has made the region a global hot spot for depend on the river for drinking water, whose along the Neretva and other purity could be threatened by rivers, with fish and other or- toxic organisms that thrive in ganisms losing 30% to 70% of Going with the flow stagnant water, he notes. And, their current habitat. he adds, “Many don’t have the Researchers from across Europe converged on the Neretva River on 28 June for a money to go to the seaside on During the science week, “science week” aimed at surveying wildlife and building the case for conservation. vacation, so they spend their Weiss will be surveying popu- lations of the endangered leisure time on the rivers.” soft-mouthed trout (Salmo Sarajevo Merdan and others hope the obtusirostris) and other en- data harvested during the sci- demic fish species. Dams BOSNIA ence week will help catalyze CREDITS: (PHOTO VERA KNOOK; (MAP N. DESAI/SCIENCE would block the movements support for a new national of the rare trout and fragment ITALY park to preserve the Neret- populations, he says. Sediment va’s headwaters. The goal, from some reservoirs would Neretva River Eichelmann says, is not “safe- be flushed downstream, bury- guarding one small and scenic ing habitat. New lakes could Neretva Science Week stretch of it, but protecting the become home to invasive fish, fieldwork areas whole network of the river, such as carp, that compete which I like to compare to a with native species. tree and its branches.” j The river’s invertebrate Adriatic Sea 0 100 Richard Schiffman is a journalist residents will be the focus of km in New York City. biogeochemist Gabriel Singer 14 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

NEWS | IN DEPTH BIOMEDICINE Funds dwindle for NIH program for puzzling cases Patient groups, hospitals urge continued support for the Undiagnosed Diseases Network By Jocelyn Kaiser “I want to see the UDN sites not only Like other Common Fund programs be- continue but to [also] grow and make fore it, the UDN needed to find a home T en years ago, an athletic 12-year-old even more discoveries and … impacts on within NIH’s 27 institutes. The current from Affton, Missouri, named Mitchell the lives of patients and families,” Michele plan is for the National Institute of Neuro- Herndon began to experience muscle Herndon, Mitchell’s mother, recently wrote logical Disorders and Stroke (NINDS) to weakness that eventually put him in a to a staffer for Senator Roy Blunt (R–MO). lead a new data and coordinating center, wheelchair. After years of visits to spe- with four other institutes helping provide an The UDN emerged from an effort cialists failed to diagnose his neuro- launched in 2008 by the NIH Clinical Cen- annual $5 million budget for 5 years. NIH logical symptoms, he enrolled in a National ter in Bethesda, Maryland, to study people sees the UDN “evolving into a larger, self- Institutes of Health (NIH)-funded program with puzzling symptoms using exhaustive sustained network,” a notice says. that studies patients with debilitating mys- clinical workups and exome sequencing, a The current sites can apply to join—but tery diseases. Researchers eventually found then-new tool that scours a person’s protein- the agency plans to directly fund only the an explanation for Mitchell’s condition: a coding DNA for a culprit gene. The program’s intramural site at NIH. In part, that’s be- mutated gene that causes certain brain cells success led NIH’s Common Fund, dedicated cause genome sequencing has become a to produce an overactive protein routine part of medicine that that leads to neuron damage. is often covered by insurance, Mitchell died 3 years ago at an NIH spokesperson notes, al- age 19. Since then, 14 more peo- though UDN researchers say only ple have been identified with the some insurers cover it. same disease, dubbed Mitchell The new NINDS coordinating syndrome, and his family has center will fund small research started a foundation that hopes to grants, but scientists say this develop a treatment. won’t be enough to compensate His case is one of hundreds for the network’s existing research cracked by a highly regarded NIH resources. Those include model program called the Undiagnosed organism screening centers, a me- Diseases Network (UDN) over tabolomics center, and research at the past 9 years. Now, however, the clinical sites such as RNA se- funding is winding down for the quencing. Without these research network—and some, including pa- components, the UDN will be “less tient advocates, are scrambling to robust,” says clinical geneticist persuade Congress to restore full Vandana Shashi, who heads Duke funding or keep at least parts of University’s UDN site. it afloat. Also troubling to UDN scien- The UDN supports teams of tists and advocates is the fact that clinicians, geneticists, and other more than 1300 cases remain un- experts who study patients with solved, often because scientists medical cases that have con- need to create an animal model or founded their doctors and spe- find another patient to confirm a cialists. It was designed to sunset suspected disease mutation. “Re- 10 years after being established in Mitchell Herndon’s puzzling neurological disorder was diagnosed search is still needed to find an an- 2013, and a new NIH program to by the National Institutes of Health’s Undiagnosed Diseases Network. swer,” LeBlanc says. carry on its work will get less than The NIH spokesperson says the one-third as much as its current funding. to new programs, to launch a national net- agency is “working with Congress on other With their NIH support ending in a year, work that grew to include the NIH intra- models to expand [the UDN’s] impact,” par- seven of the network’s 12 clinical sites are mural program and 11 medical centers ticularly in underserved communities where turning away new patients and focusing on around the country. Funding rose from many patients can’t get the basic diagnostic current cases. $10 million in 2013 to about $30 million workup required to qualify for the UDN. “The significant funding cut is a chal- for several years, then tapered to an esti- Meanwhile, some sites have cobbled to- PHOTO: MICHELE HERNDON lenge,” says genetic counselor Kimberly mated $16 million this year. gether donations, parts of other NIH grants, LeBlanc, director of the UDN Coordinating It is an undisputed success: The network and other support and expect to reopen in Center at Harvard Medical School. But she has solved about 30% of nearly 1900 cases a few months. Others are still figuring out and others hope federal lawmakers will so far, finding hundreds of novel disease mu- whether they can keep going. restore more UDN funding in NIH’s 2023 tations and nearly 50 new disorders. It has “We hope to continue this work in any way spending bill, which is working its way published more than 175 papers and drawn a possible, since we are passionate and com- through Congress. stream of positive TV and press stories. mitted to this mission,” Shashi says. j SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 15

Over time, the work of cheesemakers, like this one in Switzerland, has domesticated bacteria. MICROBIOLOGY ability to break down starches and to tolerate the alcohol produced by fermentation. “The Foodmaking microbes bear restructuring of metabolism appears to be a marks of domestication hallmark of domestication in fungi,” he re- ported last week at Microbe 2022, the annual Bacteria and fungi behind cheese, soy, and more share meeting of the American Society for Micro- genomic traits wth domesticated plants and animals biology. For example, domesticated Aspergil- lus strains may have up to five times more By Elizabeth Pennisi creasing interest in fermented foods,” says copies of a gene for metabolizing starches as PHOTO: DENIS BALIBOUSE/REUTERS microbial ecologist Ariane Peralta of East their ancestor—“a brilliant way for evolution T he burst of flavor from summer’s first Carolina University. to turn up this enzyme,” Wolfe says. sweet corn and the proud stance of a show dog both testify to the power The yeasts used in making bread have long The genes of domesticated A. oryzae also of domestication. But so does the been seen as domesticated because they have display little variation, and the genome has microbial alchemy that turns milk into lost genetic variation and can’t live in the lost some key genes, including those for tox- cheese, grain into bread, and soy into wild. But for other microbes, scientists have ins that would kill the yeast needed to com- miso. Like the ancestors of the corn and the been “lacking clear evidence of domestica- plete fermentation—and which can make dog, the fungi and bacteria that drive these tion … in part because [their] microbial com- humans sick. Domestication has apparently transformations were modified for human munities can be hard to study,” says graduate made A.oryzae more human friendly, just as use. And their genomes have acquired many student Vincent Somerville of the University it bred bitter flavors out of many food plants. of the classic signatures of domestication, re- of Lausanne. searchers reported in two talks last month at Somerville reported at the meeting that a meeting in Washington, D.C. Somerville and John Gibbons, a genomicist he has seen much the same pattern in pro- at the University of Massachusetts, Amherst, karyotes, or organisms without nuclei, in- Microbes can’t be “bred” in the normal independently focused on food fermenta- cluding in bacteria used to make cheese. sense, because unlike peas or pigs, individual tion, which helped early farmers and herders Early cheesemakers established “starter” microbes with desired traits can’t be chosen transform fresh produce and milk into prod- bacterial cultures, which people in Swit- and mated. But humans can grow microbes ucts that can last months or years. Gibbons zerland use to make Gruyère and other and select variants that best serve our pur- took a close look at the genome of Aspergillus cheeses. Since the 1970s, cheesemakers have poses. The studies show the process, repeated oryzae, the fungus that jump-starts produc- banked samples of their starter cultures to over thousands of years, has left genetic tion of sake from rice and soy sauce and miso evaluate their cheese and keep quality high. hallmarks similar to those in domesticated from soybeans. Somerville sequenced the genomes of more plants and animals: The microbes have lost than 100 samples. genes, evolved into new species or strains, When farmers cultivate A. oryzae, the and become unable to thrive in the wild. fungus—a eukaryote, with its DNA enclosed “The exciting thing from this work was in a nucleus—reproduces on its own. But having samples over time,” Wolfe says. The studies “are getting to the mecha- when humans take a little finished sake and “You can see the shaping of diversity,” with nisms” of how microbial domestication transfer it to a rice mash to begin fermenta- changes in the past 50 years hinting at the works, says Benjamin Wolfe, a microbiologist tion anew, they also transfer cells of the fun- trajectory of change over past centuries. at Tufts University. By revealing which genes gal strains that evolved and survived best are key to microbes’ prized traits—and which during the first round of fermentation. All the samples had low genetic diversity, can be lost—the work could help further with just a few strains of two dominant spe- improve the organisms that fashion much Gibbons compared the genomes of scores cies, Somerville reported. Those few persis- of our food and drink, “especially [with] in- of A. oryzae strains with those of their wild tent strains are probably important to cheese ancestor, A. flavus. Over time, he found, se- quality, Gibbons said. The cultures had also lection by humans had boosted A. oryzae’s lost genes since the 1970s, including some needed to make certain amino acids, which are required to assemble proteins. But amino acids are costly to make—and these microbes live in protein-rich milk. “They were able to let go of a bunch of genes they didn’t need,” Wolfe says. Somerville also found extensive gene swapping among the microbes, one way to acquire new genes. Putting the studies together, Gibbons concludes the genomes of “domesticated prokaryotes and microbial eukaryotes are very similar” to each other and to multi- cellular domesticated organisms. Peralta cautions that the analogy to crops and animals isn’t perfect. Microbes can evolve far more quickly and so can more easily be “rewilded.” Still, as researchers fine-tune domesticated microbes, she hopes for even better tasting sake and cheese. j 16 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

NEWS | IN DEPTH GLOBAL HEALTH WHO holds off on global alarm for monkeypox Critics blast agency for not declaring a Public Health Emergency of International Concern By Kai Kupferschmidt monkeypox outbreak doesn’t deserve PHEIC gests its authors declined to recommend a status. The International Health Regula- PHEIC even though all criteria were met, T he World Health Organization (WHO) tions, a global treaty updated in 2005, de- says Clare Wenham, a global health expert may have very high aspirations—“the fine a PHEIC—pronounced as “fake”—as an at the London School of Economics. “We attainment by all peoples of the high- “extraordinary event which is determined have seen this inconsistent application of est possible level of health”—but when to constitute a public health risk to other the criteria of a PHEIC throughout its his- a new human disease begins to spread, States through the international spread of tory,” she says. The yes-or-no nature of the or a known one behaves in unusual, disease and to potentially require a coordi- decision probably leads experts to be cau- threatening ways, it has few levers to pull. nated international response.” With more tious, Youde says: “It’s tricky, because it’s One important decision it can make, how- than 4000 monkeypox cases since May such a blunt instrument.” ever, is declaring a Public Health Emergency in more than 40 countries where it is not How helpful a PHEIC truly is remains of International Concern (PHEIC), a designa- normally seen, global spread is clearly a a matter of debate as well. The declara- tion that gives WHO some additional powers concern, and the panel says the outbreak re- tion obligates member countries to follow and serves as a global wake-up call. quires “collaborative international efforts.” WHO’s recommendations, such as sharing After a meeting behind data on cases, and allows the closed doors, a WHO expert agency to issue travel advice. panel announced on 25 June “To date there is no scien- that the rapidly growing tific evidence on the effect a monkeypox epidemic does PHEIC has,” Wenham says. not yet warrant that status— But declaring a PHEIC a verdict the agency has puts the spotlight on a patho- accepted. The panel’s con- gen, Phelan says: “I worry clusion was widely criticized what waiting a few weeks by virologists, epidemio- before sufficiently grabbing logists, and public health political attention will mean experts, and it has triggered for community transmission.” a new debate about the A delay can also let an out- purpose of the PHEIC, an break grow so big that coun- instrument created to help tries are more likely to hoard improve the response to in- vaccines and other resources. ternational health threats. “As more countries become “I think they made a big affected, they’re less able to mistake,” says Yale School help countries affected early of Public Health epidemio- on,” Phelan says. And there logist Gregg Gonsalves, is no evidence that calling a who advised the committee. People line up at a New York City pop-up clinic offering a monkeypox vaccination. PHEIC early has downsides, “They punted.” Youde says. WHO has previously come under fire That leaves just one criterion in doubt, The panel acknowledged that some of its for waiting too long to declare a PHEIC says Alexandra Phelan, a lawyer at George- own members disagreed with the decision for COVID-19 and Ebola epidemics in town University who specializes in global and said it will reconsider the issue if there West Africa and the Democratic Republic health policy: whether the surge is an “ex- is new evidence that monkeypox is spread- of the Congo. The agency’s “track record traordinary event.” That determination is ing to other countries or new groups, or is that they tend to be on the later side of tricky because monkeypox is an endemic, that the severity of the disease is increas- PHOTO: TAYFUN COSKUN/ANADOLU AGENCY/GETTY IMAGES things,” says Jeremy Youde, a global health if neglected, disease in some African coun- ing. Signs the virus is establishing new researcher at the University of Minnesota, tries. “It is unjust and unethical to deter- animal reservoirs outside Africa might also Duluth. “Right now PHEICs send the mes- mine an event is only extraordinary if it is warrant a reconsideration. sage that WHO is the last institution to now occurring in high-income countries,” “I think some of these criteria will be grasp that a newly identified outbreak is Phelan says. Rather than holding off on a met almost immediately,” Gonsalves says. indeed a public health emergency of inter- PHEIC, however, WHO should re-examine The list of affected countries is growing al- national concern,” adds biologist Michael how equitable the criteria are, she says. most daily and there have already been re- Worobey of the University of Arizona. Emory University virologist Boghuma ports of the disease in children. The panel’s “The window may already have closed on Titanji notes that the question isn’t just report mentions a potential re-evaluation stopping the establishment of a new sexu- where monkeypox is spreading, but also in 21 days, Gonsalves notes, “but I hope ally transmitted disease worldwide, but a how. The vast majority of recent cases have [WHO’s] director-general is smart enough PHEIC has not even been declared.” been in men who have sex with men, a pat- to convene people again in a much more The panel didn’t fully explain why the tern not seen before. The panel’s report sug- timely manner.” j SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 17

NEWS FEATURES SEA CHANGE Can former pirates help scientists study troubled waters? By David Grimm L aura Sánchez Alòs had been at sea began to throw rocks, iron sinkers, and Mo- ers from across the globe. With a dozen PHOTOS: (LEFT TO RIGHT MELISSA ROMAO/SEA SHEPHERD; JA for less than 20 minutes when the lotov cocktails. The cutter blasted the attack- vessels and a $20 million annual budget, it motorboats attacked. In late Janu- ers with firehoses, but a large rock crashed hopes to fill an urgent scientific need: fer- ary 2019, the 24-year-old Spanish through the ship’s front window, showering rying scientists, especially those from less conservation biologist was on board glass across the bridge. A few minutes later, a developed nations, to understudied parts the Farley Mowat, a former U.S. Molotov cocktail set fire to the Mowat’s port of the ocean. There they can survey endan- Coast Guard cutter, in Mexican wa- side. The ship turned its hoses on itself to gered animals, search for new species, and ters in the northern Gulf of Califor- extinguish the flames, then zoomed out of even board illegal vessels to collect first- nia. She was the ship’s scientist, part the fray, pockmarked but intact. “Either they hand data on overfishing. of a campaign by the Sea Shepherd Con- couldn’t follow us anymore,” Sánchez Alòs servation Society to study and protect the says, “or they ran out of rocks.” “We can’t do what we want going for- vaquita, the world’s smallest porpoise and ward without science driving us,” says most endangered marine mammal. Since The incident was a turnabout for an or- Pritam Singh, who effectively took over for 2015, the organization had been patrolling ganization used to being on the offensive. Watson in 2014. “Science will be our primary this region—and making local fishers in- For more than 3 decades, Sea Shepherd mission—not an afterthought.” creasingly angry. had made a name for itself as a militant conservation group, sinking whaling ves- The pivot couldn’t come at a better time Sánchez Alòs was here to document the sels, throwing its own projectiles at illegal for marine research. The U.S. government’s size and number of nets placed in the water fishing boats, and generally conducting it- scientific fleet has shrunk by one-third over to snag the 100-kilogram totoaba, a fish so self as a vigilante of the high seas. Interna- the past couple of decades, according to highly valued for its swim bladder in tra- tional courts branded the group’s head, Paul some estimates. Time on research vessels ditional Chinese medicine and cuisine, it’s Watson, a pirate and a terrorist. can take years to procure—if investigators known as the “cocaine of the sea.” But the can get on at all. And overfishing, pollution, illegal nets snare vaquitas as well, and she Yet the Sea Shepherd Conservation Soci- and climate change are roiling the seas in and her colleagues were also yanking up the ety appears to have undergone a dramatic ways researchers are struggling to measure. nets and destroying them. transformation in the past 8 years. It has abandoned militant tactics in favor of new “There are a lot of good ocean scientists, Suddenly, nearly two dozen motorboats leadership and a new mission: Protect the but they’re stranded on shore,” says Douglas surrounded the Mowat. The men aboard oceans not with violence, but with science. McCauley, a marine ecologist at the Univer- hurled insults, calling the Sea Shepherd crew Call it a sea change. sity of California, Santa Barbara. invaders and slicing their hands across their throats in an “I’ll kill you” gesture. Then they The group has just hired its first director Sea Shepherd’s vessels could be their of science and begun recruiting research- route to sea. But most of its ships are rela- tively small and only outfitted with basic 18 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

NEWS Sea Shepherd Conservation Society ships monitor a vaquita refuge in the Gulf of California, where scientists aboard the Sharpie (far left), scan for the rare porpoises. scientific equipment. And the organiza- globe. But by the early 2010s, Interpol had The Sea Shepherd movement turned more tion itself will need to shed its past and declared Watson an internationally wanted of its focus toward overfishing and began commit to robust and transparent science, fugitive and a U.S. federal court labeled his to collaborate with foreign governments to McCauley says. “It will take a rather sig- crew “pirates.” Critics also charged that the help them monitor their waters. A major nificant about-face, but it could be really group’s tactics had largely backfired, bol- turning point came in 2015 when Sea Shep- transformative,” he says. “We are looking at stering pro-whaling sentiment in places like herd Global’s Bob Barker—a former whaling a rough next few decades for the ocean, and Japan and Iceland. “[Watson’s] involvement ship painted with shark jaws on the bow— we need all hands on deck.” in all of this is an absolute disaster,” Sidney chased an illegal fishing vessel, Thunder, for Holt, one of the main architects of the first 110 days and 10,000 nautical miles. The pur- SEA SHEPHERD TRACES its roots to 1977, whaling moratorium, told The New Yorker suit, the longest in maritime history, ended when Watson was ousted from the board in 2007. “Almost everything he has been do- with the scuttling of the trawler and the ar- of Greenpeace for his controversial tac- ing has had blowback for those who want to rest of its captain. A U.S. Navy report later tics. He formed Sea Shepherd that year see an end to whaling.” called the campaign a “game changer” for and soon developed—and embraced—a the Sea Shepherd movement. “It was now reputation as a brash and militant leader. Watson, who contends his efforts saved operating with nation states in a legitimate He wore a captain’s uniform, holstered a countless marine animals, stepped away protection of fisheries,” the report stated. knife, and flew a skull and crossbones on from the Sea Shepherd Conservation So- “The organization has succeeded in counter- the ships he commanded. ciety in 2014, although he continues to ing illegal fishing where private maritime se- direct other arms of the movement, in- curity companies had hoped but failed.” For the next several decades, Sea Shep- cluding Amsterdam-based Sea Shepherd herd crews operated like vigilantes in the Global. Singh, a wealthy developer and The Sea Shepherd Conservation Society name of conservation. They dropped spiky environmentalist, and Roger Payne, a lead- added more ships to its fleet and launched steel “net rippers” onto the ocean floor to ing expert on whale behavior, had recently a campaign of what Singh calls “radical col- tear up trawling nets, lobbed smoke bombs joined the board of the U.S.-based Sea laboration,” inking agreements with a num- onto boat decks, and threw rancid butter Shepherd Conservation Society, and began ber of Latin American countries to fight to taint whale meat. From 1979 to 1994, to steer a new course. “By the summer of poaching and overfishing. It also began its Watson claims his group sunk five whaling 2014, we were re-evaluating how best to first forays into science. The group dedi- ships and scuttled two more. accomplish our mission of protecting ma- cated the Martin Sheen, a 23-meter yacht, rine wildlife,” Singh says. “It required a exclusively to research, and started to con- The campaigns, chronicled in the TV se- complete change of direction in terms of duct preliminary science missions on other ries Whale Wars, disrupted illegal fishing, culture and approach.” vessels, including surveys of the vaquita. dolphin hunts, and whaling around the SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 19

NEWS | FEATURES Singh credits the science push to Payne. gal, unregulated, and unreported fishing. ies at the University of Washington, Seattle. “Roger wanted to know how many species Up to one out of every five fish may be “They could survey the seas in ways no one were being overfished, how many sharks thrown back dead as “bycatch,” and about else can.” were being killed for finning, and whether one-third of the world’s fish are caught at Sea Shepherd can also offer marine sci- Sea Shepherd’s efforts were affecting these unsustainable levels (Science, 11 January entists a faster, cheaper route to sea. The numbers,” he says. “In many countries, 2019, p. 112). U.S. Academic Research Fleet encompasses no one is collecting this data. We realized Yet those numbers—used to inform every- 18 vessels, and other federal agencies such we had the resources to do this for the thing from government regulations to con- as the National Oceanic and Atmospheric first time.” servation efforts—are just estimates, Payne Administration (NOAA) also operate ships But first, the group needed a chief scientist. notes. A single 2009 study is still the most of various sizes used for research. But it cited paper on the global extent of illegal can take up to 5 years to secure a grant to JOHN PAYNE, then an independent re- fishing, he says. “The oceans are cloaked in get on these boats, and costs can exceed searcher, ran into Singh by chance last sum- mystery,” he says. “It’s hard to do anything $100,000 per day on a large research ves- mer in Vermont. The son of Roger, he spent about illegal fishing because we don’t know sel. “A 2-week expedition can eat up an en- his early life around whales and became the scope of the problem.” tire grant,” McCauley says. Sea Shepherd crews are mostly volunteer, which keeps costs down. Payne says scientists should be able to board its ships in a matter of months, not years. The organization also prom- ises to bring researchers to rarely frequented marine pro- tected areas, giant swaths of ocean that restrict fishing and other activities. “Many devel- oping countries don’t have the resources to patrol their areas, so even their own scien- tists have trouble getting out to these locations,” Payne says. Sea Shepherd ships already do- ing conservation work could bring researchers onboard to document animal populations and behavior, as well as water conditions such as temperature and salinity. The same could go for the open ocean. “There are a lot of places in the world where we have no idea what the fishing A beaked whale surfaces during a survey by the Sea Shepherd Conservation Society’s Martin Sheen off Baja California. impacts are,” says Les Watling, a biological oceanographer at the University of Hawaii, a marine ecologist. He had no interest in That’s where the Sea Shepherd Conserva- Manoa. “It would be absolutely delicious to joining Sea Shepherd under Watson’s reign. tion Society’s navy comes in. Its dozen ves- go somewhere no one has been.” “If Paul had asked, I would have said no,” sels range from a 17-meter catamaran to a Sea Shepherd’s preliminary scientific ef- he says. “Their confrontational approach 56-meter former Japanese research ship. forts have borne fruit. The Martin Sheen has wasn’t a good match for my skill set.” The ships venture into remote waters oth- been sailing to the Guadalupe Island Bio- Singh invited the younger Payne to his ers often avoid because of violence or harsh sphere Reserve, which encompasses several lodge in southeastern Alaska, where the two weather, such as the northern Gulf of Cali- small islands off the Pacific coast of Baja Cali- watched salmon swim up the region’s riv- fornia and parts of the Southern Ocean. Sea fornia, since 2016. On the trips, marine bio- ers. Like his father, Payne sought hard data. Shepherd groups also have unique partner- logist Gustavo Cárdenas Hinojosa of Mexico’s “I object to the way a lot of animal rights ships with several countries that allow them National Commission of Natural Protected and conservation organizations are care- to board fishing vessels and gather catch Areas studies the behavior and vocalizations less with facts,” says Payne, who became Sea data. In the waters off Liberia and Peru, for of elusive beaked whales, which are vulner- Shepherd’s director of science in October example, Sea Shepherd crew, in conjunction able to sonar and other humanmade noise. PHOTO: GUSTAVO CÁRDENAS 2021. “I wanted to help, and I wanted to with the countries’ coast guards, are autho- Before he got involved with Sea Shepherd, make sure what we said was accurate.” rized to inspect cargo holds, cataloging the he says, his trips were so limited, it took him Numbers on the state of the oceans size and types of fishing nets and the weight, 3 years just to spot 31 whales. In his first are blurry. It’s thought, for example, that number, and species of fish being caught. 3 weeks on the Martin Sheen, he saw 45. global fish consumption has doubled over “I don’t know anyone else who can do With photographs, underwater micro- the past 50 years, driven largely by ille- that,” says Ray Hilborn, an expert on fisher- phones, and DNA samples from tissue 20 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

(obtained with darts), Cárdenas Hinojosa gravity meters, and long-range Doppler so- chasing bad guys across the ocean.” and his colleagues have uncovered new in- nar. It can also accommodate underwater Hilborn also worries the group won’t pub- sights into beaked whale birthing patterns, remotely operated vehicles (ROVs), hosts lish results that conflict with its mission— family structure, and socialization. They well-equipped laboratories, and carries if it finds, for example, an abundance of have also identified a possible new species. a paid scientific crew to operate instru- species in an area thought to be overfished. “We simply would not be able to do this ments. “Doing science right takes an ex- It could create an impartial scientific work without Sea Shepherd,” he says. traordinary amount of work,” he says. board to help design and evaluate studies, A handful of other scientists have used Payne admits Sea Shepherd ships can’t he suggests. Sea Shepherd ships to study the impact rival the Revelle. Still, he says, they “are John Payne is currently assembling an of human activity on humpback whales large, stable platforms that can operate in independent board to do just that. “We are in the Pacific, shark behavior off the coast any weather,” and will support most of the committed to full transparency,” Singh says. of Gabon, and river dolphin populations types of research his organization wants to “Your data is your data. We don’t censor.” in the Amazon. Other studies have tested do, such as surveying biodiversity, verifying Appelgate would rather the Sea Shepherd sperm whales in the Gulf of California for catch data, and observing marine animal Conservation Society used its money to pollutants, which John Payne says “may be behavior. Hilborn adds that Sea Shepherd fund more established scientific ventures. the biggest threat to whales The organization could cover post-whaling.” ship time for scientists, for ex- But these projects are just a ample, or partner with Scripps drop in the ocean. What Payne as another nonprofit has done. needs now is for more scien- Still, he says, if the group tists to climb aboard. plunges deeply into its own research, he would judge it on WHEN IT COMES TO Sea Shep- its merits. “I would pay more herd’s past, Hilborn doesn’t attention to the scientific rigor mince words. “A bunch of lu- than to, ‘Hey, these guys used natics conducting campaigns to wear pirate masks.’” that were internationally crim- inal and a total waste of time,” JOHN PAYNE NOW spends his he says. (Watson counters that days calling up scientists and he and his colleagues have mapping out his organization’s never been convicted of a fel- research future. After reaching ony.) But Hilborn is cautiously out to more than 100 academ- optimistic about the Sea Shep- ics around the world, he says, herd Conservation Society’s “there is a lot of interest in us- change in direction. “Shedding ing Sea Shepherd ships for sci- Watson gives them a lot of op- ence. I think we’ll be turning portunity for rebranding,” he away a lot of people.” says. He adds that John Payne He aims to request research is “a good choice” as director proposals for ship time by the of science. (Hilborn served end of the year and hopes to on Payne’s Ph.D. committee collaborate with hundreds of and has worked with him as scientists within 5 years. a consultant.) Peter Hammarstedt, a captain with Sea Shepherd Global, investigates the Interest from the develop- Still, Hilborn and others cargo hold of a fishing trawler off the coast of West Africa. ing world is especially high, say the organization faces he says, as academics there steep challenges if it wants to become a could easily add more instrumentation. struggle even more for access to research scientific powerhouse. One is equipment. “It’s all solvable by money.” vessels. What Sea Shepherd could pro- High-powered binoculars are among Sea The Sea Shepherd Conservation Society vide in these regions is “very important,” Shepherd’s fanciest scientific devices. In currently brings in (and spends) about Cárdenas Hinojosa says. contrast, traditional research vessels have $20 million per year in donations. Payne Sánchez Alòs agrees. Undeterred by her dedicated scientific equipment, personnel, hopes to use some of that on a $100,000 run-in with the fishers, she’s still trying to and labs. On the Farley Mowat, “a laptop echosounder to acoustically measure fish track vaquitas in the Gulf of California. is really pushing it,” says Barbara Taylor, populations. “We don’t have unlimited Sea Shepherd’s interactions with the locals a biologist with NOAA’s Southwest Fisher- money for equipment,” Singh says. “But if have become less intense, she says. That ies Science Center who surveyed vaquitas we needed something like an ROV, we’d try may be because the organization no longer from the ship. to make it work.” yanks nets from the water; now it just tells Bruce Appelgate echoes those concerns. Hilborn is more concerned about the the Mexican navy where to find them. He leads ship operations at the Scripps In- organization’s ability to balance its scien- Sánchez Alòs is also helping build and PHOTO: SEA SHEPHERD stitution of Oceanography, which operates tific goals with conservation. After all, its maintain a database of all of the informa- three major scientific vessels and a collec- donors and volunteers are motivated by tion Sea Shepherd ships are collecting. tion of smaller coastal research ships. His a desire to save the whales, not measure “We’re trying to paint a better picture biggest, the 83-meter Roger Revelle, bris- salinity. “You need to go back to the same of what’s going on in our seas,” she says. tles with high-tech scientific instruments, place over and over again for scientific sur- “I’m sure the science is just going to keep including a deep-water mapping system, veys,” he says. “You can’t do that if you’re growing—it’s what the world needs.” j SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 21

INSIGHTS Herbert et al. report on a new method for reconstructing atmospheric CO2 concentrations over the past 20 million years. Their findings support a long-term covariance of atmospheric greenhouse gases and the global mean temperature. PERSPECTIVES assuming atmospheric CO concentrations in 2 PA L E O C L I M AT E excess of 850 ppm (5). Herbert et al. present Can the Miocene climate inform the future? newly reconstructed CO concentrations of 2 Another climate reconstruction shows a correlation between temperature and CO2 500 to 1100 ppm during much of the early By Anna S. von der Heydt plays the most prominent role. Quantitative Miocene, including the MCO, suggesting that ILLUSTRATION: MAURICIO ANTON/SCIENCE SOURCE comparisons of future projected climates A tmospheric CO concentrations are between different geological epochs have re- the CO amounts in climate models were not 2 vealed the Pliocene climate [~3 million years 2 rapidly rising. To reliably predict the ago (Ma)] as the most similar to the projected future, researchers have looked at climate under the RCP4.5 scenario, which is unrealistically high. Most notably, their re- past climates with comparable CO a likely greenhouse gas trajectory according 2 to the Intergovernmental Panel on Climate construction considers the rate at which oce- concentrations, dating back millions Change (IPCC). (RCP stands for representa- of years. Although these past climates tive concentration pathway, with the number anic crust is produced to be directly related representing the level of radiative forcing in are not perfect analogs of the future, they the atmosphere by 2100, measured as watts to tectonic degassing rates of CO . In previ- still provide information about how the cli- per square meter.) Under the less optimistic 2 mate system functions under increased CO RCP8.5 scenario, the world may then stabi- lize in an Eocene-like climate circa 50 Ma (3). ous studies, tectonic degassing rates were 2 However, during the Eocene, polar ice sheets were absent, and geographical boundary mostly assumed to be constant over time, but concentrations. Because there are no direct conditions were substantially different from observations of past climate states, climate those today, which makes direct comparison Herbert et al. suggest that tectonic degassing variables need to be inferred from geological with future projected climates more difficult. data, generally referred to as proxies. On page was substantially higher up until the MCO, 116 of this issue, Herbert et al. (1) present a re- A more recent warm climate episode in the construction of the evolution of atmospheric past is the Miocene, from roughly 23 to 5.3 after which degassing rates declined along CO concentration over the past 20 million Ma. One puzzling element of Miocene climate is that its global temperature seemed to be with global cooling. The authors arrive at an 2 higher than what one would expect given its atmospheric CO concentration (4). Proxies even warmer estimate of MCO global mean years. Their data provide a consistent expla- nation for the long-term evolution of global 2 surface temperatures by using organic prox- temperature and ice sheets on Earth and give a glimpse into its climate future. suggest global sea surface temperature dur- ies from higher-latitude sites only. They care- ing the Miocene Climatic Optimum [(MCO), The global average surface temperature is about 15 Ma] to be 11.5°C warmer than that of fully chose the proxies because during warm expected to rise between 1.4° and 4.4°C by the the preindustrial period, although estimates end of this century relative to the preindus- of atmospheric CO suggest relatively low lev- climates, organic proxies can become satu- trial temperature, with substantial impacts expected on every aspect of natural ecosys- 2 rated in tropical and mid-latitude sites and tems and human societies (2). The anticipated warming depends on how Earth responds els of 450 to 550 parts per million (ppm) (5). can therefore lead to unreliable results. to radiative perturbations driven by green- Thus far, climate models have failed to rec- house gases in the atmosphere, of which CO Hebert et al.’s reconstructed atmospheric oncile such warm MCO temperatures without 2 CO evolution over the past 20 million years 2 Institute for Marine and Atmospheric Research, Utrecht University, Utrecht, Netherlands. Email: [email protected] tracks with estimated global mean surface temperatures. Therefore, the Miocene cli- mate appears less like an exception to the rule (4). With their model for the Miocene providing a temperature and global ice vol- ume evolution that follows the atmospheric CO concentration, different episodes in the 2 Miocene may provide climate states with similarity to future projected climate states. The authors used a carbon budget model to explore how decreasing the tectonic degas- sing source of CO could lead to declining 2 CO concentrations. Over long time scales, 2 the degassing CO source is balanced by a 2 temperature-dependent sink resulting from the weathering of silicate rocks, extracting CO from the atmosphere (6). Because tem- 2 perature depends on atmospheric CO , two 2 parameters enter the carbon budget model— Earth system sensitivity (ESS) and weather- ability. ESS relates global temperature and at- mospheric CO on long time scales. It differs 2 from a parameter that is more widely used for the future called equilibrium climate sen- sitivity (ECS). ESS includes slower processes, such as tectonically driven land-ocean distri- bution, vegetation cover, and land-ice distri- bution (7, 8), whereas ECS quantifies only the faster responses to CO doubling. By varying 2 the ESS and weatherability within plausible ranges, Herbert et al. arrived at their CO evo- 2 lution, which includes uncertainty estimates that mostly stem from uncertainty in ESS. 26 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

Despite extensive research, both ECS and NEUROSCIENCE ESS are subject to considerable uncertainty Sleeping off stress (9). Improving the understanding of climate Social defeat activates midbrain cells, promoting sleep and reducing anxiety in mice sensitivity and its evolution on long time By Marian Joëls1,2 and E. Ronald de Kloet3 tivity up to several hours after social defeat scales—e.g., throughout the past 65 million and project to the lateral hypothalamus. W hen a mouse is placed in the cage Activation of this pathway is both necessary years—is therefore an important challenge of an aggressive conspecific (the and sufficient to promote rapid eye move- “resident”), usually the intruder ment (REM) and non-REM sleep onset, as for the field of paleoclimate studies (10, 11). is quickly defeated. This experi- well as sleep duration, after social defeat. ence of social defeat causes stress The authors found that sleep after social de- The evolution of atmospheric CO and tem- to the intruder. When social de- feat normalizes raised plasma corticosterone 2 feat takes place during the inactive phase concentrations and keeps anxiety at bay. of the day, most of the defeated animals Conversely, sleep deprivation (or any inter- perature throughout the past 20 million subsequently fall asleep. On page 63 of this ference with VTAVgat-Sst cell-mediated activa- issue, Yu et al. (1) show that a small group tion of the lateral hypothalamus) sustains years suggests that the Miocene climate is of cells in the ventral tegmental area (VTA), stress-induced elevation of corticosterone projecting to the lateral hypothalamus, is concentrations and anxiety-like behavior. less exceptional than previously thought. activated by social defeat. This pathway is key to restorative sleep after social defeat, Exactly how sleep is induced after social Global temperature, land and sea ice volume, preventing a lasting state of anxiety. defeat remains unresolved, as is the nature of the cells to which the VTAVgat-Sst cells pro- and atmospheric CO seem to covary on long These VTA cells are g-aminobutyric acid ject. It might seem straightforward that 2 (GABA) neurons, and not the classical dopa- these VTA interneurons project onto mine neurons that regulate reward process- GABAergic cells in the lateral hypothalamus, time scales in ways that are not too differ- ing and reinforcement learning (2), social which are known to locally inhibit orexin- competence (3), motivation, and stress cop- producing cells (5). Orexin is a neuropep- ent before and after the Miocene. Declining ing (4). Yu et al. find that after social defeat tide that, among other things, is important in mice, input from brain areas such as the for arousal and wakefulness. By inhibiting CO concentrations over the Cenozoic pe- paraventricular nucleus of the hypothala- orexin-producing cells, faster sleep onset, lon- 2 mus, the lateral preoptic area, and periaq- ger sleep duration, and reduction of anxiety ueductal gray activates 15 to 20% of all VTA would be predicted. However, attempts by Yu riod reached a first threshold at the end of GABAergic cells that express the vesicu- et al. to demonstrate a role of orexin blockade lar GABA transporter (VTAVgat). These are on, for example, anxiety were inconclusive. the Eocene (34 Ma), crossing a tipping point particularly somatostatin-expressing cells (VTAVgat-Sst) and not parvalbumin-expressing The relationship between social defeat– that resulted in a large ice cap on Antarctica. cells. The VTAVgat-Sst cells show increased ac- induced sleep, restoration of plasma corti- costerone concentrations, and prevention of Although this CO threshold remains subject 2 Social defeat activates interconnected brain systems to considerable (model-based) uncertainty, Somatostatin (Sst)-expressing g-aminobutyric acid (GABA) neurons in the mouse ventral tegmental area (VTAVgat-Sst) that project to the lateral hypothalamus (LH) are necessary and sufficient to promote sleep the previously reconstructed low Miocene and attenuate anxiety after social defeat. Social defeat also activates other pathways, connecting the VTA mesocorticolimbic dopaminergic (DA) system to, e.g., the amygdala, nucleus accumbens (ACC), prefrontal CO amounts were at odds with the observa- cortex (PFC), paraventricular nucleus (PVN), and hippocampus. These systems are often interconnected, 2 processing various elements intrinsic to a social defeat experience. tion that the East Antarctic Ice Sheet largely PFC Hippocampus Other Reinforcement Context disappeared during the MCO. VTA-DA GRAPHIC: KELLIE HOLOSKI/SCIENCE ACC PVN VTAVgat-Sst Within the paleoclimate community, the Reward Neuroendocrine mounting Miocene proxy data continue to regulation drive the need for a coordinated effort to VTAVgat-Sst Amygdala LH afferent and Anxiety Sleep compare different Miocene models (12). The efferent connections Miocene climate could also provide informa- tion and understanding of nonlinear or tip- ping point behavior of specific climate sub- systems—such as polar ice caps, the global ocean circulation, or tropical rainforests—rel- evant for future climate change (13). A better understanding of the Miocene climate will provide important insights for understand- ing the future climate of Earth. j REFERENCES AND NOTES 1. T.D.Herbert et al.,Science 377,116 (2022). 2. Intergovernmental Panel on Climate Change,Climate Change 2021:The Physical Science Basis.Contribution ofWorking Group I to the SixthAssessment Report of the Intergovernmental Panel on Climate Change,V.Masson- Delmotte et al.,Eds.(Cambridge Univ.Press,2021). 3. K.D.Burke et al.,Proc.Natl.Acad.Sci.U.S.A.115,13288 (2018). 4. J.E.Tierney et al.,Science 370,eaay3701 (2020). 5. N.J.Burls et al.,Paleoceanogr.Paleocimatol.36, e2020PA004054 (2021). 6. J.C.G.Walker et al.,J.Geophys.Res.86,9776 (1981). 7. PALAEOSENS Project Members,Nature 491,683 (2012). 8. D.J.Lunt et al.,Nat.Geosci.3,60 (2010). 9. S.C.Sherwood et al.,Rev.Geophys.58,e2019RG000678 (2020). 10. A.S.von der Heydt et al.,Curr.Clim.Change Rep.2,148 (2016). 11. A.M.Haywood et al.,Earth Syst.Environ.3,1 (2019). 12. DeepMIP-Miocene,The Deep-Time Model Intercomparison Project; www.deepmip.org/ deepmip-miocene/. 13. H.J.Schellnhuber et al.,Nat.Clim.Chang.6,649 (2016). ACKNOWLEDGMENTS A.S.v.d.H. acknowledges support by the program of the Netherlands Earth System Science Centre (NESSC), finan- cially supported by the Ministry of Education, Culture and Science (OCW) and the TiPES project (TiPES contribution no. 161), which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 820970. 10.1126/science.abq6542 SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 27

Despite extensive research, both ECS and NEUROSCIENCE ESS are subject to considerable uncertainty Sleeping off stress (9). Improving the understanding of climate Social defeat activates midbrain cells, promoting sleep and reducing anxiety in mice sensitivity and its evolution on long time By Marian Joëls1,2 and E. Ronald de Kloet3 tivity up to several hours after social defeat scales—e.g., throughout the past 65 million and project to the lateral hypothalamus. W hen a mouse is placed in the cage Activation of this pathway is both necessary years—is therefore an important challenge of an aggressive conspecific (the and sufficient to promote rapid eye move- “resident”), usually the intruder ment (REM) and non-REM sleep onset, as for the field of paleoclimate studies (10, 11). is quickly defeated. This experi- well as sleep duration, after social defeat. ence of social defeat causes stress The authors found that sleep after social de- The evolution of atmospheric CO and tem- to the intruder. When social de- feat normalizes raised plasma corticosterone 2 feat takes place during the inactive phase concentrations and keeps anxiety at bay. of the day, most of the defeated animals Conversely, sleep deprivation (or any inter- perature throughout the past 20 million subsequently fall asleep. On page 63 of this ference with VTAVgat-Sst cell-mediated activa- issue, Yu et al. (1) show that a small group tion of the lateral hypothalamus) sustains years suggests that the Miocene climate is of cells in the ventral tegmental area (VTA), stress-induced elevation of corticosterone projecting to the lateral hypothalamus, is concentrations and anxiety-like behavior. less exceptional than previously thought. activated by social defeat. This pathway is key to restorative sleep after social defeat, Exactly how sleep is induced after social Global temperature, land and sea ice volume, preventing a lasting state of anxiety. defeat remains unresolved, as is the nature of the cells to which the VTAVgat-Sst cells pro- and atmospheric CO seem to covary on long These VTA cells are g-aminobutyric acid ject. It might seem straightforward that 2 (GABA) neurons, and not the classical dopa- these VTA interneurons project onto mine neurons that regulate reward process- GABAergic cells in the lateral hypothalamus, time scales in ways that are not too differ- ing and reinforcement learning (2), social which are known to locally inhibit orexin- competence (3), motivation, and stress cop- producing cells (5). Orexin is a neuropep- ent before and after the Miocene. Declining ing (4). Yu et al. find that after social defeat tide that, among other things, is important in mice, input from brain areas such as the for arousal and wakefulness. By inhibiting CO concentrations over the Cenozoic pe- paraventricular nucleus of the hypothala- orexin-producing cells, faster sleep onset, lon- 2 mus, the lateral preoptic area, and periaq- ger sleep duration, and reduction of anxiety ueductal gray activates 15 to 20% of all VTA would be predicted. However, attempts by Yu riod reached a first threshold at the end of GABAergic cells that express the vesicu- et al. to demonstrate a role of orexin blockade lar GABA transporter (VTAVgat). These are on, for example, anxiety were inconclusive. the Eocene (34 Ma), crossing a tipping point particularly somatostatin-expressing cells (VTAVgat-Sst) and not parvalbumin-expressing The relationship between social defeat– that resulted in a large ice cap on Antarctica. cells. The VTAVgat-Sst cells show increased ac- induced sleep, restoration of plasma corti- costerone concentrations, and prevention of Although this CO threshold remains subject 2 Social defeat activates interconnected brain systems to considerable (model-based) uncertainty, Somatostatin (Sst)-expressing g-aminobutyric acid (GABA) neurons in the mouse ventral tegmental area (VTAVgat-Sst) that project to the lateral hypothalamus (LH) are necessary and sufficient to promote sleep the previously reconstructed low Miocene and attenuate anxiety after social defeat. Social defeat also activates other pathways, connecting the VTA mesocorticolimbic dopaminergic (DA) system to, e.g., the amygdala, nucleus accumbens (ACC), prefrontal CO amounts were at odds with the observa- cortex (PFC), paraventricular nucleus (PVN), and hippocampus. These systems are often interconnected, 2 processing various elements intrinsic to a social defeat experience. tion that the East Antarctic Ice Sheet largely PFC Hippocampus Other Reinforcement Context disappeared during the MCO. VTA-DA GRAPHIC: KELLIE HOLOSKI/SCIENCE ACC PVN VTAVgat-Sst Within the paleoclimate community, the Reward Neuroendocrine mounting Miocene proxy data continue to regulation drive the need for a coordinated effort to VTAVgat-Sst Amygdala LH afferent and Anxiety Sleep compare different Miocene models (12). The efferent connections Miocene climate could also provide informa- tion and understanding of nonlinear or tip- ping point behavior of specific climate sub- systems—such as polar ice caps, the global ocean circulation, or tropical rainforests—rel- evant for future climate change (13). A better understanding of the Miocene climate will provide important insights for understand- ing the future climate of Earth. j REFERENCES AND NOTES 1. T.D.Herbert et al.,Science 377,116 (2022). 2. Intergovernmental Panel on Climate Change,Climate Change 2021:The Physical Science Basis.Contribution ofWorking Group I to the SixthAssessment Report of the Intergovernmental Panel on Climate Change,V.Masson- Delmotte et al.,Eds.(Cambridge Univ.Press,2021). 3. K.D.Burke et al.,Proc.Natl.Acad.Sci.U.S.A.115,13288 (2018). 4. J.E.Tierney et al.,Science 370,eaay3701 (2020). 5. N.J.Burls et al.,Paleoceanogr.Paleocimatol.36, e2020PA004054 (2021). 6. J.C.G.Walker et al.,J.Geophys.Res.86,9776 (1981). 7. PALAEOSENS Project Members,Nature 491,683 (2012). 8. D.J.Lunt et al.,Nat.Geosci.3,60 (2010). 9. S.C.Sherwood et al.,Rev.Geophys.58,e2019RG000678 (2020). 10. A.S.von der Heydt et al.,Curr.Clim.Change Rep.2,148 (2016). 11. A.M.Haywood et al.,Earth Syst.Environ.3,1 (2019). 12. DeepMIP-Miocene,The Deep-Time Model Intercomparison Project; www.deepmip.org/ deepmip-miocene/. 13. H.J.Schellnhuber et al.,Nat.Clim.Chang.6,649 (2016). ACKNOWLEDGMENTS A.S.v.d.H. acknowledges support by the program of the Netherlands Earth System Science Centre (NESSC), finan- cially supported by the Ministry of Education, Culture and Science (OCW) and the TiPES project (TiPES contribution no. 161), which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 820970. 10.1126/science.abq6542 SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 27

INSIGHTS | PERSPECTIVES anxiety, as reported by Yu et al., is not equivo- in turn exacerbate the susceptibility to new HEALTH TECHNOLOGY cal: Are these phenomena causally linked or episodes and progression of such disorders do they occur in parallel? A causal relation- (12, 13). However, there may be two impor- Cooling the pain ship is suggested by the observation that tant differences between such pathological VTAVgat-Sst stimulation during artificial sleep conditions and the one described by Yu et A miniaturized, flexible deprivation after social defeat cannot restrain al. Single stressors may have different con- cooling device can be used anxiety, nor (fully) normalize stress hormone sequences than the wear and tear caused for precise analgesia concentrations in plasma. Yet, chemogenetic by a chronic state of (unpredictable) stress. stimulation of VTAVgat-Sst cells (in the absence Furthermore, the induction of sleep may By Shan Jiang1,2 and Guosong Hong1,2 of social defeat) increases sleep but does not be specific for stressful situations such affect concentrations of the stress hormones as social defeat that have little ambiguity, A s one of the most critical health corticotropin-releasing factor (CRF) and cor- whereas stressors with a more uncertain problems, pain afflicts one in five ticosterone. This suggests that parallel path- outcome may affect sleep negatively. Even adults in the world (1). Despite the ways might regulate sleep and anxiety, which though social defeat is a negative live event, efficacy of opioids in treating pain, is also supported by recent studies showing it is relatively straightforward: The defeated opioid use disorder and overdose the importance of a reciprocal loop between mouse knows exactly what the consequence have motivated the development of the VTA and parts of the amygdala in social is—i.e., a subordinate position. nonopioid alternatives, such as other an- defeat–induced anxiety (6, 7). The parallel algesics (2), electrical stimulation (3), and pathways of VTA–lateral hypothalamus to Not all individuals may respond to social acupuncture (4) for pain management. regulate sleep and VTA-amygdala to regulate defeat with a bout of sleep. Recent findings Among these alternatives, analgesic nerve anxiety are reminiscent of the observation showed that social stress promotes sleep- cooling offers an effective and reversible that glucocorticoid receptor deletion in pre- like inactivity in mice, with a large degree of strategy to alleviate pain (5). On page 109 frontal dopaminoceptive neurons decreases variation among experimental animals (14). of this issue, Reeder et al. (6) report a min- social avoidance but not anxiety and fear This variation is also noticeable in the experi- iaturized and implantable cooling system memories after mice were subjected to 10 ments by Yu et al.: About half of the animals that integrates state-of-the-art microfluidic days of social defeat (8). showed a strong increase in REM sleep du- and flexible electronic technologies in a ration, whereas the remaining mice slept biodegradable platform for localized tem- It could be hypothesized that sleep in- the same amount as controls. This requires perature control and precise pain relief. duced by the hypothalamus and activation of further investigation in larger groups of mice the hypothalamic–pituitary–adrenal (HPA) (15), which would also be helpful to probe the Analgesic nerve cooling leverages the axis (which eventually causes a rise in cir- robustness of the current explorative study. temperature dependence of chemical reac- culating corticosterone concentration) may The source of interindividual variation could tion rates to effectively reduce the meta- affect social aversion, and through a paral- arise from the animal’s sex (the social defeat bolic, electrogenic, and ionic activity in the lel pathway involving limbic regions, reduce model is optimized for male mice), and ge- neural tissue at lower temperatures (7). A anxiety (9, 10). Thus, during sleep, events netic predisposition, and be modulated by moderate temperature decrease in nerves to experienced while awake are replayed, bind- life events, affecting the sleep pattern, per- 15°C has been reported to block the trans- ing elements of the experience in various sonality, stress responsivity, ability to con- mission of compound nerve action poten- parts of the brain and forming a memory textualize, and so on—or any combination tials, whereas a complete nerve conduction of the situation (11). Such memory-enhanc- of these. Knowing the essential steps in the block can be achieved at 5°C (8). The risk ing effects of sleep are particularly strong brain may help steer future interventions of inducing nerve damage at an even lower for locations with an aversive connotation, in rodents and perhaps even humans after temperature calls for precise control of local as in the case of a social defeat experience. stressful experiences, be it through cognitive cooling. Conventional nerve-cooling meth- Eventually this results in the formation of therapy or pharmacotherapy or maybe, one ods rely on precooled liquids, such as meth- gist-like memories. REM sleep is proposed day, genetic interference. j anol, delivered through a metal or silicone to depotentiate amygdala reactivation loop or a thermoelectric device (9). These (which is associated with anxiety), tuning REFERENCES AND NOTES interfaces are constrained by their bulky down amygdala inputs to the hippocampus and rigid structures, nonspecific cooling, (12). This would allow contextual elements 1. X.Yu et al., Science 377, 63 (2022). and high-power requirement, thus limiting to be stored, freed from the anxious con- 2. W. Schultz, P. Dayan, P. R. Montague, Science 275, 1593 their chronic application in the peripheral text. Overall, interconnected parallel loops nervous system. appear to be involved in the processing of (1997). various elements that are intrinsic to a so- 3. S. Ghosal, C. Sandi, M.A. van der Kooij, An implantable cooling device with on- cial defeat experience (see the figure). demand local analgesia will be a game Neuropharmacology 159, 107498 (2019). changer for long-term pain management. Sleep and stress entertain a complex 4. C. Bouarab, B.Thompson,A. M. Polter, Front Neural Reeder et al. capitalized on their expertise courtship. Intuitively, falling asleep after in advanced flexible microsystems (10) to experiencing stress may not sound logical: Circuits 13, 78 (2019). create a microfluidic cooling device with Almost all mood and anxiety disorders are 5. L. L. Ferrari et al., J. Neurosci. 38, 1588 (2018). real-time temperature feedback. Compared characterized by sleep abnormalities, which 6. N. Dedic et al., Front. Neurosci. 13, 986 (2019). 7. C. Morel et al., Nat. Commun. 13, 1532 (2022). 1Department of Materials Science and Engineering, 1Department of Translational Neuroscience, University 8. J. Barik et al., Science 339, 332 (2013). Stanford University, Stanford, CA 94305, USA. 2Wu Tsai Medical Center Utrecht, Utrecht University, Utrecht, 9. P. Belujon,A.A. Grace, Int.J. Neuropsychopharmacol. 20, Neurosciences Institute, Stanford University, Stanford, CA Netherlands. 2University Medical Center Groningen, 94305, USA. Email: [email protected] University of Groningen, Groningen, Netherlands. 3Leiden 1036 (2017). Academic Center for Drug Research, Leiden University 10. E. H. Douma, E. R. de Kloet, Neurosci. Biobehav. Rev. 108, Medical Center, Leiden University, Leiden, Netherlands. Email: [email protected] 48 (2020). 11. J. G. Klinzing, N. Niethard,J. Born, Nat. Neurosci. 22, 1598 (2019). 12. A. N. Goldstein, M. P.Walker, Annu. Rev. Clin. Psychol. 10, 679 (2014). 13. C. Baglioni et al., Psychol. Bull. 142, 969 (2016). 14. M. Nagai, H. Nagai, C. Numa,T. Furuyashiki, Sci. Rep. 10, 19800 (2020). 15. V. Bonapersona, H. Hoijtink, R.A. Sarabdjitsingh, M. Joëls, Nat. Neurosci. 24, 470 (2021). 10.1126/science.adc9782 28 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

INSIGHTS | PERSPECTIVES anxiety, as reported by Yu et al., is not equivo- in turn exacerbate the susceptibility to new HEALTH TECHNOLOGY cal: Are these phenomena causally linked or episodes and progression of such disorders do they occur in parallel? A causal relation- (12, 13). However, there may be two impor- Cooling the pain ship is suggested by the observation that tant differences between such pathological VTAVgat-Sst stimulation during artificial sleep conditions and the one described by Yu et A miniaturized, flexible deprivation after social defeat cannot restrain al. Single stressors may have different con- cooling device can be used anxiety, nor (fully) normalize stress hormone sequences than the wear and tear caused for precise analgesia concentrations in plasma. Yet, chemogenetic by a chronic state of (unpredictable) stress. stimulation of VTAVgat-Sst cells (in the absence Furthermore, the induction of sleep may By Shan Jiang1,2 and Guosong Hong1,2 of social defeat) increases sleep but does not be specific for stressful situations such affect concentrations of the stress hormones as social defeat that have little ambiguity, A s one of the most critical health corticotropin-releasing factor (CRF) and cor- whereas stressors with a more uncertain problems, pain afflicts one in five ticosterone. This suggests that parallel path- outcome may affect sleep negatively. Even adults in the world (1). Despite the ways might regulate sleep and anxiety, which though social defeat is a negative live event, efficacy of opioids in treating pain, is also supported by recent studies showing it is relatively straightforward: The defeated opioid use disorder and overdose the importance of a reciprocal loop between mouse knows exactly what the consequence have motivated the development of the VTA and parts of the amygdala in social is—i.e., a subordinate position. nonopioid alternatives, such as other an- defeat–induced anxiety (6, 7). The parallel algesics (2), electrical stimulation (3), and pathways of VTA–lateral hypothalamus to Not all individuals may respond to social acupuncture (4) for pain management. regulate sleep and VTA-amygdala to regulate defeat with a bout of sleep. Recent findings Among these alternatives, analgesic nerve anxiety are reminiscent of the observation showed that social stress promotes sleep- cooling offers an effective and reversible that glucocorticoid receptor deletion in pre- like inactivity in mice, with a large degree of strategy to alleviate pain (5). On page 109 frontal dopaminoceptive neurons decreases variation among experimental animals (14). of this issue, Reeder et al. (6) report a min- social avoidance but not anxiety and fear This variation is also noticeable in the experi- iaturized and implantable cooling system memories after mice were subjected to 10 ments by Yu et al.: About half of the animals that integrates state-of-the-art microfluidic days of social defeat (8). showed a strong increase in REM sleep du- and flexible electronic technologies in a ration, whereas the remaining mice slept biodegradable platform for localized tem- It could be hypothesized that sleep in- the same amount as controls. This requires perature control and precise pain relief. duced by the hypothalamus and activation of further investigation in larger groups of mice the hypothalamic–pituitary–adrenal (HPA) (15), which would also be helpful to probe the Analgesic nerve cooling leverages the axis (which eventually causes a rise in cir- robustness of the current explorative study. temperature dependence of chemical reac- culating corticosterone concentration) may The source of interindividual variation could tion rates to effectively reduce the meta- affect social aversion, and through a paral- arise from the animal’s sex (the social defeat bolic, electrogenic, and ionic activity in the lel pathway involving limbic regions, reduce model is optimized for male mice), and ge- neural tissue at lower temperatures (7). A anxiety (9, 10). Thus, during sleep, events netic predisposition, and be modulated by moderate temperature decrease in nerves to experienced while awake are replayed, bind- life events, affecting the sleep pattern, per- 15°C has been reported to block the trans- ing elements of the experience in various sonality, stress responsivity, ability to con- mission of compound nerve action poten- parts of the brain and forming a memory textualize, and so on—or any combination tials, whereas a complete nerve conduction of the situation (11). Such memory-enhanc- of these. Knowing the essential steps in the block can be achieved at 5°C (8). The risk ing effects of sleep are particularly strong brain may help steer future interventions of inducing nerve damage at an even lower for locations with an aversive connotation, in rodents and perhaps even humans after temperature calls for precise control of local as in the case of a social defeat experience. stressful experiences, be it through cognitive cooling. Conventional nerve-cooling meth- Eventually this results in the formation of therapy or pharmacotherapy or maybe, one ods rely on precooled liquids, such as meth- gist-like memories. REM sleep is proposed day, genetic interference. j anol, delivered through a metal or silicone to depotentiate amygdala reactivation loop or a thermoelectric device (9). These (which is associated with anxiety), tuning REFERENCES AND NOTES interfaces are constrained by their bulky down amygdala inputs to the hippocampus and rigid structures, nonspecific cooling, (12). This would allow contextual elements 1. X.Yu et al., Science 377, 63 (2022). and high-power requirement, thus limiting to be stored, freed from the anxious con- 2. W. Schultz, P. Dayan, P. R. Montague, Science 275, 1593 their chronic application in the peripheral text. Overall, interconnected parallel loops nervous system. appear to be involved in the processing of (1997). various elements that are intrinsic to a so- 3. S. Ghosal, C. Sandi, M.A. van der Kooij, An implantable cooling device with on- cial defeat experience (see the figure). demand local analgesia will be a game Neuropharmacology 159, 107498 (2019). changer for long-term pain management. Sleep and stress entertain a complex 4. C. Bouarab, B.Thompson,A. M. Polter, Front Neural Reeder et al. capitalized on their expertise courtship. Intuitively, falling asleep after in advanced flexible microsystems (10) to experiencing stress may not sound logical: Circuits 13, 78 (2019). create a microfluidic cooling device with Almost all mood and anxiety disorders are 5. L. L. Ferrari et al., J. Neurosci. 38, 1588 (2018). real-time temperature feedback. Compared characterized by sleep abnormalities, which 6. N. Dedic et al., Front. Neurosci. 13, 986 (2019). 7. C. Morel et al., Nat. Commun. 13, 1532 (2022). 1Department of Materials Science and Engineering, 1Department of Translational Neuroscience, University 8. J. Barik et al., Science 339, 332 (2013). Stanford University, Stanford, CA 94305, USA. 2Wu Tsai Medical Center Utrecht, Utrecht University, Utrecht, 9. P. Belujon,A.A. Grace, Int.J. Neuropsychopharmacol. 20, Neurosciences Institute, Stanford University, Stanford, CA Netherlands. 2University Medical Center Groningen, 94305, USA. Email: [email protected] University of Groningen, Groningen, Netherlands. 3Leiden 1036 (2017). Academic Center for Drug Research, Leiden University 10. E. H. Douma, E. R. de Kloet, Neurosci. Biobehav. Rev. 108, Medical Center, Leiden University, Leiden, Netherlands. Email: [email protected] 48 (2020). 11. J. G. Klinzing, N. Niethard,J. Born, Nat. Neurosci. 22, 1598 (2019). 12. A. N. Goldstein, M. P.Walker, Annu. Rev. Clin. Psychol. 10, 679 (2014). 13. C. Baglioni et al., Psychol. Bull. 142, 969 (2016). 14. M. Nagai, H. Nagai, C. Numa,T. Furuyashiki, Sci. Rep. 10, 19800 (2020). 15. V. Bonapersona, H. Hoijtink, R.A. Sarabdjitsingh, M. Joëls, Nat. Neurosci. 24, 470 (2021). 10.1126/science.adc9782 28 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

with other approaches to achieving nerve for precise control of local temperatures. blocks of rat sciatic nerves, as observed blocks, their device outperforms conven- In achieving spatiotemporally precise by electromyography, compound nerve tional in vivo cooling methods for several action potential, and muscle-force mea- reasons (see the figure). Composed of ser- cooling, Reeder et al. demonstrate the surements. Furthermore, the stretchable pentine architectures and elastomeric ma- power of engineering advances in address- cooling device achieved analgesia in freely terials with similar elasticity to those of pe- ing unmet biomedical needs. The evapora- moving rats with neuropathic pain over ripheral nerves, the device is soft, flexible, tive cooling scheme has been applied in several weeks after implantation, as dem- and stretchable. Because of its tissue-like the thermal management of high-density onstrated in von Frey anesthesiometer mechanical properties, this device readily electronics (11). However, its application in measurements and histological analyses. wraps around the nerve like a cuff elec- pain management in living organisms has This stable interface, along with its degra- trode, forming an intimate interface to fa- so far been limited. This is largely because dation over time, enables on-demand pain cilitate effective heat transfer. The device of the shape mismatch at the thermal in- management with long-term utility while terface because these devices usually come obviating the need for surgical extraction after the period of intervention. The flexible and bioresorbable microfluidic cooler for nerve blocks Besides the demonstrated strengths of the miniaturized, flexible cooling device With embedded microfluidics and microelectronics, this bioresorbable for pain mitigation, the technology pre- device can achieve precise and reversible pain mitigation through local sents further opportunities for neurosci- coolant evaporation in the microfluidic channel, where the neighboring ence research and neurological practice. temperature sensor monitors real-time temperature changes. Specifically, cortical cooling has been used as a nongenetic means to silence neural Nerve Bioresorbable activities and investigate circuit dynam- platform ics in the brain (14). The localized, revers- Acute pain ible cooling effect represents an attractive signals Microfluidic method for manipulating neural activi- system ties with high spatiotemporal resolutions, Nitrogen flow to chronic utility, and minimal invasiveness trigger the evaporation in nonhuman primates and even humans. of perfluoropentane In addition, this technology offers a non- opioid alternative for targeted, on-demand Temperature pain relief in current hospital settings. A sensor wearable cooling device with a more com- pact integration of its components helps GRAPHIC: V. ALTOUNIAN/SCIENCE is also bioresorbable; it dissolves in physio- in the form of rigid parallel plates (12), achieve point-of-care pain management. logical fluids over months and yields a min- making them less than ideal for accompa- By leveraging the latest advances in flex- imal inflammatory response in the tissue. nying nerves, which, by contrast, are soft ible and stretchable bioelectronics, an The gradual biodegradation of the device and geometrically complex. all-in-one nerve interface with cooling, is attributed to a bioresorbable elastomer temperature monitoring, and electrophysi- known as poly(octanediol citrate), which is Reeder et al. applied evaporative cooling ological recordings may be possible in the used to build the microfluidic system. In in a soft and stretchable microfluidic plat- future, offering real-time adjustment of addition, the device leverages an evapora- form, which has previously been used for cooling temperatures, duration, and inter- tive mechanism to produce rapid cooling, drug delivery in the nervous system. The mittency to achieve desired physiological in contrast to conventional precooled liq- bioinertness of perfluoropentane and its and therapeutic effects. j uids with slower temperature reduction clinically approved use as an intravenous kinetics. Because the spatial spread of ultrasound contrast agent justify its use as a REFERENCES AND NOTES heat diffusion scales with time, more rapid biocompatible liquid coolant in vivo. By tak- cooling, along with the low heat capacity of ing advantage of the low boiling point and 1. D. S. Goldberg, S.J. McGee, BMC Public Health 11, 770 exhaust gas, yields greater spatial confine- high enthalpy of vaporization of perfluoro- (2011). ment and more localized analgesia down pentane (13) alongside the use of dry nitro- to the millimeter scale. Lastly, this device gen gas, the device created by Reeder et al. 2. N. B. Finnerup, N. Engl.J. Med. 380, 2440 (2019). incorporates a temperature sensor in an achieved a maximum cooling rate of 38C/s. 3. M.Johnson, Rev. Pain 1, 7 (2007). electronic layer alongside the microfluidic 4. B. M. Berman, H. M. Langevin, C. M.Witt, R. Dubner, system, which provides real-time feedback When tested on rats, their device pro- duced highly localized cooling and enabled N. Engl.J. Med. 363, 454 (2010). efficacious and reversible conduction 5. E. Ernst,V. Fialka, J. Pain Symptom Manage. 9, 56 (1994). 6. J.T. Reeder et al., Science 377, 109 (2022). 7. R.Janssen, Neurosci. Biobehav. Rev. 16, 399 (1992). 8. T. Morgan et al., J. Neurophysiol. 123, 2173 (2020). 9. S. G. Lomber, B. R. Payne,J.A. Horel, J. Neurosci. Methods 86, 179 (1999). 10. E. Song,J. Li, S. M.Won,W. Bai,J.A. Rogers, Nat. Mater. 19, 590 (2020). 11. M. M. Nahar et al., Appl.Therm. Eng. 194, 117109 (2021). 12. A. Bar-Cohen, G. Sherwood, M. Hodes, G. Solbreken, Microelectron. Reliab. 37, 502 (1997). 13. J. S. Chickos,W. E.Acree Jr., J. Phys. Chem. Ref. Data 32, 519 (2003). 14. C. R. Ponce, S. G. Lomber, R.T. Born, Nat. Neurosci. 11, 216 (2008). 10.1126/science.abm8159 SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 29

INSIGHTS | PERSPECTIVES TSUNAMIS The wave blown around the world The atmospheric wave from the Tonga eruption drove faster-than-normal tsunamis By Emily E. Brodsky and Thorne Lay develop forecasting and warning systems simultaneously compressing (like a sound O n 15 January 2022, unusual waves for tsunamis that now produce reasonably wave) while having an accompanying appeared in Earth’s atmosphere and oceans (1–3). The origin of the accurate predictions after earthquakes of buoyancy force at the air-sea interface. In waves was clearly the catastrophic volcanic eruption in Tonga, which when and where tsunamis will occur as effect, the air wave blew the tsunami wave pummeled the atmosphere with the largest eruptive plume since the 1883 erup- well as how high the waves will be. across the ocean, even passing over conti- tion of Krakatoa, Indonesia. On page 95 of this issue, Matoza et al. (4) show that the Surprisingly, the first tsunami arrivals nents and driving new tsunamis when the 2022 Tonga eruption generated waves in the water, air, and even in the ionosphere produced by the Tonga eruption were ob- ocean was again encountered. that wrapped around Earth multiple times. Tsunamis appeared to hop across served several hours earlier than antici- This rare method of tsunami genera- the land into all of the major ocean basins. And on page 91 of this issue, Kubota et al. pated. Kubota et al. explain that the fast tion has a precedent in the last eruption (5) explain that the tsunamis arrived much earlier than expected on the basis of con- and complex tsunamis result from how the that produced such strong atmospheric ventional tsunami modeling, and the wave trains lasted much longer than for even ocean interacts with the atmosphere after waves. Like the 2022 eruption in Tonga, the largest earthquakes (5). a volcanic eruption (see the figure). They the 1883 Krakatoa event also produced Tsunamis are ocean waves with several- hundred-kilometer-long wavelengths that show that the atmospheric and oceanic an intense atmospheric acoustic-gravity are usually caused by sudden perturba- tions of the ocean. Giant earthquakes, dynamics are intimately connected. The wave and infrasound that could be heard such as the 2004 magnitude 9.2 Suma- tra earthquake, can produce abrupt sea- atmospheric waves were accompanied by up to 3000 miles away (4). In 1955, Press floor movements that extend as much as 1500 km along the fault rupture on a coupled oceanic wave that traveled at a and Ewing (6) noted that air-pressure in- a tectonic plate boundary, displacing the overlying ocean and generating a dev- speed that exceeded that of conventional creases were coincident with initial oce- astating tsunami. But earthquakes are not the only events that trigger tsunamis— tsunami gravity waves in the ocean (~200 anic waves observed around the world. In landslides and volcanic eruptions can also displace large volumes of water in the m/s). The coupled wave can be modeled as 1967, Harkrider and Press (7) went on to ocean and produce tsunami waves. an acoustic-gravity wave, which travels by analyze the coupled motion of the ocean Once the water is displaced, tsuna- mis travel as ordinary gravity waves and atmosphere to quantify with buoyancy providing the re- storing force. Gravity waves in the the mechanistic connection. ocean include the familiar waves on the sea surface that break Multiple tsunami generation mechanisms Of course, the data from 1883 on the seashore. Tsunamis are were difficult to analyze and usually governed by the same The January 2022 Tonga eruption generated waves in the oceans, the Krakatoa observation stood physics. However, because of atmosphere, and ionosphere as reported by Matoza et al., including as an oddity in the annals of their long wavelengths, the unusual tsunamis blown by atmosphere at the air-sea interface as tsunami generation until the speed and path of the grav- shown by Kubota et al. ity waves are determined by the variable depth of 2022 eruption in Tonga pro- the ocean. Investments in tsunami modeling, duced extensive global obser- motivated by the events of the 2004 Indian Ocean Infrasound Tonga volcano Ionosphere vations (4). tsunami and the 2011 Tohoku waves and The wavefield that resulted tsunami in Japan, have helped atmosphere was captured with unprece- dented resolution as explained Ocean by Matoza et al. The rich data make it clear that very large- Earth scale atmospheric transients of eruptions or atmospheric im- pacts should be expected to pro- duce large, fast, and complex tsunamis around the world. The volcanic blast produced a Island Ordinary tsunamis nondispersive wave in the at- Continent are gravity waves in the mosphere that traveled along ocean generated by the Earth’s surface with a pressure displacement of water oscillation lasting over 2000 s GRAPHIC: V. ALTOUNIAN/SCIENCE near the volcano. that expanded away from the source at about 315 m/s (4, 5, Driven tsunamis are 8–11). Slower acoustic waves coupled acoustic-gravity were of high enough frequen- waves that travel along cies (>20 Hz infrasound) that the air-sea interface. they could be heard by people Scattered tsunamis in Alaska, more than 6000 are generated by the interaction of the tsunami Department of Earth and Planetary waves with islands and Sciences, University of California Santa other obstacles. Cruz, CA, USA Email: [email protected] 30 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

miles away from the erupting volcano. N E U R O D E G E N E R AT I O N In addition, conventional tsunami waves Elucidating the causes of were generated near the source in response neurodegeneration to the initial ocean displacement, and scat- tered tsunami waves were generated as Investigating phase separation in neurodegeneration the driven wave encountered variations highlights evidence needed for causation in ocean depth across the Pacific. This combination of generation mechanisms By Gregory A. Petsko1 and Scott A. Small2 (whether key molecules of the pathway are produced the very long-lasting sequence dysregulated in the disease), cellular biol- of tsunami waves, including the largest H ow can a given gene, or gene prod- ogy (when disrupted, whether the pathway waves, which were twice as large as the ini- uct, or the cellular pathway it serves causes the disease’s cardinal cellular pa- tial atmospherically coupled one (11). Even be determined as causal for neuro- thologies), and anatomical biology (when more elastic waves were produced in the degenerative diseases instead of be- disrupted, whether the pathway causes the solid earth and were observed on seismom- ing a consequence of the underlying disease’s cardinal anatomical pathology). In eters globally (12). pathology? There are questions about the case of Alzheimer’s disease, the hypoth- the current theories that explain neurode- esis that misprocessing of the amyloid-b The 2022 Tonga eruption reawakens generation, with therapeutic strategies pro- precursor protein (APP) produces cytotoxic curiosity about processes crossing tradi- ducing disappointing results. On page 46 of extracellular amyloid plaques fulfills parts tional boundaries between Earth systems. this issue, Zhou et al. (1) attempt to address of the first two criteria. But amyloid plaque Atmosphere–Ocean–Solid Earth coupling whether the aberrant phase separation of deposition is not primarily observed in the is a major focus of climate research, yet protein domains of low amino acid sequence trans-entorhinal cortex (TEC), where neuro- observations that directly sample their complexity are causally pathogenic in sev- degeneration begins in Alzheimer’s disease— interaction may have been underutilized. eral neurodegenerative diseases, including a an anatomical mismatch between plaques Volcanic eruption studies show that the form of frontotemporal dementia. Their ap- and neurodegeneration noted by Alzheimer tools of infrasound and seismology that proach has potential application in identify- himself (4). The TEC is important in short- have traditionally been used to study the ing causative factors in a range of disorders, term memory and navigation, which become solid Earth potentially have much broader as well as to the formation of membraneless disrupted in Alzheimer’s disease. Two prom- uses. New technologies and networks in organelles in normal cells. ising new hypotheses for the causes of neu- a data-rich world are providing windows rodegeneration in Alzheimer’s disease—dys- into dynamic interactions between Earth’s In 1884, Robert Koch and Friedrich function of the innate immune system in the systems. Oceans, rivers, glaciers, and hur- Loeffler proposed postulates to establish brain (5) and defects in endosomal protein ricanes all produce distinctive waves that that a microorganism caused an infec- trafficking (6)—are not mutually exclusive; are now routinely recorded on global net- tious disease (2). Despite many iterations of the latter may fulfill all three criteria (7). works (13–15). Earth’s systems are broad- Kochs’ postulates since (3), the concept of a casting their interactions through multiple set of criteria that should be satisfied to de- Zhou et al. describe experiments aimed types of waves, and now instrumentation termine causality for an infectious disease at satisfying these criteria in an attempt is in place to receive their signals. It is up remains useful. Nowhere is such rigor more to resolve an ongoing controversy about to the scientific community to reach out needed than in the case of neurodegenera- how low-complexity sequence domains across the disciplinary boundaries and use tive diseases. The complexity, chronicity, and form membraneless organelles (8) but also the data to ask the right questions about relative inaccessibility to experimentation of to identify a causal mechanism for several the entire Earth system. j the human brain, and lack of good animal neurodegenerative diseases. It has been models, as well as the phenotypic heteroge- known for more than a century that eukary- REFERENCES AND NOTES neity and age dependence of most of these otic cells contain phase-separated liquid- disorders make finding causal biological like droplets, but interest in their composi- 1. D.Adam, Nature 601, 497 (2022). pathways very difficult. Consequently, spe- tion and function waned. However, in 2009, 2. D. R.Themens et al., Geophys. Res. Lett. 49, cific criteria to establish causality for a neu- germline P granules in Caenorhabditis el- rodegenerative disease and to validate a egans were shown to be liquid droplets that 2022GL098158 (2022). target and therapeutic approach might be displayed similar behavior to that of oil in 3. D.A.Yuen et al., Earthquake Res.Adv. 10.1016/j. useful. Ideally, given the complexity of the water (9). Further work revealed that such problem, such postulates should reflect an phase separation was common, especially eqrea.2022.100134 (2022). integrative biology approach (see the figure). for some protein-RNA complexes, and it 4. R. S. Matoza et al., Science 377, 95 (2022). was proposed that the resulting membrane- 5. T. Kubota et al., Science 377, 91 (2022). A set of criteria are proposed, integrat- less organelles likely played important 6. M. Ewing, F. Press, Trans.Am. Geophys. Union 36, 53 ing evidence from human molecular biology functional roles in the regulation of gene expression and nuclear import (10) by pro- (1955). 1Ann Romney Center for Neurologic Diseases, Department viding a way to temporarily organize criti- 7. D. Harkrider, F. Press, Geophys.J. Int. 13, 149 (1967). of Neurology, Brigham & Women’s Hospital and Harvard cal components without the complexity of 8. S. Otsuka, Geophys. Res. Lett. 49, e2022GL098324 Medical School, Boson, MA, USA. 2Taub Institute for transporting molecules across a membrane. Research on Alzheimer’s Disease and the Aging Brain, (2022). Department of Neurology, Columbia University, New York, In 2012, amyloid-like fibers were identi- 9. A.Amores et al., Geophys. Res. Lett. 49, NY, USA. Email: [email protected]; fied in hydrogels formed from low-complex- [email protected] e2022GL098240 (2022). 10. J.-T. Lin et al., Geophys. Res. Lett. 49, e2022GL098222 (2022). 11. M. Carvajal, I. Sepúlveda,A. Gubler, R. Garreaud, Geophys. Res. Lett. 49, 2022GL098153 (2022). 12. P. Poli, N. M. Shapiro, Geophys. Res. Lett. 49, e2022GL098123 (2022). 13. K. L. Cook, M. Dietze, Annu. Rev. Earth Planet. Sci. 50, 183 (2022). 14. H. R. Shaddox, E. E. Brodsky, S. R. Ramp, K.A. Davis, AGU Adv. 2, e2021AV000475 (2021). 15. T.Tanimoto,A. Lamontagne, Geophys. Res. Lett. 41, 7532 (2014). 10.1126/science. abq5392 SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 31

miles away from the erupting volcano. N E U R O D E G E N E R AT I O N In addition, conventional tsunami waves Elucidating the causes of were generated near the source in response neurodegeneration to the initial ocean displacement, and scat- tered tsunami waves were generated as Investigating phase separation in neurodegeneration the driven wave encountered variations highlights evidence needed for causation in ocean depth across the Pacific. This combination of generation mechanisms By Gregory A. Petsko1 and Scott A. Small2 (whether key molecules of the pathway are produced the very long-lasting sequence dysregulated in the disease), cellular biol- of tsunami waves, including the largest H ow can a given gene, or gene prod- ogy (when disrupted, whether the pathway waves, which were twice as large as the ini- uct, or the cellular pathway it serves causes the disease’s cardinal cellular pa- tial atmospherically coupled one (11). Even be determined as causal for neuro- thologies), and anatomical biology (when more elastic waves were produced in the degenerative diseases instead of be- disrupted, whether the pathway causes the solid earth and were observed on seismom- ing a consequence of the underlying disease’s cardinal anatomical pathology). In eters globally (12). pathology? There are questions about the case of Alzheimer’s disease, the hypoth- the current theories that explain neurode- esis that misprocessing of the amyloid-b The 2022 Tonga eruption reawakens generation, with therapeutic strategies pro- precursor protein (APP) produces cytotoxic curiosity about processes crossing tradi- ducing disappointing results. On page 46 of extracellular amyloid plaques fulfills parts tional boundaries between Earth systems. this issue, Zhou et al. (1) attempt to address of the first two criteria. But amyloid plaque Atmosphere–Ocean–Solid Earth coupling whether the aberrant phase separation of deposition is not primarily observed in the is a major focus of climate research, yet protein domains of low amino acid sequence trans-entorhinal cortex (TEC), where neuro- observations that directly sample their complexity are causally pathogenic in sev- degeneration begins in Alzheimer’s disease— interaction may have been underutilized. eral neurodegenerative diseases, including a an anatomical mismatch between plaques Volcanic eruption studies show that the form of frontotemporal dementia. Their ap- and neurodegeneration noted by Alzheimer tools of infrasound and seismology that proach has potential application in identify- himself (4). The TEC is important in short- have traditionally been used to study the ing causative factors in a range of disorders, term memory and navigation, which become solid Earth potentially have much broader as well as to the formation of membraneless disrupted in Alzheimer’s disease. Two prom- uses. New technologies and networks in organelles in normal cells. ising new hypotheses for the causes of neu- a data-rich world are providing windows rodegeneration in Alzheimer’s disease—dys- into dynamic interactions between Earth’s In 1884, Robert Koch and Friedrich function of the innate immune system in the systems. Oceans, rivers, glaciers, and hur- Loeffler proposed postulates to establish brain (5) and defects in endosomal protein ricanes all produce distinctive waves that that a microorganism caused an infec- trafficking (6)—are not mutually exclusive; are now routinely recorded on global net- tious disease (2). Despite many iterations of the latter may fulfill all three criteria (7). works (13–15). Earth’s systems are broad- Kochs’ postulates since (3), the concept of a casting their interactions through multiple set of criteria that should be satisfied to de- Zhou et al. describe experiments aimed types of waves, and now instrumentation termine causality for an infectious disease at satisfying these criteria in an attempt is in place to receive their signals. It is up remains useful. Nowhere is such rigor more to resolve an ongoing controversy about to the scientific community to reach out needed than in the case of neurodegenera- how low-complexity sequence domains across the disciplinary boundaries and use tive diseases. The complexity, chronicity, and form membraneless organelles (8) but also the data to ask the right questions about relative inaccessibility to experimentation of to identify a causal mechanism for several the entire Earth system. j the human brain, and lack of good animal neurodegenerative diseases. It has been models, as well as the phenotypic heteroge- known for more than a century that eukary- REFERENCES AND NOTES neity and age dependence of most of these otic cells contain phase-separated liquid- disorders make finding causal biological like droplets, but interest in their composi- 1. D.Adam, Nature 601, 497 (2022). pathways very difficult. Consequently, spe- tion and function waned. However, in 2009, 2. D. R.Themens et al., Geophys. Res. Lett. 49, cific criteria to establish causality for a neu- germline P granules in Caenorhabditis el- rodegenerative disease and to validate a egans were shown to be liquid droplets that 2022GL098158 (2022). target and therapeutic approach might be displayed similar behavior to that of oil in 3. D.A.Yuen et al., Earthquake Res.Adv. 10.1016/j. useful. Ideally, given the complexity of the water (9). Further work revealed that such problem, such postulates should reflect an phase separation was common, especially eqrea.2022.100134 (2022). integrative biology approach (see the figure). for some protein-RNA complexes, and it 4. R. S. Matoza et al., Science 377, 95 (2022). was proposed that the resulting membrane- 5. T. Kubota et al., Science 377, 91 (2022). A set of criteria are proposed, integrat- less organelles likely played important 6. M. Ewing, F. Press, Trans.Am. Geophys. Union 36, 53 ing evidence from human molecular biology functional roles in the regulation of gene expression and nuclear import (10) by pro- (1955). 1Ann Romney Center for Neurologic Diseases, Department viding a way to temporarily organize criti- 7. D. Harkrider, F. Press, Geophys.J. Int. 13, 149 (1967). of Neurology, Brigham & Women’s Hospital and Harvard cal components without the complexity of 8. S. Otsuka, Geophys. Res. Lett. 49, e2022GL098324 Medical School, Boson, MA, USA. 2Taub Institute for transporting molecules across a membrane. Research on Alzheimer’s Disease and the Aging Brain, (2022). Department of Neurology, Columbia University, New York, In 2012, amyloid-like fibers were identi- 9. A.Amores et al., Geophys. Res. Lett. 49, NY, USA. Email: [email protected]; fied in hydrogels formed from low-complex- [email protected] e2022GL098240 (2022). 10. J.-T. Lin et al., Geophys. Res. Lett. 49, e2022GL098222 (2022). 11. M. Carvajal, I. Sepúlveda,A. Gubler, R. Garreaud, Geophys. Res. Lett. 49, 2022GL098153 (2022). 12. P. Poli, N. M. Shapiro, Geophys. Res. Lett. 49, e2022GL098123 (2022). 13. K. L. Cook, M. Dietze, Annu. Rev. Earth Planet. Sci. 50, 183 (2022). 14. H. R. Shaddox, E. E. Brodsky, S. R. Ramp, K.A. Davis, AGU Adv. 2, e2021AV000475 (2021). 15. T.Tanimoto,A. Lamontagne, Geophys. Res. Lett. 41, 7532 (2014). 10.1126/science. abq5392 SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 31

INSIGHTS | PERSPECTIVES ity domains (11). Low-complexity domains sheet structure is the mechanism that drives tion, Zhou et al. looked for disease-causing are stretches of protein sequence compris- both membraneless organelle formation and mutations in proline residues in other low- ing only a few different amino acids; they pathogenesis in certain neurodegenerative complexity domains (the molecular biology have been found in most of the proteins diseases. In so doing, they solve a thorny criterion). They found such mutations in in membraneless organelles. Many have problem: how to test the role of the polypep- neurofilament light chain (NFL): When Pro22 also been linked to neurologic disorders, tide chain backbone when virtually any mu- or Pro8 are mutated, NFL forms stable aggre- the prevailing hypothesis being that this tation will leave that backbone intact. They gates that cause Charcot-Marie-Tooth disease self-association sequesters critical proteins stitched synthetic peptides with one modified (an inherited peripheral nerve disorder). from their normal function and recruits backbone residue into the middle of the low- Moreover, capping the residues replacing other key cellular components into the fi- complexity domain in the RNA binding pro- the proline with backbone-nitrogen methyl groups restored normal NFL be- havior in biochemical assays. Integrative biology as evidence for causation in neurodegeneration Similar analyses of disease- causing mutations in prolines in Three main criteria should be met for establishing causation in neurodegenerative diseases: Key molecules of a biological the tau protein, which give rise to frontotemporal dementia, and pathway should be dysregulated in the disease (molecular biology), and when disrupted, the pathway should cause the disease’s cardinal cellular pathologies (cellular biology) and explain the disease’s anatomical vulnerability (anatomical biology). in heterogeneous nuclear ribo- Molecular biology Cellular biology Anatomical biology nucleoprotein A2 (hnRNPA2), which cause Paget’s disease, are Stage I-II Stage III-IV consistent with the model that cross–b sheet formation is im- portant for low-complexity do- Mixed phase Glial Stage V-VI main labile self-association. The cells Trans- results also suggest that making Liquid droplet these dynamic structures too sta- entorhinal ble—for example, when the stra- cortex tegically placed proline residues Irreversible Dying that keep the structure labile solid aggregate neurons are mutated—is pathogenic be- cause the dynamic assembly and For example, mutated low-complexity Neurodegeneration and neuro- For example, neurodegeneration begins disassembly of low-complexity domain proteins form less dynamic inflammation are cardinal cellular in the trans-entorhinal cortex in domain proteins with their part- membraneless organelles in several pathologies in neurodegenerative Alzheimer's disease and then spreads ners is essential for the normal neurodegenerative diseases. diseases. across the brain. function of the cell. Work such as that of Zhou et al., as well as by bril. But unlike the amyloid fibrils observed tein TDP-43 (TAR DNA-binding protein 43). others, on protein aggregation has brought in Alzheimer’s disease and other neurode- TDP-43 mutations cause amyotropic lateral new rigor to understanding neurodegenera- generative diseases, the fibers in hydrogels sclerosis and frontotemporal dementia.  The tive diseases, and consequently, prospects for had few interfacial hydrophobic residues authors made 24 synthetic peptides, each of finding definitive causes and effective thera- and were highly labile. which put a methyl cap on a single-peptide pies are brighter. At least for some disorders, Controversy has arisen around the role of backbone nitrogen atom, blocking its ability finding ways to maintain reversible phase secondary and tertiary structures in the self- to form the interstrand hydrogen bonds of a separation of low-complexity domains now association of low-complexity domains and b sheet.  By adding this modification across seems an attractive strategy. j consequent phase separation. Two compet- the predicted cross–b sheet–forming region, REFERENCES AND NOTES GRAPHIC: KELLIE HOLOSKI/SCIENCE ing models have been proposed. In one (12), they map the precise region that requires low-complexity domain self-association is backbone hydrogen bonding and confirm 1. X.Zhou et al., Science 377, eabn5582 (2022). driven by the formation of a labile cross–b that the labile cross–b sheet structure medi- 2. R. Koch, Verhandlungen des X Internationalen sheet structure stabilized by hydrogen bonds ates self-association. That removal of a single between N–H and C=O groups of adjacent backbone hydrogen bond could disrupt the Medichinischen Congresses, Berlin 1, 35 (1890). strands of the polypeptide backbone. Because entire structure shows just how weak—and 3. A. L. Byrd,J.A. Segre, Science 351, 224 (2016). the polypeptide backbone is the same for therefore dynamic and reversible—the self- 4. A.Alzheimer, Z. Gesamte Neurol. Psychiatr. 4, 356 each residue, in this model specificity as to association actually is. which chains associate, and in what register, (1911). arises from some side chain interactions, as The authors go on to resolve how various 5. Y. Shi, D. M. Holtzman, Nat. Rev. Immunol. 18, 759 (2018). observed in crystal structures of amyloid-like low-complexity domain missense mutations 6. S.A. Small, G.A. Petsko, Sci.Transl. Med. 13, eabb1717 fibers (13). In the other model (14), specific in three different proteins are causative of secondary structure plays little or no role, several neurodegenerative diseases, showing (2020). and backbone interactions are not thought that all of them add stability to their cog- 7. S. Simoes et al., Cell Rep. 37, 110182 (2021). to be essential; coalescence is proposed to nate structures in a manner understandable 8. M. Kato,X.Zhou, S. L. McKnight, RNA 28, 3 (2022). through the lens of structural biology. Noting 9. C. P. Brangwynne et al., Science 324, 1729 (2009). 10. S. Frey, D. Görlich, Cell 130, 512 (2007). 11. M. Kato et al., Cell 149, 753 (2012). 12. S.Xiang et al., Cell 163, 829 (2015). 13. E. L. Guenther et al., Nat. Struct. Mol. Biol. 25, 463 (2018). 14. K.A. Burle et al., Mol. Cell 50, 231 (2015). be driven by stabilizing interactions between that mutating Pro320 in the TDP-43 low-com- ACKNOWLEDGMENTS specifically spaced side chains. plexity domain to Gly, Ser, and Ala (proline G.A.P. and S.A.S. are cofounders of Retromer Therapeutics, Zhou et al. have, in essence, applied the has no free backbone N–H to form an inter- which is developing treatments for neurodegenerative strand hydrogen bond; all other residues do) diseases. molecular biology and cell biology criteria to demonstrate that formation of the cross–b caused precipitation and stable fiber forma- 10.1126/science.adc9969 32 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

VIEWPOINT: COVID-19 endemic state at lower incidence. Other in- fections may display several years of altered The hiatus of the handshake seasonal patterns. Indeed, this is consistent with out-of-season respiratory syncytial vi- Human contact has been altered in ways that may affect rus (RSV) epidemics already documented endemic infections for years to come in summer 2021. For other infections, how- ever, it is likely that the current period of By Kristin Nelson1 and Ben Lopman1,2 contacts averaging less than five per day in very low incidence may be followed by re- early 2022—less than half of pre-pandemic surgence, and historical data may provide T he response to the COVID-19 pan- levels (1–3). This reduction so far seems sus- insight into what to expect. demic prompted abrupt and poten- tained, despite a return to workplaces and tially lasting changes to human be- the resumption of in-person schooling, so- For childhood infections that ceased to havior, including the types of direct cial activities, and large gatherings. circulate among the youngest children over contact that enable transmission of the past several years, first infections will common pathogens. Although the Not only are people interacting less, but occur at older ages and disease profiles for handshake and other types of physical con- where those interactions take place has some may be less severe. For example, the tact are gradually returning, they have been shifted. The move toward increased remote generally lower severity of dehydrating di- on an extended hiatus. Such changes have work options has de-densified workplaces, arrhea in a 5-year-old compared with an already altered the epidemiology of a broad reducing the number of contacts reported infant under 1 year of age. But for some in- range of infectious diseases, including in- at work, and is likely to reduce the contri- fections, such as varicella (chickenpox), dis- fluenza, measles, and norovirus, and will bution of these settings to disease transmis- ease is more likely to be severe at older ages. likely continue to affect their age distribu- sion. By contrast, school-based contacts are The increasing severity of poliomyelitis in tion, severity, and typical seasonal patterns. likely to return to typical, pre-pandemic the US in the 1950s was most likely the Changes to contact patterns may also nudge patterns (4). When they occur, interactions result of improvements in sanitation that the evolutionary trajectory of pathogens, may be somewhat less likely to transmit reduced environmental transmission and as they adapt to new norms of less human infection than those that occurred prior the risk of exposure at younger ages, which contact. Initiatives to measure social con- to the pandemic. Data show that contacts drove infections into older age groups in tact patterns through time and track their are less likely to involve physical touch now which paralysis is more common (7). effects on the epidemiology of endemic than before the pandemic and that masking pathogens are essential to both manage the remains common: ~30% of the US popu- For infections with strong seasonal pat- potential for resurgence of common infec- lation reports routinely masking at work, terns, persistently lower contact rates may tions and to reenergize control efforts. and ~25% of children are still masking at shift the timing of peaks. For example, school (5). However, studies from other lower levels of transmission may result in a There are two fundamental determi- countries suggest that these measures are delayed peak of seasonal infections, result- nants of the dynamics of directly transmit- now less common, underscoring the need to ing in stresses on the health care system ted infectious diseases: the human contact better understand how behaviors differ by at new times of the year. Any intervention that enables transmission and a pathogen’s location (6). Although it is uncertain how that reduces circulation of a pathogen may biological natural history. Reductions in long current levels of masking and physi- result in changes to its dynamics. For ex- human contact that occurred during the cal distancing will continue, the widespread ample, the introduction of rotavirus vac- COVID-19 pandemic have substantially normalization of this behavior suggests that cination—which protected vaccinated chil- affected patterns of circulation of other they are likely to continue in some form, dren and reduced transmission—in 2006 pathogens (see the figure). Reported inci- perhaps on public transport, in health care reduced overall rotavirus incidence and has dence of most directly transmitted infec- settings, and among people at high risk for since perturbed seasonal patterns (8). tions fell to virtually zero in early 2020 severe respiratory illness. amid initial lockdown measures. Although Sustained changes in human contact may these declines may have partially been due Even if these reductions in contact are also have the potential to drive the evolu- to gaps in reporting, they mostly reflect true modest, impacts on endemic diseases may tion of endemic pathogens. Those with reductions in disease incidence. As restric- be substantial. Many pathogens maintain a high transmissibility, either because of a tions were relaxed, circulation of certain fine balance of endemic equilibrium; that is, lower average infectious dose or a better infections resumed—in some cases, with with an effective reproduction number (the survival profile outside the host, could have shifted seasonal patterns—but they have yet number of cases caused by an infection in a an increasingly strong evolutionary advan- to return to their pre-pandemic levels. population with some immunity) close to 1. tage. Alternatively, pathogens with more Lower contact rates mean reduced trans- prolonged infectious periods that lead to Despite the widespread relaxation of non- mission and a disruption of this balance for more opportunities for transmission may pharmaceutical interventions, a return to the many pathogens that are transmitted also be more successful in a new normal pre-pandemic “normal” has yet to fully ma- directly from person to person. A near-com- defined by less human-to-human contact. terialize. Studies of specific populations in plete return to pre-pandemic contact rates Changes in the severity of endemic infec- the US are consistent with those from gen- after 2 years could result in considerable tions due to evolutionary pressures may be eral European populations, which report changes to transmission dynamics. Some harder to anticipate. The COVID-19 pan- pathogens that confer lifelong immunity demic underscores that the evolutionary 1Department of Epidemiology, Rollins School of Public may resurge to higher than pre-pandemic trajectory of pathogens does not always Health, Emory University, Atlanta, GA, USA. 2Gangarosa levels after an extended period of low cir- follow predictable patterns. The emergence Department of Environmental Health, Rollins School of culation, resulting from a buildup of sus- of the Delta severe acute respiratory syn- Public Health, Emory University, Atlanta, GA, USA. ceptible individuals, before settling into an drome coronavirus 2 (SARS-CoV-2) variant, Email: [email protected] which was more severe than its precursor, Alpha, was closely followed by less-severe Omicron variants (9, 10), illustrating that SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 33

INSIGHTS | PERSPECTIVES the evolution of virulence is not The effects of reduced contact on diseases terpretation is critical because constrained in one direction. caused by endemic pathogens multiple factors are at play— For pathogens that employ key among them, changing Weekly case reports of a selection of common pathogens in Germany are shown from health care seeking and test- multiple routes of transmis- January 2018 through May 2022 [source: SurvStat database (https://survstat.rki.de/)]. ing practices, which can bias sion, variants that are transmit- ted via environmental routes, 2000 Rotavirus traditional surveillance data. such as contaminated water, 1000 Nonetheless, combining robust soil, or objects, might outcom- Beginning of widespread case surveillance with genomic pete those that rely on direct 0 social distancing in Germany data and phylogenetic analysis contact. For example, geno- can provide signals of pathogen group 1 noroviruses, which 1000 Respiratory syncytial virus evolution and their potential are more often transmitted by impact on public health. food and water, may increase 500 At its core, infectious disease in prevalence relative to geno- epidemiology is the study of group 2 noroviruses, which Cases 0 person, place, and time: who are predominantly transmitted 40 Measles becomes sick, where infection through person-to-person con- and transmission occur, and tact (11). Notably, the incidence 20 when disease incidence rises of enteric pathogens such as 0 or falls. Substantial changes to Salmonella, which transmit human behavior in response to through routes that do not re- 500 Salmonella the COVID-19 pandemic stand quire direct person-to-person to affect all three, producing contact, were less affected by 250 ripple effects for many endemic social distancing. In the most 0 diseases and upending the cur- extreme scenario, fewer infec- 2018 2019 2020 2021 2022 rent understanding of their tions may slow or even stop the epidemiology. To adapt, modern evolution of endemic infections Possible future trajectories Lifelong immunity surveillance activities should if the effective reproductive ...with vaccination do more than count cases, it number is suppressed below 1 Accrual of susceptible people from reduced contact may should include human behav- for a sufficient amount of time. cause resurgence, which is slower for illnesses against which Temporary immunity ioral and pathogen genomic During the lull in influenza vi- populations have vaccine-induced protection. Pathogens for ...and seasonal data to provide a rich picture of rus circulation in the wake of which the susceptible population is maintained by loss of the changing epidemiology of immunity are less affected. Seasonal infections may display years of disrupted patterns. the pandemic, the influenza B/ Incidence Pre-pandemic Severely reduced Slightly reduced endemic pathogens. The scien- Yamagata lineage has virtually contact contact contact Pre-pandemic tific community has spent the disappeared, leading to specu- mean incidence past 2 years characterizing the lation that it has gone extinct epidemiology of a novel infec- (12). The current period of low tion—it is time to ensure that incidence may also present a disease surveillance systems will rare opportunity to eliminate Time be ahead of more familiar foes. j local transmission of eradicable pathogens, such as measles. In these cases, senting a key data gap. Instead, data de- REFERENCES AND NOTES redoubled vaccination efforts are also re- scribing contact patterns in specific groups 1. K.Prem et al., PLOS Comput.Biol.13,e1005697 (2017). quired to overcome immunity gaps and (4, 13, 14) and proxies for social contact, 2. A. Gimma et al., PLOS Med. 19, e1003907 (2022). temporary falls in vaccine coverage that oc- including mobility data that is passively 3. C.Y. Liu et al., Epidemiology 32, 781 (2021). curred during the pandemic. collected from mobile devices, has been 4. M. C. Kiti et al., Epidemics 36, 100481 (2021). heavily relied on. Geolocation data from 5. Kaiser Family Foundation, KFF COVID-19 Vaccine To ascertain whether changes in social Monitor; http://www.kff.org/coronavirus-covid-19/ contact will be long-standing and broadly mobile devices, which can be used to infer dashboard/kff-covid-19-vaccine-monitor-dashboard/. impactful on infectious disease epidemiol- the proximity among people, may provide a 6. D.Thindwa et al., medRxiv 10.1101/2021.12.16.21267959 ogy, two data streams are pertinent. The more accurate accounting of social contact first is direct measurement of contact. that is relevant for transmission risk (15). (2021). 7. N. Nathanson,J. R. Martin, Am.J. Epidemiol. 110, 672 (1979). Despite human contact being the proximate However, such data lack information on the 8. J. E.Tate et al., Pediatr. Infect. Dis.J. 32, 741 (2013). social determinant of infectious disease physicality of contact and whether masks 9. J.A. Lewnard et al., Nat. Med. 10.1038/s41591-022- transmission, it is rarely measured in a way were worn. that ensures population representative- 01887-z (2022). The second data stream required to un- 10. K.A.Twohig et al., Lancet Infect. Dis. 22, 35 (2022). 11. L.Verhoef et al., Emerg. Infect. Dis. 21, 592 (2015). ness, and even more rarely, longitudinally. derstand how changing social contact af- 12. M.Koutsakos et al.,Nat.Rev.Microbiol.19,741 (2021). In Europe, the CoMix study has provided fects disease epidemiology is case surveil- 13. T. Chin et al., medRxiv 10.1101/2021.09.25.21264082 GRAPHIC: N. DESAI/SCIENCE near–real time data during the pandemic lance data, providing a direct measure of (2021). through large, weekly online surveys on the disease patterns and trends in the sizes and number and nature of contacts (2), but no locations of outbreaks. A key metric to be 14. D. M. Feehan,A. S. Mahmud, Nat. Commun. 12, 893 (2021). 15. O. Morozova et al., Sci. Rep. 11, 20271 (2021). such data source exists for the US or many monitored is the average age and severity ACKNOWLEDGMENTS other countries. Notably, there is little to of cases of a given infectious disease. Lower no data available from low- and middle- transmission, because of fewer potentially The authors thank J. de Roode for helpful comments. income countries, where the burden of infectious contacts, will result in an older B.L. serves as a consultant to Epidemiological Research and Methods, LLC. many of these infections is highest, repre- average age of cases. Of course, careful in- 10.1126/science.abp9316 34 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

POLICY FORUM Rubric usage and hiring patterns We started with a faculty candidate evalua- DIVERSITY tion template from the University of Michi- gan STRIDE program (Strategies and Tactics Can rubrics combat gender for Recruiting to Improve Diversity and Ex- bias in faculty hiring? cellence), which is funded by the National Science Foundation (NSF). This template in- Some bias persisted, but rubric use should be encouraged cludes widely accepted criteria for faculty at research-intensive universities (5). By Mary Blair-Loy1, Olga V. Mayorova1, strongly encourage rubric usage, in which Pamela C. Cosman2, Stephanie I. Fraley3 faculty evaluators systematically rate each We worked with the department un- candidate on a set of previously agreed-on der study to adapt the template to fit its R esearch has documented the presence criteria. This process is believed to coun- searches. Its rubric evaluated faculty candi- of bias against women in hiring, in- teract the bias of individual evaluators by dates across six dimensions: research pro- cluding in academic science, technol- promoting slower, more deliberative, and ductivity, research impact, teaching ability, ogy, engineering, and mathematics analytical thinking and by focusing them contributions to diversity, potential for col- (STEM). Hiring rubrics (also called on skill sets that directly affect job per- laboration, and overall impression (see fig. criterion checklists, decision sup- formance rather than on impressions and S1). Rubric scores ranged from excellent to port tools, and evaluation tools) are widely intuitions (4, 5). However, we are aware poor for each evaluation category (we trans- recommended as a precise, cost-effective of only one study, conducted in a labora- lated these ratings into a numerical vari- remedy to counteract hiring bias, despite a tory setting, in which participants rated able: excellent = 4, good = 3, neutral = 2, paucity of evidence that they actually work candidate summaries, which shows that fair = 1, and poor = 0). Written commentary (see table S8). Our in-depth case study of ru- agreeing on rubric criteria in advance re- was also encouraged. bric usage in faculty hiring in an academic duces evaluation bias (6). We are aware of engineering department in a very research- no studies that analyze the effect of rubric Department faculty agreed to fill out the active university found that the rate of hir- use on bias in real-world hiring, in which rubric as a tool in their evaluation of the ing women increased after the department actual evaluators assess voluminous can- semifinalist list compiled by the recruit- deployed rubrics and used them to guide ho- didate files to make actual high-stakes ment committee. In four faculty search cy- listic discussions. Yet we also found evidence decisions. Real-world case studies are im- cles over four recent academic years, faculty of substantial gender bias persisting in some portant because the effectiveness of inter- used the rubric to evaluate written materials rubric scoring categories and evaluators’ ventions depends on the social context and supporting applications of 62 semifinalists written comments. We do not recommend the identities of all involved (7). (32 women and 30 men; gender was self- abandoning rubrics. Instead, we recom- reported by candidates in their application mend a strategic and sociologically astute Despite this paucity of evidence, many file). At the beginning of each faculty meet- use of rubrics as a department self-study tool fields have developed rubrics to standard- ing that was focused on selecting finalists, a within the context of a holistic evaluation of ize candidate assessment and have pro- faculty member summarized and presented semifinalist candidates. moted rubrics as a best practice for EDI in rubric scoring results and commentary, hiring. In policy guides for academic hir- with evaluators anonymized, filtering out Although academic STEM aspires to be a ing, several applied treatises and websites any inaccurate or off-topic content. meritocracy, its taken-for-granted cultural provide sample rubrics (see table S8) (5). A schemas of merit smuggle in biases (1), recent influential review of faculty hiring Our analysis next compared the propor- which contribute to a dearth of diversity lists “mandatory use” of rubrics as one of tion of women hired during the 8-year pe- that undermines scientific innovation and the interventions that the authors “view as riod immediately before rubric use (which impact (see table S8). In academic engineer- having the most promise for [university] in- we refer to as “Phase One”) with the propor- ing, one of the most male-dominated STEM stitutions seeking to improve inclusivity in tion hired during the four academic years of fields, on average 17.6% of engineering fac- hiring across disciplines” (4). rubric use (“Phase Two”). Near the outset of ulty positions are held by women (2). Al- Phase One, the campus implemented three though the percent of women engineering CASE STUDY OF RUBRIC USAGE EDI interventions: Faculty serving as equity doctorates increased from 15.8% in 2000 To help address this knowledge and policy advisers took on administrative oversight to 24% in 2019 (3), these increases will not gap, we developed an in-depth case study of shortlisted candidates, applicants’ “Con- be matched by gains in the professoriate if of an engineering department in a research- tributions to Diversity Statements” (C2D) women face unfair barriers at hiring. intensive (Carnegie classification R1), were added to application files, and equity highly ranked university. Like other R1s, advisers began giving diversity training to Academic policy-makers and EDI (eq- this department strongly values research search committee members. Such training uity, diversity, and inclusion) specialists productivity when evaluating faculty can- focused on evaluating C2D statements and didates (8). Like most academic engineer- an overview of research on implicit biases. 1Department of Sociology, University of California, San ing departments, our case department was Nonetheless, during Phase One, the depart- Diego, La Jolla, CA, USA. 2Department of Electrical and male dominated; women composed 18% of ment conducted eight searches and hired Computer Engineering, University of California, San Diego, the faculty, which is close to the 17.6% na- eight men and one woman. La Jolla, CA, USA. 3Department of Bioengineering, tional average (2). University of California, San Diego, La Jolla, CA, USA. At the outset of Phase Two, the depart- Email: [email protected]; [email protected] ment introduced an additional intervention: rubrics used as described above. During Phase Two, the department conducted four faculty searches and hired three women and six men. The number of women hired increased from only one per nine hires in Phase One to three per nine hires in Phase SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 35

INSIGHTS | POLICY FORUM Two. The phase with the increased hiring of To test for gender bias, we constructed same across the range of number of articles women coincides with the period when ru- ordinary least squares (OLS) regression published. (The rubric scores are mostly brics were used. (We cannot fully attribute models to predict rubric scores of research clustered at the middle to high portion of this increase to rubric utilization because productivity, controlling for the indepen- the scale, between 2 and 4; within this range, unmeasured factors may also have changed.) dently measured categories of seniority and there is an approximately 18% penalty for be- number of articles or H-index (see table ing a woman.) Analysis of rubric scoring S2). We found that women candidates, on All 62 semifinalist candidates received ru- average, received statistically significantly Yet when controlling for H-index and se- bric scores from 6 to 21 faculty, with a mean lower productivity rubric scores than those niority, the gender penalty is harshest among of 13.5 and a median of 12. There was no of men, even after controlling for seniority candidates with the lowest H-indices (see the statistically significant gender difference in (measured as number of years since PhD) first figure, right), who are disproportion- the number of scores received. and number of articles published [unstan- ately junior (see table S4, footnote). At the dardized b coefficient (B) = –0.36, P # 0.01] lowest tail of the H-index distribution, men Analysis of the rubric scoring patterns for (see table S2, model 1). Similarly, women re- receive research productivity rubric scores men and women candidates revealed statis- ceive significantly lower scores on average that are on average 0.7 points higher than tically significant differences in three of the than men while controlling for seniority the scores of women with the same seniority. six evaluation categories (see table S1.A): and H-index (B= –0.29, P< 09.05) (table S2, At this end of the H-index distribution, the Women were scored lower than men in re- model 3). Thus, rubric scoring alone did not rubric scores are mostly clustered between 1 search productivity and research impact but appear to fully mitigate gender bias. These and 3; for these candidates, there is an ap- higher than men in contributions to diver- findings mirror the gender bias detected proximately 35% penalty for being a woman. sity. In the other categories, including the in other academic peer-review processes overall impression category, scores for men (10, 11). Because the H-index itself has been The gender difference in rubric scoring and women were not significantly different. found to incorporate bias against women gradually decreases by about 0.01 point for (see table S8), our findings should be inter- each 1 point of H-index gained. Yet women To determine whether gender bias was preted as additional bias. do not catch up to men in how productive incorporated into rubric scores, we analyzed they are rated in the rubrics until reaching the research productivity category because it Social psychology literature on double an H-index of 17.5, a productivity index well can be most directly compared with external standards finds that among more junior above the 12.8 average and achieved by only metrics. We chose two metrics calculated for candidates, women are often held to higher a handful of candidates. Because rubric the candidate’s application year. First, we tal- standards of competence than men in ways scores for men and women in the overall lied from candidate curricula vitae the num- that sometimes change for candidates impression category were not statistically ber of articles published (and confirmed this with more experience (12). We thus tested significantly different (see table S1), evalu- tally in the Web of Science database). Sec- whether the effect of gender on rubric ators may have combined category scores ond, we pulled from the Web of Science the scores is contingent on the value of the ex- so that women’s higher average scores on H-index, a dominant measure of researcher ternal metric (see table S2, models 2 and 4). contributions to diversity offset their lower output that incorporates productivity and average scores on productivity and impact. impact in a single number that can be com- Women’s productivity rubric scores are pared across faculty of all seniority levels (9). consistently below those of men who have Content analysis of qualitative comments We call research productivity, a rubric cat- the same number of articles and seniority Next, we conducted what to our knowledge egory that can be measured independently, a (see the first figure, left). Women face an av- is the first content analysis of qualitative “calibration category” (see table S2, footnote). erage 0.36-point penalty, which remains the rubric comments in a real faculty search context. Candidates received written com- Indication of gender bias in rubric scores on research productivity mentary alongside their rubric scores. An average of three and a maximum of nine Graphs show predicted values by gender from ordinary least squares regression models regressing rubric evaluators wrote comments on each candi- scores of research productivity on independent productivity metrics, controlling for seniority. n = 62 date. The number of comments received did semifinalist candidates (see table S2, models 1 and 4). not differ by candidate gender. Women’s scores Women’s predicted scores Men’s scores Men’s predicted scores In our content analysis, we prepared a dataset of comments, in which candidate 44 gender was concealed, by removing gender y = 3.3 indicators such as pronouns. We then com- bined an inductive exploration for emergent 33 themes with deductive searches for specific patterns found in previous literature on let- ters of recommendation. We conducted hand coding, which some research suggests is su- perior to computer-assisted coding for stud- ies such as ours with new analyses (13). Many comments contained evaluative notes on the quality, number, authorship order, or impact of the publications. Induc- tively, we coded these as either negative (for example, “some gaps in the pubs.” and “only one paper from a postdoc of three- plus years”) or positive (for example, “strong publication record, letters attest to research Research productivity rubric score Research productivity rubric score GRAPHIC: K. FRANKLIN/SCIENCE 22 1 1 0 x = 17 0 20 40 60 0 Number of articles 0 10 20 30 40 H-index 36 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

output and collaboration”). We POLICY TEMPLATE also searched deductively for the Using rubrics for EDI hiring In light of our findings that presence of two themes men- gender bias remains endemic tioned in previous literature on Recommended process for rubric use to improve EDI in faculty hiring. Steps even in this seemingly objective other types of evaluation. One 1, 3, and 6 are conducted by faculty evaluators while steps 2, 4, and 5 are evaluation process, it is vital that code is “standout” language conducted by faculty on the search committee with administrative support. rubric usage be accompanied by (13, 14). Examples in the rubric Evaluators Process managers strategic application in depart- comments include “outstanding Work as a group to determine 1 Ensure that rubric includes a mental meetings to counteract productivity and quality” and rubric categories and weights, 2 calibration category, i.e., one that individual bias and check inter- “probably the best [search spe- in accordance with disciplinary 3 is independently quantifiable. actional bias during the discus- cialty] candidate out there this schemes of merit, to mitigate 4 sion of candidates. Our results cycle.” The last code is “doubt evaluation bias. 5 Compile and analyze rubric suggest that using rubrics ac- raisers” (15), when a seemingly 6 results, comparing calibration cording to this process frame- positive or neutral comment is Individually complete rubrics category scores to independent work can improve diversity in accompanied by language that for all candidates to mitigate metrics to detect any remaining hiring. Thus, we recommend a minimizes the accomplishment individual bias. individual bias. strategic and sociologically as- or raises concerns (for example, tute use of rubrics as a depart- “several publications, but... some Use findings to guide holistic Start the meeting of evalutors ment self-study tool within the impact factors are very mod- discussion of candidates, by presenting rubric results context of a holistic evaluation est”). We turned these four codes futher reducing individual to mitigate first speaker bias, of the short-listed candidates into four dichotomous measures bias and mitigating noting high inter-evaluator (see the second figure). interactional bias. variance and any large inconsistencies of scores with independent metrics. of the presence or absence of We have studied this process comments in each category. (See with regard to gender. Given table S3 for details on coding methods, inter- At the beginning of the meeting to dis- the otherwise limited diversity among can- coder reliability, dichotomous measure ratio- cuss the semifinalist list and choose fi- didates in our study, we were unable to ad- nale, and robustness check.) nalists to invite for interviews, a faculty dress whether rubrics could also be a tool to Candidate gender was subsequently un- member presented rubric numeric scores promote and check on the fairness of evalu- masked, and the percentages of women and and comments with the identity of the ations with regard to race/ethnicity or other men who had received at least one posi- evaluators anonymized. It was explained minoritized identities. This suggests priori- tive comment, negative comment, standout to faculty that this step aimed to enable ties for future research. j term, and doubt raiser were calculated (see all viewpoints to be heard while avoiding REFERENCES AND NOTES table S3). We found that 86% of men but first-speaker bias, in which initial speak- only 63% of women candidates received ers set the tone for discussion. However, 1. M.Blair-Loy,E.Cech,Misconceiving Merit: Paradoxes of at least one positive comment. Men were faculty were not discouraged from making Excellence and Devotion inAcademic Science and Engi- half as likely to receive a negative comment additional comments or claiming or echo- neering (Univ.Chicago Press,2022). (25%) compared with women (50%). Men ing their support for particular comments were 3.5 times more likely to receive stand- after the presentation. Most survey re- 2. J.Roy,C.Wilson,A.Erdiaw-Kwasie,C.Stuppard,“Engineer- out language (32%) compared with women spondents said that this practice prompted ing and engineering technology by the numbers 2019” (9%). A x2 test indicates statistically sig- meeting attendees to focus on more objec- (American Society for Engineering Education,2020). nificant gender differences for these three tive criteria (78%), improved the climate of variables. Thirteen percent of women and the meeting (80%), and reduced the first 3. J.Falkenheim,“Doctoral Recipients from U.S.Universities: 25% of men received a doubt-raising com- speaker effect (67%) (see fig. S2). 2019”(National Science Foundation,2019). ment. This pattern was not expected, yet this gender difference is not statistically Additionally, some commented in open- 4. K.O’Meara,D.Culpepper,L.L.Templeton,Rev.Educ.Res. significant (see table S3). Overall, the gen- ended survey responses that meeting time 90,311 (2020). dered patterns in rubric quantitative scores was used efficiently to quickly identify align with the qualitative comments and candidates with strong consensus and 5. University of Michigan,in Advance Program, University of with previous research on other evaluative then spend more time on those with high Michigan,Ed.(University of Michigan Office of the Provost, language (13–15). variance in ratings [whom we determined 2018). were disproportionately women (see table Survey of faculty S1.B)]. Taken together, these results suggest 6. E.Uhlmann,G.L.Cohen,Psychol.Sci.16,474 (2005). At the conclusion of Phase Two, we con- that beginning the faculty meeting with 7. R.H.Thaler,C.R.Sunstein,Nudge: Improving Decisions ducted an anonymous survey of department rubric results reduced interactional bias faculty, to which 56% of the professors re- emergent in the faculty meeting. By open- About Health,Wealth,and Happiness (Yale Univ.Press, ing with a neutral reading of the full set 2008). 8. National Research Council,Gender Differences at Critical Transitions in the Careers of Science,Engineering,and Mathematics Faculty (NationalAcademies Press,2010). 9. V.Koltun,D.Hafner,PLOS ONE 16,e0253397 (2021). 10. C.Wenneras,A.Wold,Nature 387,341 (1997). 11. E.R.Andersson,C.E.Hagberg,S.Hägg,Front.Res.Metr. Anal.6,594424 (2021). 12. M.Foschi,Annu.Rev.Sociol.26,21 (2000). 13. S.J.Correll,K.R.Weisshaar,A.T.Wynn,J.D.Wehner,Am. Sociol.Rev.85,1022 (2020). 14. T.Schmader,J.Whitehead,V.H.Wysocki,Sex Roles 57,509 (2007). 15. J.M.Madera,M.R.Hebl,H.Dial,R.Martin,V.Valian,J.Bus. Psychol.34,287 (2019). GRAPHIC: C. SMITH/SCIENCE sponded. Our check for selection bias in re- of both positive and negative rubric com- ACKNOWLEDGMENTS sponses revealed no statistically significant ments, the impact was blunted of any first difference in the two indicators we have for speakers, often senior men, attempting to This work was supported by the National Science Foundation, respondents and nonrespondents: gender vociferously promote or shoot down a can- grant 1661306 (M.B.-L.). Any opinions,findings,and conclu- and tenure status (see table S6). Most re- didate. The faculty meeting format may sions or recommendations expressed in this material are those ported that rubric usage helped them evalu- have mitigated gender bias in the research of the authors and do not necessarily reflect the views of the ate candidates in a more organized fashion productivity scores and the selection of National Science Foundation.S.I.F.is a cofounder and scientific (78%) and may have helped them be more finalists; 47% of women semifinalists and adviser for MelioLabs and holds equity in the company. SUPPLEMENTARY MATERIALS objective (78%), potentially reducing indi- 37% of men semifinalists advanced to the science.org/doi/10.1126/science.abm2329 vidual bias (see fig. S2 and table S5). finalist stage. 10.1126/science.abm2329 SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 37

INSIGHTS Tech jobs performed on large corporate campuses like Apple’s should be decentralized, argues Khanna. Although it comes with a “parsimony” caveat, Susskind’s “digital republicanism” in- verts traditional concerns about state power. The primary threat to be contained, in his view, emanates from private industry, and democratically guided state action is neces- sary to curtail it. The private power held by the technology sector is all the more insidious because it of- ten operates covertly, argues Susskind. Coding practices can produce relations of domination, for example, even when coders act in good faith. Even potential coercion, he maintains, is a serious problem—it is not enough to rely on the goodwill of individuals in the tech sector or on market discipline. We must build institu- tions that afford democratic citizens a robust BOOKS et al. say in the forces that affect them. Susskind’s thesis is thus more general than Khanna’s, and his policy proposals are appli- cable beyond the United States. His book in- SCIENCE AND SOCIETY cludes an entire chapter defending an inter- The digital citizen nationalist component of his approach. But reading these two books together further en- hances the value of each. While Khanna links Two new books advocate for technological agency our private lives as workers and our public lives as citizens, he offers more detailed policy proposals related to the former. Susskind’s proposals, meanwhile, tend to emphasize By Michael Neblo1,2 and Avery White2 to high-paying tech jobs often face a real (but changes that might be put in place on the pub- ultimately unnecessary) choice between aban- lic side. The two books provide a full picture of M any people initially regarded the doning their communities and foregoing the what it would mean to govern technology well. radical ideas espoused by Charles work and wealth afforded by the tech industry. It is also worthwhile to consider more Darwin about evolution and Henry The indignity of that choice, and the resulting Ford about automation technology economic inequality, drive much of the recent radical notions of digital spaces. In his re- as threats to what was understood increase in political polarization, he main- cent book, Reality+, for example, philosopher David Chalmers argues that virtual entities to be, respectively, humankind’s tains. This process is further catalyzed by the are no less real for being digital. If we accept proper place in the world and dignified work. often insidious effects that social media itself this as true, we should regard such spaces as By adjusting our ideas and practices, how- has had on our political discourse. new venues in which to live a good ever, we have (mostly) been able to reconcile He proposes instead a policy to life, rather than as distractions ourselves to the upheavals wrought by the decentralize the tech industry geo- from the “real” world. evolutionary worldview and the economics graphically and an “Internet Bill of Khanna rightly values an in- of industrial automation. Two new books, Ro Rights” incentivizing industry to dividual’s ability to establish and Khanna’s Dignity in a Digital Age and Jamie promote healthy public discourse. maintain roots in a particular Susskind’s The Digital Republic, aim to help Khanna’s vision sometimes gets place. His strictly physical inter- today’s society adapt to the social, economic, lost in the litany of proposals he pretation of “place,” however, un- and political upheavals underway as a result puts forward, but the insight it of- Dignity in a Digital Age dervalues the ways virtual spaces PHOTO: NOAH BERGER/REUTERS/ALAMY STOCK PHOTO of rapid changes in digital technology. fers is potentially profound. Ro Khanna enable experiments in living that keep liberal democracies robust Khanna—a US congressman whose dis- Dignity plays a different role for Simon & Schuster, and vibrant. Similarly, Susskind trict includes Silicon Valley—synthesizes a Susskind, who titles his opening 2022. 368 pp. remarkable range of philosophy, economics, chapter “The Indignant Spirit.” He rightly emphasizes the need to tech knowledge, and savvy politics in his plan grounds his thesis in the “republi- avoid technological domination, to reduce economic inequality (part I) and can” tradition of political philoso- but, at times, his position de- partisan polarization (part II), while preserv- phy, which emphasizes avoiding emphasizes positive human ing people’s ability to establish and maintain subjection to the arbitrary power agency—the power to experiment roots in the communities of their choice. He of others. Citizens become indig- with different ways of living. Efforts argues that people in regions without access nant when they are subject to to govern the tech industry should The reviewers are at the 1Department of Political governmental or private power, he The Digital Republic also promote technology’s power Science and 2Institute for Democratic Engagement and argues, and should feel the same Jamie Susskind to enable previously undiscovered Accountability, The Ohio State University, Columbus, OH when big tech similarly encroaches ways to live lives of dignity. j 43210, USA. Email: [email protected] on their freedom. Pegasus, 2022. 304 pp. 10.1126/science.abq6958 38 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

BIOCHEMISTRY Bringing inanimate matter to life A biochemist probes the origins and vital nature of the Krebs cycle By Joseph Moran pathways and mechanisms. He lays bare the Transformer: human side of science, telling of pioneering The Deep Chemistry T he incredible scientific advances cen- biochemists such as Frederick Gowland Hop- of Life and Death tered around DNA, RNA, and pro- kins, Peter Mitchell, Jennifer Moyle, Melvin Nick Lane teins have left many people with the Calvin, Andrew Benson, and others caught Norton, 2022. 400 pp. impression that the essence of life is up in intellectual battles with larger-than- found in genetic information. Yet a life personalities and nearly thwarted by the cell that died seconds ago contains whims of political currents and (un)fortun- Moving on to early life, Lane reasons that the same genes that it did moments earlier, ate timing. Lane does not feed readers the many of the key evolutionary transitions suggesting that there are other processes textbook story, instead wading through the in deep time can be understood by consid- at play that bring the inanimate to life. In messy process of discovery and the debates ering how geological changes or biological his latest book, Transformer, biochemist that predated the modern consensus over innovations affected the Krebs cycle. Subse- Nick Lane reminds readers in accessible how the central metabolic pathways work. quent chapters paint a fresh perspective on prose that it is life’s dynamic chemistry, its The reader next learns how chemical the centrality of the Krebs cycle to disease, metabolism, that draws inanimate matter forerunners to these biological pathways aging, and even what it means to be an indi- into the living state and vidual. Some of these ideas back again. As Lane puts are undoubtedly speculative it, metabolism is not just but are undeniably stimulat- “what keeps us alive—it is ing—the mark of good popu- what being alive is.” lar science writing. The main hero of the Biased by my own inter- book is the Krebs cycle, a est in the chemical origins sequence of chemical reac- of metabolism, I found my- tions that most of us were self riveted, especially by the taught releases energy from first half of the book. Lane molecules obtained from the does a masterful job of ex- breakdown of sugars or fats, plaining the needed chem- expelling CO as a waste istry in plain language, but I 2 suspect that readers without product. However, Lane points out that this perspec- such a background will find tive obscures this vital pro- themselves flipping back in cess’s place at the heart of all places to refresh their mem- biology and life itself. ories on chemical names. Few laypeople know that In a few spots, I could not the Krebs cycle can run in tell which ideas came from reverse, fixing CO and hy- other researchers and which 2 were Lane’s—a literary tac- drogen gas to produce all the key building blocks of tic, I presume, to keep things biochemistry—a process as straightforward. Those who natural and thermodynam- Hydrothermal vents like this one may have facilitated early biochemical processes. want to know to whom each ically favored as water flow- theory and discovery is at- ing downhill. Some versions of this reverse likely gave rise to life. Experiments from tributed can peruse the more than 60 pages Krebs cycle contain a feedback loop that my own lab and conducted by others are of annotated references that cap the book. amplifies the quantity of its own chemical now starting to support such ideas (1). But these are minor quibbles. With constituents. Rather than simply being an Lane and others, such as Jack Corliss, Transformer, Lane has managed to write engine for the synthesis of the molecules Günter Wächtershäuser, Mike Russell, and a book about the Krebs cycle that jumps of life, it may thus be more accurate to say Bill Martin, speculate that deep-sea hydro- fresh off the page, overturning any residual PHOTO: RALPH WHITE/GETTY IMAGES that life is what one can make from the thermal vents were life’s birthplace. Some antipathy for biochemistry one might still Krebs cycle. of these researchers argue that a primitive be holding on to from his or her student Lane begins by taking readers on a thrill- form of the Krebs cycle led to the first liv- days. The book brings to life the chemistry ing tour of the remarkable stories behind the ing systems and that the cycle may have that brings us to life. j discoveries of some of life’s key metabolic initially run in the reverse direction. The REFERENCES AND NOTES proton gradients between the inorganic 1. K. B. Muchowska, S.J.Varma,J. Moran, Chem. Rev. 120, The reviewer is at the Institute of Supramolecular membranes found within these vents may 7708 (2020). Science and Engineering (ISIS), University of Strasbourg, have been key to promoting the chemistry 67000 Strasbourg, France. Email: [email protected] of life, argues Lane. 10.1126/science.abp8953 SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 39

INSIGHTS Flexible schedules ILLUSTRATION: ROBERT NEUBECKER LETTERS My organization has embraced a hybrid work model: Employees can choose to Pandemic-inspired policies come to the office for only 2 or 3 days a week (or fewer in the case of parents The COVID-19 pandemic disrupted long-standing routines, creating of newborns). As the institution under- myriad challenges and opportunities. Now that many restrictions stands the importance of both flexibility have been lifted, a new normal is taking shape. We asked young and creating a strong network within the scientists to describe positive changes their institutions have made, team, team-building games are conducted or should make, based on lessons learned during the pandemic. remotely. This strategy helps people to Read some of the best responses here. Follow NextGen Voices on relax in the midst of hectic work, thereby Twitter with hashtag #NextGenSci. —Jennifer Sills building a healthy and friendly work atmosphere. 22 1 JULY 2022 • VOL 377 ISSUE 6601 Nandhini Kesavan Experian Services India Pvt. Ltd., Mumbai 400070, India. Email: [email protected] Before the pandemic, all lab members were expected to be present in the lab, even outside working hours and on week- ends. People who were present for long hours were considered smart and hard working. The pandemic showed that it is possible to collaborate and work effec- tively in a remote setup. Now, researchers have the much-welcomed flexibility to work from home when writing an article or thesis. Senthilkumar Seenuvasaragavan Mumbai 400076, India. Email: [email protected] My university has realized that if you are sick, you should stay home, and that this principle applies to everyone—stu- dents, staff, and faculty. This is a much kinder and safer policy than the previous expectation that sick people should drag themselves to campus despite their own needs and the risk of contagion. Katie Burnette Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA. Email: [email protected] Remote learning options My department has continued to use a hybrid format for departmental seminars and colloquia. Hybrid seminars are acces- sible; they allow for people to partake in the community-building, in-person format that was common before the pandemic but also offer an opportunity for those who cannot physically be there to stay involved and informed. Even when the speaker is presenting remotely, my depart- ment often offers a space for people to view seminars in person. Hybrid seminars can also diversify the speakers. By invit- ing remote speakers without needing to consider travel logistics, we can greatly science.org SCIENCE

INSIGHTS | LETTERS broaden the demographics and expertise home countries. Providing international penalties for not showing up. However, for of our presenters. students with the option to temporarily me, this change promotes accountability, Ashley Barbara Heim continue their work remotely could allevi- adds structure to the day, and has led to ate stress for those who need to travel better time management. Department of Ecology and Evolutionary home in the future. Biology, Cornell University, Ithaca, NY 14853, Xiangkun (Elvis) Cao Kathryn K. Oi USA. Email: [email protected] Department of Chemistry, University Department of Chemical Engineering, of Zurich, 8057 Zürich, Switzerland. Before the pandemic, few profes- Massachusetts Institute of Technology, Email: [email protected] sors recorded their lectures or offered Cambridge, MA 02139, USA. Twitter: @Elvis_Cao synchronous livestreams. The normaliza- My organization has established a mobile tion of video streaming and recording Mental health services sports platform for employees and applications has offered students who students to plan personal fitness and exer- have to miss class the opportunity to stay The pandemic lockdowns began shortly after cise. With this software, people can make on track. As a result, students struggling I arrived in China to begin my postdoc. I was personalized indoor exercise training to attend for any reason are less likely isolated in a new place, far from family, and plans and view professional guidance at to fall behind, and students who are sick my mental health suffered. My institution home. The benefits of helping employees know that they can stay home to recover, could have helped by providing psychiatrist meet their fitness goals will long outlast improving their health and protecting consultations for foreign postdocs. With the pandemic. their classmates. more support, I could have adjusted more Rishi Jai Patel quickly and been more productive. Such Yuan Zhi services should always be available to those School of Economics, Guizhou University, Guiyang, Department of Chemistry, University of experiencing stress, especially foreign stu- Guizhou 550025, China. Pennsylvania, Philadelphia, PA 19104, USA. dents and employees. Email: [email protected] Email: [email protected] Hafiz Arbab Sakandar Online tools Financial support Food Engineering Department, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, Before the pandemic, most faculty at my During the pandemic, our department China. Email: [email protected] university didn’t know how to use online learned to be more responsive to students teaching software, and the university didn’t in financial crisis. When a remote student’s After the pandemic lockdowns, my have an online teaching resource database. laptop was stolen (and shipping a library institution began to pay more attention During the pandemic, the office of academic loaner device wasn’t feasible), we con- to the mental health of students, espe- affairs conducted systematic training for firmed that they were eligible for a grant cially those who faced stalled projects or teachers and students, made a series of to replace the equipment. Immediately, the difficulties finding a job. I was one of the teaching videos, and established corre- department provided cash for the purchase, “Psychological Committee” volunteers, sponding websites for students to browse allowing the student to buy a new laptop recruited by the Students Counseling and study. This online teaching platform and return to class. Weeks later, when the and Mental Health Center. We organized provides crucial resources that both faculty grant was fully approved, the department activities to help students relieve stress and students continue to use. received a reimbursement for the expense. and make friends. The committee also This quick response demonstrated that answered mental health questions on Yujie Diao prompt financial support is possible. social media. During this time, I received Department of Blood Transfusion, The First Juliet Johnston training from the university on how to Affiliated Hospital of Anhui Medical recognize and respond to psychologi- University, Hefei, Anhui 230022, China. Department of Civil and Environmental cal crises, which helped me support my Email: [email protected] Engineering, University of California, Berkeley, classmates. The university has also made Berkeley, CA 94720, USA. professional psychological consultants Because of the pandemic, digital innova- Twitter: @queermsfrizzle available to students. Both the services tions in higher education that would have offered and the training I received should otherwise taken years to implement were My PhD institution, Cornell University, be made widely available going forward. introduced in a matter of days. The changes offered continued financial support to were examples of “creative destruction,” a international graduate students who Yan Zhuang concept originated by economist Joseph were stranded in their home countries Peking-Tsinghua Center for Life Sciences, Schumpeter. My institution started using due to government-imposed travel Peking University, Beijing 100871, China. educational technology driven by artificial restrictions. The support included Email: [email protected] intelligence that predicts the navigational options such as graduate teaching assis- behavior of learners in an online course and tantship (for online courses), graduate Facilitation of exercise identifies pedagogically valuable behaviors research assistantship (for studies that in real time. The technology serves as an could be done remotely), and support for My university sports center adapted online tutor that can assess a student’s students to attend online conferences. to pandemic concerns by starting an strengths and weaknesses and deliver per- This innovative change made it possible electronic sign-up and sign-in system to sonalized individual instructions, extending for international students to maintain use the facilities. At first a way to limit the capacity of a classroom teacher. progress toward their research degrees capacity and conduct contact tracing, during the COVID-19 disruptions. Some the system is still in place today. Some Wadim Strielkowski students also had the opportunity to con- may find the requirements burdensome, Department of Agricultural and Resource duct research with collaborators of their given that walk-in attendance was pos- Economics, University of California, advisers at institutions in the students’ sible before the pandemic and there are Berkeley, Berkeley, CA 94720, USA. Email: [email protected] 24 1 JULY 2022 • VOL 377 ISSUE 6601 10.1126/science.add2046 science.org SCIENCE

RESEARCH the liver based on proximity to blood vessels. —YN IN SCIENCE JOURNALS Science, abi9547, this issue p. 47 Edited by Michael Funk N A N O M AT E R I A L S NEURODEVELOPMENT Trapping and A model for dendrite branching recovering organics H ighly complex branched dendritic arbors allow neurons to integrate many inputs, but it Hydrogels consist of cross- has been difficult to analyze how such variable structures form. Shree et al. combined linked organic polymers that live imaging of the dendrites of sensory neurons in Drosophila larvae with computa- can swell to hold up to 90% tional modeling to derive the rules that drive their development. A model in which the water, making them useful as tips of dendrites randomly switch between growing, shrinking, and pausing can repro- absorbents and for tissue engi- duce the observed patterns of growth. The model also reveals the importance of branching neering. Zhang et al. synthesized for increasing the size of dendritic trees and identifies properties that may give different inorganic nanowires from poly- types of neurons their morphologies. —JET Sci. Adv. 10.1126/sciadv.abn0080 (2022). oxometalates, calcium ions, and oleylamine and found that these Fluorescence microscopy image of a fruit fly larva revealing the nanowires readily formed three- branching patterns of sensory neuron dendrites dimensional networks. The networks swell when exposed to IMAGE: SHREE ET AL. EVOLUTION effects of cis- and trans-reg- physiological ones such as insu- a range of volatile organic com- ulatory mutations affecting lin secretion and pathological pounds added at fractions even From one mutation, expression of the TDH3 gene in ones involved in the metabolic below 1% to form organogels. many effects yeast. They found that trans- syndrome. mTORC1 is a key pro- The gels are stable to physical regulatory mutations do indeed tein that is also involved in many squeezing without a substan- New mutations introduce have more pleiotropic effects aspects of metabolism and tial loss of liquid. However, the genetic variation into a popula- and are more deleterious. — senses leucine through proteins liquids can be recovered using tion, and if the genetic changes LMZ and DJ called sestrins. Some aspects distillation and centrifuga- persist, they can provide of this signaling pathway were tion, and the nanowires can be raw material for evolution- Science, abj7185, this issue p. 105 previously observed in cultured reused, making possible the ary change. Pleiotropy, or the cells, but now Cangelosi et al. trapping and recovery of organic number of traits altered by a NUTRIENT METABOLISM have identified what happens in solvents. —MSL mutation, is often assumed vivo in a mammal. The authors to affect the probability that a Leucine sensing clarified the signaling steps Science, abm7574, this issue p. 100 mutation survives the test of in the zone involved in mTORC1 sensing time. Vande Zande et al. now of leucine through sestrins in HUMAN GENOMICS provide a framework with which Leucine is an essential amino mice and determined that the to test such assumptions by acid that plays an important regulation of this pathway varies Human migrations empirically determining and role in a variety of metabolic between different zones within into Micronesia comparing the pleiotropic processes, including both The movements of ancient humans can be difficult to ascer- tain from their current population genetic structure. Studying the peopling of the Micronesian islands, Liu et al. examined 164 ancient human remains from five different archaeological sites in remote Oceania from different prehistoric time frames, along with 112 present-day individuals from the same area. They com- bined these new data with the results of previous studies and also compared their results with linguistic studies. Their analysis revealed successive movements from island Southeast Asia that differ from those in the southwest Pacific. Furthermore, co-analysis of Micronesian and southwest Pacific ancient DNA indicates that the first people who colonized the Pacific islands had a population SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 41

RESEARCH | IN SCIENCE JOURNALS structure in which men moved to ocean temperature over the past IN OTHER JOURNALS find their mates, whereas women 65 million years. They found that rarely moved to join men. —LMZ deep ocean temperatures were Edited by Caroline Ash generally higher and more vari- and Jesse Smith Science, abm6536, this issue p. 72 able than earlier work suggests. Their results have implications VISION PHYSIOLOGY for our understanding of deep sea temperature responses to Nimble neurons Balancing liver repair atmospheric carbon dioxide con- enable nimble flight and regeneration centrations, climate sensitivity, and ocean structure during times B irds analyze optic flow with the help of two visual The related cytokines transform- of minimal continental ice. —HJS pathways in the midbrain, and mammals have ing growth factor-b (TGF-b) homologous components in their visual systems. and bone morphogenic protein Science, abk0604, this issue p. 86 Smyth et al. have found unanticipated diversity (BMP) can exert protective among birds in this visual pathway. For instance, or detrimental effects during NEUROSCIENCE in flight maneuvers, pigeons are a lumbering bus liver injury. Stavropoulos et al. compared with the zebrafinch and the hummingbird. investigated the contributions Microglia can cause Finches may be nimble, but hummingbirds outshine of the TGF-b and BMP pathways chronic pain them in their ability to hover and dart rapidly with in the response to acetamin- breathtaking changes in speed and direction. The ophen-induced liver injury in Peripheral nerve injury leads to authors found that hummingbird neurons preferred reporter-expressing mice. Both long-lasting pain hypersensitivity. faster stimuli than did zebrafinch or pigeon neurons. pathways were induced near Treatment of chronic pain contin- Such differences in how birds’ neurons are tuned to areas of necrosis in hepatocytes ues to be unsatisfactory because perceive motion may reflect the behaviors of the birds. that also showed an increase we still don’t fully understand the The sensitivities of the hummingbird neurons may in autophagy, and both path- underlying processes. Tansley et convey a greater ability to interpret the large, rapidly ways were required to stimulate al. discovered a new mechanism moving retinal images that would arise as the bird darts autophagy. Although inhibiting by which peripheral nerve injury and hovers around nearby objects, for example, when signaling through both pathways causes pain. A subpopulation of feeding on flowers. —PJH Curr. Biol. 32, 2772 (2022). initially worsened the damage, projection neurons in the spinal it ultimately accelerated tissue cord dorsal horn that are critical Neurons in the visual system of the adult Anna’s regeneration and recovery. —AMV for transmission of pain signals hummingbird, Calypte anna (a male is shown here), to the brain, but not other cell are tuned to their specific flight behavior. Sci. Signal. 15, eabn4395 (2022). types in superficial dorsal horn, are selectively surrounded by SIGNAL TRANSDUCTION combined contribution of bacte- PA L E O C L I M AT E specialized extracellular matrix rial cells to the common pool of structures called perineuronal Signaling the autoinducer molecules. —LBR Warmer than realized nets. Nerve injury–activated bacterial vote microglia degrade perineuronal Nat. Commun. 13, 2772 (2022). Past climates may hold impor- nets around projection neurons, Quorum sensing, the mecha- tant clues about how the planet which increases projection nism by which bacteria monitor ELECTROCHEMISTRY might respond to ongoing neuron activity, subsequently the size of their population by climate warming. Meckler et al. causing pain. —PRS responding to signaling mol- Toward CO2-free use clumped isotope thermom- ecules (autoinducers) produced ammonia synthesis etry on benthic foraminifera to Science, abl6773, this issue p. 80 by individual cells, may resemble reinterpret the record of the deep more of a community vote than Lithium-mediated electrochemi- a simple count of the number of cal ammonia synthesis (LiMEAS) Fossil foraminifera, seen here with scanning electron microscopy, can be analyzed bacteria. Bettenworth et al. found is thought to be a promising CREDITS: (LEFT TO RIGHT MECKLER ET AL.; DAN SUZIO/SCIENC to determine the ocean temperature millions of years ago. that the bacterium Sinorhizobium alternative to the traditional meliloti produces SinI, the thermochemical Haber-Bosch enzyme that makes its autoin- process because it can operate ducer (a homoserine lactone), in at ambient temperature and a stochastic, pulsatile manner. pressure conditions and without The Sin regulatory system acts CO2 emissions. However, little as a probabilistic switch that is known about its complex activates relatively rarely but is mechanism. Using standardized influenced by the cell’s response high-resolution gas chromatog- to physiological cues such as raphy−mass spectrometry and growth conditions, which can nuclear magnetic resonance change the pulse frequency. imaging, Sažinas et al. analyzed A quorum-sensing response the stabilizing effect of oxygen occurs, depending on the in LiMEAS. They determined the 42 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

RESEARCH ALSO IN SCIENCE JOURNALS Edited by Michael Funk GUT PHYSIOLOGY contacts between neurons and 1883 Krakatau eruption. Kubota to mitigate the transmission microglia, which may explain et al. detail how this lamb of severe acute respiratory Regulating the why certain genes are associ- wave contributed to the global syndrome coronavirus 2 (SARS- redox swamp ated with neurodegenerative tsunami waves arriving much CoV-2) has also affected the diseases. —LMZ and PJH earlier than expected. The erup- transmission and epidemiology The diversity and abundance tion also generated long-range of various other endemic infec- of organisms that live in the Science, abm1741, this issue p. 56 infrasounds and ionospheric tious diseases that are spread human gut are well known. We interations, along with a global from person to person. Because also have some idea of associa- NEUROSCIENCE tsunami. This set of observations human contacts remain different tions between microbial taxa and will be helpful for disentangling from what they were before the host disease, but we have failed Sleep as a response the event and understanding the COVID-19 pandemic, it is possible to consistently translate this to stress propagation of waves through that these endemic diseases understanding into therapeutic the atmosphere and ocean (see may also adapt to changes in options. Redox reactions, which Stress-induced sleep has the Perspective by Brodsky and social contacts. This may result in are governed by the availability been hypothesized to dampen Lay). —BG changes in seasonality, and other of respiratory electron accep- stress responses and to help infections may become less or tors, are the drivers of bacterial mental processing of the Science, abo4364, abo7063, more severe as susceptible age community composition. Lee et stressful events. However, the this issue p. 91, p. 95; groups change. In a Perspective, al. reviewed the literature on bac- mechanisms underlying these Nelson and Lopman discuss terial colonization of regions of phenomena are not understood. see also abq5392, p. 30 the impacts of reduced social the gut and concluded that colo- Yu et al. discovered a specific contacts on the transmission of nization is primarily regulated circuit in the mouse midbrain MUSCULAR DYSTROPHY endemic infectious diseases and by host physiology controlling dedicated to detecting stress whether there is an opportunity to electron acceptor availability and inducing restorative sleep Macrophages modulate eradicate them altogether. —GKA rather than by microbial activity. (see the Perspective by Joëls muscular dystrophy Although diet shapes microbiota and de Kloet). A subset of Science, abp9316, this issue p. 33 composition, its effects are specialized neurons receive The role of resident macro- largely mediated by its effect on stress inputs and induce rapid phages in skeletal muscle BIOCHEMISTRY host homeostasis. Intervening eye movement (REM) and regeneration after injury has with host gut physiology could non-REM sleep through the previously been difficult to Keeping things dynamic thus offer a more tractable route lateral hypothalamus. Transient study. Babaeijandaghi et al. to translational solutions for gut stress enhanced the activity of used parabiosis, lineage tracing, Many proteins contain domains dysbiosis than trying to manipu- these neurons for several hours. and single-cell RNA-sequencing that do not adopt a stable folded late the microbiota. —CA Stress-induced sleep gener- experiments to identify a popula- structure but are involved in ated by this pathway alleviated tion of self-renewing resident protein function, sometimes Science, abp9960, this issue p. 44 stress levels and mitigated macrophages that were found to through self-association that stress-induced anxiety, restor- clear damage-induced apoptotic can drive the formation of NEUROGENOMIC IMAGING ing mental and body functions. cells early after muscle injury. phase-separated structures Sleep after stress can thus In a mouse model of Duchenne inside cells. These regions are Mouse and human cortex profoundly reduce the chronic muscular dystrophy, depletion known as low-complexity (LC) cell comparisons stress response. —PRS of macrophages through long- domains because they are term colony-stimulating factor composed of only a few different Studies of specific cellular types Science, abn0853, this issue p. 63; 1 receptor (CSF1R) inhibition types of amino acids. Zhou et and their molecular phenotype see also adc9782, p. 28 resulted in a shift in muscle al. show that the LC domain in the cortex have been espe- fiber composition toward more of the RNA-binding protein cially difficult in humans. Fang et NATURAL HAZARDS glycolytic-oxidative fibers that TDP-43 associates transiently al. applied an imaging technique were protective against con- through a labile structure, and called MERFISH to 4000 gene Going on the lamb traction-induced injury. These this behavior is required for transcripts to identify the spatial findings highlight the contribu- phase separation, which is key distributions of cell types within The Hunga Tonga undersea tion of resident macrophages to to its normal role of organizing the human and mouse cortex. volcanic eruption was one of the skeletal muscle regeneration and mRNA (see the Perspective by From this survey, they identified most powerful ever recorded, suggest a role for CSF1R inhibi- Petsko and Small). Mutation cell-type-specific association with audible sound detected tion in the treatment of muscular of a proline in the LC domain patterns that differed between more than 10,000 kilometers dystrophies. —MN caused aggregation by stabiliz- the mouse and human brain. from the source. Matoza et al. Sci. Transl. Med. 14, eabg7504 (2022). ing the labile structure. In three They found that humans have present infrasound and seismic other proteins, proline mutations more specific neurons than recordings, along with other CORONAVIRUS linked to neuronal diseases were mice, and that these cells have geophysical observations, that shown to similarly enhance the greater proximity to and interac- help to describe this event. An A new normal? stability of self-association of LC tions with similar neuronal cell atmospheric lamb wave, charac- domains. —VV types. Studying receptor-ligand teristic of energetic atmospheric The implementation of non- pairs, the authors identified likely events, circled the planet four pharmaceutical interventions Science, abn5582, this issue p. 46; times and was similar to the see also adc9969, p. 31 43-B 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

RESEARCH GENE REGULATION release mechanism is not well required. These can include understood. Yamagishi et al. used analgesic medications or local HoxA synthetic regulatory an obesity-induced HCC mouse injections to dull the pain reconstitution model to study SASP factor receptors, but may also be as release from hepatic stellate cells simple as applying something Regulatory inputs from many within tumors. Interleukin-33 cold to the location causing the elements are integrated across (IL-33) release was triggered by pain, such as ice packs for sore large genomic windows to lipoteichoic acid, which accumu- or bruised joints or muscles. control mammalian gene expres- lated in the livers of obese mice. Reeder et al. developed a soft, sion. Despite advances in gene Full-length IL-33 was cleaved into miniaturized, implantable cooler editing, generating combinato- its short, active form and released to temporarily block nerve rial variant alleles to precisely into the tumor microenvironment conduction using a liquid-to- measure the contribution of through gasdermin D N-terminal gas phase transition as the each input remains challeng- pores. Secreted IL-33 bound to cooling mechanism (see the ing. Inspired by the bottom-up ST2+ regulatory T cells, result- Perspective by Jiang and Hong). approaches of synthetic biology ing in impaired CD8+-mediated They borrowed the design and biochemical reconstitution, antitumor immunity and the of electrical nerve cuff and Pinglay et al. have established a development of HCC. These substituted electrical wires with “synthetic regulatory reconstitu- findings shed light on SASP factor a microfluidic channel carrying tion” framework for the study of release and suggest that targeting a microliter volume of bioinert gene regulation. They leveraged IL-33 release from senescent cells coolant. A thermal thin-film advances in large DNA construct may be an attractive therapy for sensor integrated within the synthesis and cell differentiation HCC. —HMI cuff enabled monitoring of the to dissect the relative contribu- temperature in real time, thus tions of the many mechanisms Sci. Immunol. 7, eabl7209 (2022). enabling closed-loop control. controlling mammalian Hox gene —MSL expression. This study opens the GPCR SIGNALING door to similar analyses of other Science, abl8532, this issue p. 109; loci in any genome. —BAP and Cholesterol’s spot in SMH chemokine receptors see also abm8159, p. 28 Science, abk2820, this issue p. 45 The activation of many G pro- tein–coupled receptors (GPCRs) PA L E O C L I M AT E is allosterically modulated by endogenous lipid molecules, Crustal effects on climate including cholesterol; however, the corresponding molecular Why was the long-term global mechanisms remain elusive. cooling trend of the Cenozoic Using cryo–electron microscopy, interrupted by a several-million- Lu et al. determined apo- and year interval of warming during ligand-bound structures of the the middle of the Miocene? signaling complex between a Herbert et al. present a recon- chemokine receptor, a repre- struction of global ocean crustal sentative of the CX3C subfamily, production to show that tectonic and its cognate Gi protein. A degassing of carbon can account distinct activation mode of the for most of the long-term ice receptor was identified, along sheet and global temperature with three cholesterol molecules evolution for the past 20 million that stabilize the active receptor years (see the Perspective by conformation and modulate sig- von der Heydt). These results naling. Structural features of both provide further support for the receptor and ligand were found idea that sea floor spreading to define selectivity, in contrast to rates can control global changes the largely promiscuous interac- in climate. —HJS tions between most chemokine receptors and chemokines. —VC Science, abl4353, this issue p. 116; see also abq6542, p. 28 Sci. Adv. 10.1126/ sciadv.abn8048 (2022). CANCER IMMUNOLOGY BIOMEDICINE Deleterious release Cooling away the pain The secretion of senescence- associated secretory phenotype After injury due to an accident (SASP) factors by senescent or medical procedure, various hepatic stellate cells promotes forms of pain relief may be the development of hepatocel- lular carcinoma (HCC), but the SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 43-C

RESEARCH | IN SCIENCE JOURNALS structure in which men moved to ocean temperature over the past IN OTHER JOURNALS find their mates, whereas women 65 million years. They found that rarely moved to join men. —LMZ deep ocean temperatures were Edited by Caroline Ash generally higher and more vari- and Jesse Smith Science, abm6536, this issue p. 72 able than earlier work suggests. Their results have implications VISION PHYSIOLOGY for our understanding of deep sea temperature responses to Nimble neurons Balancing liver repair atmospheric carbon dioxide con- enable nimble flight and regeneration centrations, climate sensitivity, and ocean structure during times B irds analyze optic flow with the help of two visual The related cytokines transform- of minimal continental ice. —HJS pathways in the midbrain, and mammals have ing growth factor-b (TGF-b) homologous components in their visual systems. and bone morphogenic protein Science, abk0604, this issue p. 86 Smyth et al. have found unanticipated diversity (BMP) can exert protective among birds in this visual pathway. For instance, or detrimental effects during NEUROSCIENCE in flight maneuvers, pigeons are a lumbering bus liver injury. Stavropoulos et al. compared with the zebrafinch and the hummingbird. investigated the contributions Microglia can cause Finches may be nimble, but hummingbirds outshine of the TGF-b and BMP pathways chronic pain them in their ability to hover and dart rapidly with in the response to acetamin- breathtaking changes in speed and direction. The ophen-induced liver injury in Peripheral nerve injury leads to authors found that hummingbird neurons preferred reporter-expressing mice. Both long-lasting pain hypersensitivity. faster stimuli than did zebrafinch or pigeon neurons. pathways were induced near Treatment of chronic pain contin- Such differences in how birds’ neurons are tuned to areas of necrosis in hepatocytes ues to be unsatisfactory because perceive motion may reflect the behaviors of the birds. that also showed an increase we still don’t fully understand the The sensitivities of the hummingbird neurons may in autophagy, and both path- underlying processes. Tansley et convey a greater ability to interpret the large, rapidly ways were required to stimulate al. discovered a new mechanism moving retinal images that would arise as the bird darts autophagy. Although inhibiting by which peripheral nerve injury and hovers around nearby objects, for example, when signaling through both pathways causes pain. A subpopulation of feeding on flowers. —PJH Curr. Biol. 32, 2772 (2022). initially worsened the damage, projection neurons in the spinal it ultimately accelerated tissue cord dorsal horn that are critical Neurons in the visual system of the adult Anna’s regeneration and recovery. —AMV for transmission of pain signals hummingbird, Calypte anna (a male is shown here), to the brain, but not other cell are tuned to their specific flight behavior. Sci. Signal. 15, eabn4395 (2022). types in superficial dorsal horn, are selectively surrounded by SIGNAL TRANSDUCTION combined contribution of bacte- PA L E O C L I M AT E specialized extracellular matrix rial cells to the common pool of structures called perineuronal Signaling the autoinducer molecules. —LBR Warmer than realized nets. Nerve injury–activated bacterial vote microglia degrade perineuronal Nat. Commun. 13, 2772 (2022). Past climates may hold impor- nets around projection neurons, Quorum sensing, the mecha- tant clues about how the planet which increases projection nism by which bacteria monitor ELECTROCHEMISTRY might respond to ongoing neuron activity, subsequently the size of their population by climate warming. Meckler et al. causing pain. —PRS responding to signaling mol- Toward CO2-free use clumped isotope thermom- ecules (autoinducers) produced ammonia synthesis etry on benthic foraminifera to Science, abl6773, this issue p. 80 by individual cells, may resemble reinterpret the record of the deep more of a community vote than Lithium-mediated electrochemi- a simple count of the number of cal ammonia synthesis (LiMEAS) Fossil foraminifera, seen here with scanning electron microscopy, can be analyzed bacteria. Bettenworth et al. found is thought to be a promising CREDITS: (LEFT TO RIGHT MECKLER ET AL.; DAN SUZIO/SCIENC to determine the ocean temperature millions of years ago. that the bacterium Sinorhizobium alternative to the traditional meliloti produces SinI, the thermochemical Haber-Bosch enzyme that makes its autoin- process because it can operate ducer (a homoserine lactone), in at ambient temperature and a stochastic, pulsatile manner. pressure conditions and without The Sin regulatory system acts CO2 emissions. However, little as a probabilistic switch that is known about its complex activates relatively rarely but is mechanism. Using standardized influenced by the cell’s response high-resolution gas chromatog- to physiological cues such as raphy−mass spectrometry and growth conditions, which can nuclear magnetic resonance change the pulse frequency. imaging, Sažinas et al. analyzed A quorum-sensing response the stabilizing effect of oxygen occurs, depending on the in LiMEAS. They determined the 42 1 JULY 2022 • VOL 377 ISSUE 6601 science.org SCIENCE

POLITICAL SCIENCE A widening ideological gap Using three unique decade-long surveys, Jessee et al. examined the ideological positioning of the Supreme Court of the United States (SCOTUS) and the perception of the Court by the US public. The authors show that SCOTUS has become much more conservative on key policy issues relative to the general public since 2020. Furthermore, although the US public has adjusted their perception of the ideological shift within SCOTUS, this adjustment on average is less than the actual shift. The researchers also found that the respondents’ perception of the SCOTUS ideology relative to their own was correlated with their support for institutional changes, but with noticeable differences between those who identified as Democrats versus those who identified as Republicans. —YY Proc. Nat. Acad. Sci. U.S.A. 119, e2120284119 (2022). optimal amount of oxygen to participants who had experienced The anterior and posterior insular PEROVSKITES enhance the chemical stability a landlord-related forced move cortex are involved in various of the system and reported the later reported higher levels of forms of recognition memory. Examining edge states underlying mechanism. This intimate partner violence (IPV) in After examining basolateral work is potentially an important their sexual relationships during a amygdala projections to the insu- The layered halide perovskites step toward a more efficient and 6-month follow-up. Furthermore, lar cortex, Chen et al. found that (LHPs) that are used in solar cells stable LiMEAS process. —YS higher IPV levels were associated the basolateral amygdala sends can undergo strain relaxation with behaviors that increased HIV dense monosynaptic projections through surface reorganization J. Phys. Chem. Lett. 13, 4605 (2022). risk (e.g., unprotected or transac- to the anterior insular cortex and form lower-energy edge tional sex). Policy makers should and only sparse projections to states (ESs) with higher charge SOCIAL INEQUITY take note of the results of this the posterior insular cortex. carrier lifetimes and lower emis- study because they reveal how Memory-enhancing norepineph- sion energies. Qin et al. showed Justice, housing eviction can also affect health by rine administration selectively that a family of two-dimensional and health altering the dynamics of sexual reduced neuronal activity within Ruddlesden-Popper LHPs formed partnerships. —EEU the anterior insular cortex during PbBr6 octahedra rotated at the Social inequities that place the postlearning consolidation crystal layer edges. These dan- women and racially marginalized Soc. Sci. Med. 305,115030 (2022). period but not in the posterior gling octahedra were the origin of renters at disproportionate risk insular cortex. Inhibition of the localized, lower-energy ESs that for evictions are associated with NEUROSCIENCE anterior insular cortex enhances helped to transport electrons out HIV risk. However, there are no the consolidation of memory, of the interior. The population longitudinal studies that identify Emotional arousal protecting it by disrupting of electrons in both the interior the pathways through which evic- promotes memory attentional reorienting toward states and ESs could be con- tions affect sexual partnerships new stimuli and thus promoting trolled with external electric fields. that raise HIV risk. Analyzing Emotional arousal induces ongoing long-term memory stor- Phonons activated by the dan- participants from the longitudi- noradrenergic activation of the age. —PRS gling octahedra interacted with nal Justice, Housing and Health basolateral amygdala, which electrons and helped to facilitate Study that were HIV-negative at promotes long-term information Proc. Natl. Acad. Sci. U.S.A. radiative recombination, unlike baseline, Groves et al. found that storage in other brain regions. midgap states in conventional 119, e2203680119 (2022). semiconductors, which normally quench luminescence. —PDS Adv. Mater. 10.1002/ adma.202201666 (2022). SCIENCE science.org 1 JULY 2022 • VOL 377 ISSUE 6601 43

RESEARCH ◥ latory reconstitution” as a framework for the study of gene regulation to address this gap. RESEARCH ARTICLE SUMMARY The synthesis of large DNA constructs (>100 kb) permits any combination of complex modifica- GENE REGULATION tions to be made, at the scale required to probe regulation across a native genomic neighbor- Synthetic regulatory reconstitution reveals principles hood. We fabricated HoxA cluster variants that of mammalian Hox cluster regulation encode various combinations of the previously identified regulatory modules and integrated Sudarshan Pinglay†, Milica Bulajić†, Dylan P. Rahe, Emily Huang, Ran Brosh, Nicholas E. Mamrak, them into an ectopic location in the mouse Benjamin R. King, Sergei German, John A. Cadley, Lila Rieber, Nicole Easo, Timothée Lionnet, genome. This enabled us to directly test the Shaun Mahony, Matthew T. Maurano, Liam J. Holt, Esteban O. Mazzoni*, Jef D. Boeke* independent ability of these variant ectopic clusters to reconstitute distinct aspects of INTRODUCTION: Despite an ever-expanding cat- Although distal enhancers, intracluster tran- HoxA regulation. alog of noncoding elements that are implicated scription factor binding, and topological orga- in the control of mammalian gene expression, nization have emerged as the major regulatory RESULTS: We harnessed the efficient homol- how the regulatory input from multiple ele- modules in establishing this expression pattern, ogous recombination machinery in yeast to ments is integrated across a genomic neigh- their relative contributions remain elusive. construct four rat HoxA variants (130 to 170 kb) borhood has remained largely unclear. This and delivered them at single copy to the house- challenge is exemplified at Hox clusters (~100 to RATIONALE: Despite the advent of a vast suite keeping Hprt1 locus of mouse embryonic stem 200 kb), which contain genes that specify po- of genome editing tools, it has remained chal- cells. Upon RA-induced differentiation, an ectopic sitional identity along the anterior-posterior lenging to simultaneously manipulate multiple HoxA cluster lacking distal enhancers (SynHoxA) axis of the developing embryo. In response to regulatory elements across large genomic win- induced both the appropriate subset of HoxA developmental morphogens such as retinoic dows to deconvolve their relative contributions. genes and the corresponding chromatin bound- acid (RA), the HoxA cluster splits into an active Taking inspiration from the bottom-up ap- ary. The presence of distal enhancers (Enhancers+ (Hoxa1–5) and inactive domain (Hoxa6–13) at proaches of synthetic biology and biochemical SynHoxA) increased transcription levels, especially the level of gene expression and chromatin. reconstitution, we developed “synthetic regu- at early time points. Further, both SynHoxA and Enhancers+SynHoxA reorganized into Bottom-up construction of locus variants active and inactive topological domains upon differentiation, mirroring the endogenous or- BACs containing region Overlapping + Synthetic DNA ganization. The mutation of just four retinoic of interest amplicons encoding variation acid response elements (RAREs) present in SynHoxA (RARED) almost completely elimi- PCR nated any response of the ectopic cluster to RA, at the levels of both gene expression and chromatin reorganization. The addition of dis- tal enhancers to RARED could not fully rescue this loss of gene expression phenotype. XX XX XX CONCLUSION: Our data suggest that at HoxA, the primary module of active gene and chro- Amplification of assembled Assembly in yeast by matin boundary specification in response to RA construct in bacteria homologous recombination is through the presence of internal transcription factor binding sites. Distal enhancers are dis- Mammalian cell 100 kb pensable for the specification of active genes but a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 synergize with intracluster activator binding to HoxA boost the amount of transcription. Therefore, Locus mammalian Hox clusters contain all the regu- latory information that is necessary to convert a HoxA morphogenetic signal into a stable transcrip- Variant tional, epigenetic, and topological state. This study showcases the power of synthetic regu- a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 latory reconstitution, a generalizable platform Bottom-up construction of variant mammalian genomic loci at the >100-kb scale. Making multiple ▪for the dissection of gene regulation at other edits on the same allele over large genomic windows has remained challenging in mammalian cells. Variant loci with an arbitrary number of changes can be constructed in yeast using synthetic DNA and site- loci in complex genomes. specifically integrated into the genome of mammalian cells to study their behavior. BAC, bacterial artificial chromosome. The list of author affiliations is available in the full article online. *Corresponding author. Email: [email protected] (E.O.M.); [email protected] (J.D.B.) †These authors contributed equally to this work. Cite this article as S. Pinglay et al., Science 377, eabk2820 (2022). DOI: 10.1126/science.abk2820 READ THE FULL ARTICLE AT https://doi.org/10.1126/science.abk2820 Pinglay et al., Science 377, 45 (2022) 1 July 2022 1 of 1

RESEARCH ◥ ulatory elements in cis. Testing the necessity of individual elements by generating loss-of- RESEARCH ARTICLE function variants has received a lot of attention. However, tests of sufficiency have remained GENE REGULATION intractable owing to the inability to precisely manipulate DNA at a scale that accurately Synthetic regulatory reconstitution reveals principles models the complexity and size of native loci of mammalian Hox cluster regulation (>100 kb) (25). Sudarshan Pinglay1†, Milica Bulajić2†‡, Dylan P. Rahe2, Emily Huang1, Ran Brosh1, Short reporter constructs enable the study Nicholas E. Mamrak1, Benjamin R. King1§, Sergei German1, John A. Cadley1, Lila Rieber3¶, of variants only over a small genomic window Nicole Easo1, Timothée Lionnet1,4,5, Shaun Mahony3, Matthew T. Maurano1,6, Liam J. Holt1,5,7, (<10 kb) and also suffer from a lack of con- Esteban O. Mazzoni2*, Jef D. Boeke1,5,7* trolled genomic context, as they are largely randomly integrated or reside on episomal Precise Hox gene expression is crucial for embryonic patterning. Intra-Hox transcription factor binding and plasmids (26). Although they can test the abil- distal enhancer elements have emerged as the major regulatory modules controlling Hox gene expression. ity of a sequence to drive expression, they lack However, quantifying their relative contributions has remained elusive. Here, we introduce “synthetic the scale to study Hox cluster chromatin do- regulatory reconstitution,” a conceptual framework for studying gene regulation, and apply it to the HoxA main formation (>100 kb). Larger bacterial or cluster. We synthesized and delivered variant rat HoxA clusters (130 to 170 kilobases) to an ectopic yeast artificial chromosomes (BACs/YACs) can location in the mouse genome. We found that a minimal HoxA cluster recapitulated correct patterns of provide more genomic context and have been chromatin remodeling and transcription in response to patterning signals, whereas the addition of distal elegantly employed to understand regulation enhancers was needed for full transcriptional output. Synthetic regulatory reconstitution could provide a at Hox clusters (27–29). However, they are not generalizable strategy for deciphering the regulatory logic of gene expression in complex genomes. easy to manipulate, making it challenging to generate a large number of variants that can M ammalian Hox genes encode deeply related with the separation of the cluster into be tested in vivo (26, 30, 31). Further, these conserved transcription factors (TFs) two domains that contain transcribed and large constructs are often randomly integrated repressed genes, respectively (8–12) (Fig. 1A). into the genome, which confounds comparison that are organized into four dense RARE mutations can lead to decreased or across different constructs as a result of posi- clusters (HoxA to HoxD) lacking other abolished expression of the neighboring HoxA tion effects and the integration of multiple coding genes (1). In response to devel- genes in the central nervous system, solidifying copies. Methods for precise, single-copy inte- opmental morphogens, Hox genes are expressed the notion that RAREs directly control Hox gration of large DNA molecules in mammalian along the anterior-posterior axis of the develop- gene expression (9, 13, 14). However, the rela- cells have not yet been applied to the study of tionship between RARE activity and chromatin Hox cluster regulation (32, 33). Despite the ing embryo in a spatial and temporal pattern domain formation is not yet well established. revolution in genome editing, it is still ineffi- cient and time-consuming to make intricate that mirrors the organization of the genes A collection of intricate genetic manipula- structural rearrangements or multiple defined within the cluster (2–4). The alteration of this tions has revealed a complex regulatory land- edits in cis, phased on a single homolog (34, 35). “colinear” Hox gene expression pattern results scape surrounding the Hox clusters (15–19). For in gross developmental defects or diseases such example, the HoxA cluster relies on several We recently described a pipeline that har- as cancer (5, 6). RA and Wnt responsive distal regulatory ele- nesses the endogenous homologous recombi- ments (enhancers) located in the gene-poor nation machinery in yeast to de novo assemble In undifferentiated cells, where no Hox region between Hoxa1 and the next gene, ~100-kb regions of mammalian genomes and genes are expressed, the entire HoxA cluster Skap2 (~300 kb away). Deleting some of these integrate them into a defined location in mouse (~130 kb) is targeted by Polycomb repressive enhancers reduces, but never eliminates, HoxA embryonic stem cells (mESCs) (36). This bottom- expression in response to RA or Wnt (20–22). up assembly of genomic loci enables the intro- complex 2 (PRC2) and marked by hetero- Distal enhancer access to the genes in the duction of an arbitrary number of variants in cis chromatin (7). Patterning signals such as ret- inactive domain is restricted by the formation that are independent of any natural template. inoic acid (RA) and Wnt activate transcription of a strong topological boundary at CCCTC- binding factor (CTCF) sites within the cluster Here, we apply and extend this technology through their downstream TFs. In response to upon differentiation. Disruption of this bound- to study the relative contributions of genomic ary results in the misexpression of posterior context, distal enhancers, and intracluster reg- RA, activated RA receptors (RARs) are bound HoxA genes in response to RA (15, 23, 24). ulatory elements to HoxA regulation. We con- structed variants of the HoxA cluster (ranging to retinoic acid response elements (RAREs) Thus, different regulatory modules are inte- from 130 to 170 kb) encoding combinations of found within the HoxA cluster. This is cor- grated to control Hox gene expression: local the previously identified regulatory modules TF binding, distal enhancers, and topological and integrated them into an ectopic locus, 1Institute for Systems Genetics, NYU Langone Health, New York, DNA organization. However, a synergistic model thereby isolating them from the native ge- NY 10016, USA. 2Department of Biology, New York describing their relative contribution and inter- nomic neighborhood. We then asked whether University, New York, NY 10003, USA. 3Center for Eukaryotic actions has remained elusive (Fig. 1B). the variant ectopic clusters were sufficient to Gene Regulation, Department of Biochemistry and Molecular reconstitute the transcriptional and epige- Biology, Pennsylvania State University, University Park, PA The relative contribution of a cis-regulatory netic HoxA response to activating patterning 16802, USA. 4Department of Cell Biology, NYU Langone Health, module could be measured by (i) generating a signals (Fig. 1C). New York, NY 10016, USA. 5Department of Biomedical variant allele that only contains the elements Engineering, NYU Tandon School of Engineering, Brooklyn, that constitute the module, and (ii) isolating Synthetic HoxA strategy and construction NY 11201, USA. 6Department of Pathology, NYU Langone the variant allele from confounding factors, Health, New York, NY 10016, USA. 7Department of such as the compensatory effect of other reg- All HoxA constructs described here were de- Biochemistry and Molecular Pharmacology, NYU Langone rived from rat (Rattus norvegicus) HoxA se- Health, New York, NY 10016, USA. quence, which shares ~90% sequence identity *Corresponding author. Email: [email protected] (E.O.M.); [email protected] (J.D.B.) †These authors contributed equally to this work. ‡Present address: Biogen Inc., Cambridge, MA 02142, USA. §Present address: Bristol-Myers Squibb Co., Lawrenceville, NJ 08648, USA. ¶Present address: Element Genomics Inc., Durham, NC 27701, USA. Pinglay et al., Science 377, eabk2820 (2022) 1 July 2022 1 of 9

RESEARCH | RESEARCH ARTICLE A mESC + Retinoic Acid (RA) Rostral Motor Neuron B HoxA regulatory modules +Sonic Hedgehog (Shh) No Hox Hoxa1-Hoxa5 chr6 expression expressed Distal Retinoic Acid Topology Enhancers Receptor Binding a1-a5 RAR binding a5/a6 | a7 topological boundary chr6 a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 HoxA response to RA What are their relative contributions? Active enhancers Euchromatin Heterochromatin ~300kb Synthetic regulatory reconstitution C - Enhancers + RAREs SynHoxA clusters (130-170kb) endogenous HoxA cluster + Enhancers + RAREs chr6 + Enhancers - RAREs - Enhancers - RAREs chrX Hprt locus ectopic SynHoxA cluster Gene expression? Chromatin boundary? chrX Step 1: Build HoxA variants to isolate the Step 2: Introduce variants to ectopic locus, Step 3: Compare ectopic variants to endoge- effect of each regulatory module isolate from endogenous genomic context nous locus and infer relative contributions Fig. 1. HoxA regulation relies on the integration of multiple regulatory modules. (A) Schematic of HoxA regulation in response to retinoic acid (RA) during in vitro mouse ES cell (mESC)–motor neuron differentiation. (B) Multiple regulatory modules, including enhancers, TF binding, and topology, are integrated to drive HoxA cluster response to RA. (C) Schematic of the synthetic regulatory reconstitution approach. Synthetic HoxA variants encoding various combinations of regulatory modules are built and integrated at an ectopic location in the genome. The response of these synthetic ectopic clusters to RA reveals their sufficiency and relative contribution in driving faithful HoxA expression. with the mouse HoxA sequence. This facili- generating the 170-kb Enhancers+SynHoxA ventral spinal cord development, including tated experiments in two distinct genetic back- construct (fig. S2). the activation of the appropriate HoxA genes grounds: (i) cells containing the endogenous (fig. S6A) (42, 43). Endogenous HoxA genes HoxA cluster (HoxA+/+), allowing direct com- DNA sequencing at each step confirmed are repressed before exposure to patterning parisons of expression levels to an internal assemblon integrity (Fig. 2C and fig. S3). We signals, and Hoxa1–5 are induced in response detected mutations at a frequency of ~1 nu- to the “anterior” RA signal (10). control, and (ii) cells lacking endogenous mouse cleotide per 6 kb, likely arising from PCR er- HoxA to eliminate potential sequence-mapping rors (fig. S3). We verified that none of these We performed RNA-seq on wild-type HoxA+/+ challenges (HoxA–/–). mutations were likely to affect the function cells containing ectopic SynHoxA variants over of the clusters in our differentiation system the course of the differentiation protocol. Com- We first constructed a 134-kb wild-type mini- described below (table S1). mal rat HoxA cluster (SynHoxA) (Fig. 2 and fig. parison to previously published control data- S1). SynHoxA contains all HoxA coding genes All constructs were delivered to the Hprt and encompasses the sequence correspond- locus on the X chromosome of both HoxA+/+ sets by principal components analysis (PCA) and HoxA–/– mESCs using Cre-mediated re- revealed that the samples grouped largely ing to the contiguous domain repressed by combination (38) (figs. S4 and S5). We reasoned according to time since RA treatment (44, 45) H3K27me3 (trimethylated histone H3 Lys27) that Hprt would be an appropriate site to at- (fig. S6B). Cells containing SynHoxA variants tempt regulatory reconstitution because it is down-regulated the expression of pluripotency in undifferentiated mESCs. We produced a housekeeping gene with little regulatory markers, up-regulated the expression of mark- polymerase chain reaction (PCR) amplicons activity in the surrounding regions, and its from BACs bearing the rat HoxA cluster, with use as a “safe harbor” site is well documented ers of motor neuron differentiation, and in- overlap between adjacent segments to enable (39, 40). Furthermore, transposing the HoxA duced Hoxa1–5 from the endogenous cluster cluster to an open locus would be the most upon exposure to RA as expected (Fig. 3, A and homologous recombination. These amplicons stringent test of its ability to recruit the C, and fig. S6, C and D). Thus, the presence of were recombined in yeast to produce the 134-kb repressive PRC2 complex in undifferentiated SynHoxA construct, termed an “assemblon” cells. We used capture sequencing to verify an ectopic synthetic cluster does not affect the (fig. S1B). Edits to the assemblon can be made that mESC clones contained the entire assem- ability of cells to differentiate appropriately blon, specifically at Hprt and in single copy by switching the wild-type amplicons with (41) (Fig. 2B). after RA treatment. synthetic DNA bearing the desired changes The ectopic Enhancers+SynHoxA cluster Induction of SynHoxA gene expression during or by editing the assemblons directly using motor neuron differentiation induced SynHoxa1–5 starting 24 hours after RA highly efficient, marker-free CRISPR/Cas9- treatment (Fig. 3B and figs. S7 and S8, A and based engineering in yeast (37). Assemblons We investigated the response of the ectopic B), whereas SynHoxa6 to SynHoxa13 re- were recovered from yeast into bacteria to clusters to RA in a widely used differentia- mained repressed throughout. Similarly, ectop- tion system that recapitulates key aspects of ic SynHoxA specifically induced SynHoxa1–5 purify large amounts of DNA (Fig. 2A). To test (Fig. 3D and figs. S7 and S8C) without mis- the contribution of distal enhancers to HoxA regulation, we fused all experimentally veri- expression of any posterior genes. Thus, neither fied distal regulatory elements directly up- endogenous genomic context nor the wide stream of the core SynHoxA assemblon, spacing of enhancer elements is strictly required Pinglay et al., Science 377, eabk2820 (2022) 1 July 2022 2 of 9

RESEARCH | RESEARCH ARTICLE A BACs containing Overlapping synthetic DNA mESCs B Integration site analysis amplicons encoding variation ectopic SynHoxA assemblon Rat HoxA Site-specific delivery to chrX mammalian cells PCR + BAC WT HoxA -/- Reads spanning assemblon and target genome BAC Left Junction Off target Right Junction Amplification of assemblons DNA SYNTHESIS SynHoxA Assembly of variants by homologous recombination 1 ... 27 Enhancers + WT mESC SynHoxA CEN/ARS 2 28 URA3 OR 1 highly efficient WT CRISPR edits BAC KANr BAC SynHoxA 2 ... 27 BAC BAC Variant 28 URA3 Enhancers + SynHoxA YEAST BAC KANr BAC HoxA -/- mESC 0 C BACTERIA 10 20 30 40 50 60 70 CEN/ARS reads per 10M Enhancers a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 170kb Enhancers + SynHoxA 134kb SynHoxA Assemblons [0 - 89] SynHoxA [0 - 63] Enhancers + SynHoxA WT mESC [0 - 182] SynHoxA [0 - 97] Enhancers + SynHoxA HoxA -/- mESC [0 - 168] SynHoxA [0 - 97] Enhancers + SynHoxA Fig. 2. Build and delivery of SynHoxA constructs. (A) Schematic of the revealed only the expected junctions with no off-target integrations. (C) Schematic process to generate mESCs bearing ectopic synthetic HoxA clusters via homologous recombination-based assembly in yeast and amplification in bacteria. (B) Analysis of the 134-kb SynHoxA and 170-kb Enhancers+SynHoxA constructs. Sequencing data of reads spanning the synthetic construct and the host genome by bamintersect for assemblon DNA isolated from bacteria (purple) and from capture sequencing after integration into wild-type (blue) and HoxA–/– (green) mESCs. for a Hox cluster to induce the appropriate duction of Hoxa2–5 from 24 to 96 hours. At (i) Hoxa5 antibody staining and (ii) RNA single- genes. 96 hours, the expression level is Hoxa2 < molecule fluorescence in situ hybridization for Hoxa3 < Hoxa4 < Hoxa5 (figs. S7 to S9). The anterior SynHoxA genes. We performed these We quantified gene induction from the ec- minimal SynHoxA cluster does not recapitulate experiments in the HoxA–/– background. Gene the temporal expression pattern of Hoxa1. expression from the ectopic clusters was not topic clusters by comparing each gene to its SynHoxa1 is expressed at low levels through- influenced by the presence or absence of the endogenous mouse HoxA counterpart (Fig. 3, out but increases steadily with time, mirroring endogenous HoxA cluster (fig. S10), and the E and F). Both ectopic clusters induced lower the regulation of SynHoxa2–5 genes. However, cells differentiated appropriately (fig. S11). SynHoxa1 transcription, whereas SynHoxa2 this is partially rescued with the addition of In both methods, the observed bulk differences induction surpassed the endogenous gene. The enhancers in Enhancers+SynHoxA. SynHoxa1 in expression were not due to a difference in induction kinetics of SynHoxa3–5 were slower expression in this context peaks at 48 hours the number of cells that express anterior than Hoxa3–5, but the mRNA levels became and decreases at 96 hours. The temporal ex- SynHoxA genes, but due to an increase in the comparable after 96 hours, particularly in the pression of SynHoxa2–5 is retained in both amount of expression per cell in the presence Enhancers+SynHoxA construct. In general, constructs (fig. S9). of the enhancers (figs. S12 to S15). Enhancers+SynHoxA induced higher levels of SynHoxa1–5 expression than SynHoxA, The observed bulk differences in gene ex- We investigated whether these findings especially at early time points (Fig. 3 and figs. pression between the ectopic clusters could be could be extended to other patterning signals beyond RA, such as the posteriorizing Wnt S7 and S8, B and C). attributed either to a change in the number of signal (10, 22). Both ectopic clusters induced cells that induce expression or to expression more posterior genes upon treatment with In our differentiation model, temporal co- Wnt, up to SynHoxa11 (fig. S16). Intriguingly, linearity of genes from the endogenous HoxA level changes in each cell. To address this, we the addition of distal enhancers does not seem cluster is exhibited by (i) an early induction of investigated the response of the synthetic Hoxa1 (peaks at 24 hours) and its subsequent down-regulation and (ii) the sequential in- clusters to RA at the single-cell level using Pinglay et al., Science 377, eabk2820 (2022) 1 July 2022 3 of 9

RESEARCH | RESEARCH ARTICLE A Enhancers + SynHoxA C SynHoxA from SynHoxa1–5. H3K27me3 was entirely cleared by 48 hours, slightly slower than the Time 24h Endogenous HoxA 24hTime Endogenous HoxA FC vs 0h -Log(adj p-val) endogenous locus, which clears by 24 hours (10). SynHoxA genes Thus, the endogenous genomic context at HoxA 48h 48h SynHoxA genes > 15 is not required to translate an extracellular sig- 0 15 nal into an accurate epigenetic chromatin state. 96h 96h Hoxa Hoxa 200 10 The minimal SynHoxA cluster also recruited gene gene H3K27ac to anterior genes upon RA activation 400 5 (Fig. 4D). Unlike the endogenous HoxA cluster B D 600 and Enhancers+SynHoxA, H3K27me3 was not entirely lost from the SynHoxa1–5 domain 24h 0 during differentiation (Fig. 4D). Nonetheless, SynHoxA formed the appropriate, albeit weak, 48h a1 a1 chromatin boundary at the SynHoxa5–a6 a2 a2 CTCF binding site (Fig. 4E and fig. S17, A 96h a3 a3 and B). Thus, the minimal SynHoxA cluster SynHoxa a4 a4 has the intrinsic ability to induce dynamic a5 a5 chromatin domains, independent of genomic gene a6 a6 context or enhancers. a7 a7 a9 a9 Topological organization of ectopic aaa111031 a10 SynHoxA clusters a11 a13 The three-dimensional structure of the HoxA cluster changes during motor neuron differ- 24h FC vs 0h -Log(adj p-val) entiation, transitioning from a single associa- tion domain to two domains containing active 48h > 15 or repressed chromatin (15, 23, 24). We investi- 0 15 gated the topological organization of the ecto- 96h pic clusters by performing Hi-C, a technique Time Time 2000 10 for detecting genome-wide chromatin inter- SynHoxa Synthetic/Endogenous Norm. Count Ratio actions, during differentiation (0 and 48 hours gene 4000 5 after RA treatment). Both clusters formed self- a1 6000 0 associating domains in undifferentiated cells a2 without generating a de novo topologically a1 a3 associating domain (TAD) boundary (fig. S18). a2 a4 Similar to the endogenous cluster, Enhancers a3 a5 +SynHoxA broke into two domains during a4 a6 differentiation, with enhancers and active genes a5 a7 in one domain and repressed genes in the other a6 a9 (fig. S18A). The minimal SynHoxA similarly a7 aaa111031 transitioned from a compact self-associated a9 state in undifferentiated cells into two domains a10 during differentiation (fig. S18B). We did not a11 observe strong evidence for trans-chromosomal a13 interactions between the ectopic locus and its endogenous enhancers (tables S2 and S3). E F Thus, the ectopic HoxA clusters have the in- trinsic ability to self-organize in three dimen- Synthetic/Endogenous Norm. Count Ratio 2 Time 2 Time sions, mirroring the expression and chromatin 0h 0h changes that occur upon differentiation. 24h 24h 48h 48h The RARE sites within the HoxA cluster are 96h 96h required for the RA response 1 1 The minimal SynHoxA transformed the RA signal into the correct transcriptional and chro- 0 0 matin programs. This behavior could theoret- SynHoxa1 SynHoxa2 SynHoxa3 SynHoxa4 SynHoxa5 SynHoxa1 SynHoxa2 SynHoxa3 SynHoxa4 SynHoxa5 ically depend on RAREs located within the Hoxa1–5 domain, other sequences within the Fig. 3. SynHoxA variants up-regulate the correct subset of genes in response to RA patterning cluster, or interactions with other regulatory signal. (A to D) Fold change (FC) of RNA-seq data for endogenous mouse HoxA [(A) and (C)] and SynHoxA elements at the ectopic locus. To distinguish [(B) and (D)] genes during RA differentiation, relative to expression before RA treatment (n = 2). SynHoxA between these possibilities, we built a third variants induce the correct genes (SynHoxa1–5) in response to RA. (E and F) Ratios of gene expression construct lacking both RAREs and enhancers for SynHoxA genes to endogenous mouse HoxA genes (n = 2). Counts for the endogenous HoxA genes were (RARED SynHoxA) and integrated it into wild- halved to normalize for two endogenous HoxA versus one ectopic SynHoxA copy. type and HoxA–/– mESCs (figs. S19 and S20) (9). to consistently modify the Wnt response across domain, forming a precise chromatin boundary SynHoxa genes as much as it did for RA. between Hoxa5 and Hoxa6 (10, 23). We investi- gated the chromatin dynamics and CTCF re- Together, these data support a model in cruitment of the relocated HoxA clusters by which the HoxA cluster contains all the nec- performing chromatin immunoprecipitation essary information to decode patterning sig- sequencing (ChIP-seq) in the HoxA–/– back- nals into the appropriate positional identity, ground to more reliably map reads to the ecto- independent of distal enhancers and the native genomic architecture. Distal enhancers are pic clusters, thereby enhancing resolution. not required to specify active genes but have Prior to differentiation, both Enhancers+ a critical role in modulating transcriptional output in response to RA. Whereas both ec- SynHoxA and SynHoxA were entirely covered topic clusters induce the correct subset of with high levels of H3K27me3. In addition, genes, additional elements may be required to fine-tune expression amplitude and timing. CTCF was recruited to the appropriate sites Chromatin reorganization at SynHoxA clusters (Fig. 4, A and B). Thus, the ability to recruit through differentiation all components for correct patterning is in- In undifferentiated cells, Hox clusters are trinsic to the HoxA cluster sequence and is carpeted with repressive H3K27me3 marks independent of endogenous genomic con- and recruit CTCF to potential boundary po- sitions established in response to extracellular text or distal enhancers. Upon RA treatment, signals. The endogenous HoxA cluster responds Enhancers+SynHoxA remodeled chromatin in a to RA by separating into an active and inactive manner that is similar to the endogenous clus- ter. H3K27me3 decreased in the SynHoxa1–5 domain and increased at SynHoxa6–13 (Fig. 4C). An increase in acetylated H3K27 (H3K27ac) complemented H3K27me3 removal Pinglay et al., Science 377, eabk2820 (2022) 1 July 2022 4 of 9

RESEARCH | RESEARCH ARTICLE A Enhancers + SynHoxA B SynHoxA H3K27me3 H3K27Ac CTCF H3K27me3 H3K27Ac CTCF [0 - 4.00] [0 - 4.00] 0h [0 - 2.00] 0h [0 - 2.00] [0 - 3.00] [0 - 3.00] Backbone Enhancers a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 Backbone Backbone a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 Backbone (ori bla) (LEU2) (ori bla) a13 (LEU2) C H3K27me3 H3K27Ac CTCF D H3K27me3 H3K27Ac CTCF Backbone [0 - 7.00] (LEU2) [0 - 7.00] 24h [0 - 2.00] 24h [0 - 2.00] [0 - 7.00] [0 - 7.00] 48h 48h [0 - 2.00] [0 - 2.00] [0 - 7.00] [0 - 7.00] 96h [0 - 2.00] 96h [0 - 2.00] [0 - 3.00] [0 - 3.00] 48h 48h Backbone Enhancers Backbone Backbone (ori bla) (LEU2) (ori bla) a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 E H3K27me3/H3K27ac Ratio H3K27me3/H3K27ac Ratio Ratio Ratio a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 a1 a2 a3 a4 a5 a6 a7 a9 a10 a11 a13 Fig. 4. Distal enhancers are required for full clearance of repressive chromatin repressive H3K27me3. Dotted lines at the anterior breakpoint between the cluster and the formation of a sharp chromatin boundary. ChIP-seq analysis (n = 2) of and the vector sequences in (B) and (D) indicate presence of enhancer sequences in activating H3K27ac (blue), repressive H3K27me3 (red), and CTCF (black) at the reference genome to which no reads are mapped. (E) RPKM (reads per kilobase SynHoxA clusters. (A and B) In undifferentiated cells, SynHoxA clusters contained per million mapped reads) normalized ratios of repressive H3K27me3 to active H3K27me3, lacked H3K27ac, and recruited CTCF to correct locations. (C and D) In H3K27ac across SynHoxA. The black line marks the Hoxa5-Hoxa6 CTCF site; gray response to RA, the SynHoxa1–5 domain contained activating H3K27ac and cleared shading indicates the windows contributing to ChIP-seq signal at the site. Cells carrying RAREDSynHoxA differenti- upstream of RARED SynHoxA (figs. S19 and S20). time points. These results are consistent with ated and induced endogenous HoxA genes In Enhancers+RARED SynHoxA, SynHoxa2–5 previous studies in which deletion of enhancers appropriately (Fig. 5A and fig. S20, D and were induced at low levels in response to RA from the endogenous locus resulted in lower Hox (Fig. 6, A and B, and fig. S8E). A faint chromatin gene transcription in response to morphogens E). The ectopic cluster was decorated with boundary formed at the appropriate location (20, 22, 46). At the time point we investigated, between SynHoxa5 and SynHoxa6 (Fig. 6, C the ectopic cluster with distal enhancers did not H3K27me3 in mESCs, indicating that RAREs and D, and fig. S17D). This suggests that the induce higher expression in response to Wnt. distal enhancers may have a weak ability to This may indicate that some Wnt-responsive are not required to recruit the repressive chro- activate HoxA gene transcription without the enhancers are missing in these constructs, or driving force provided by internal RAREs, or that the distal enhancers are ineffective in this matin machinery. However, unlike the pre- that they synergize with the poorly charac- configuration. Alternatively, earlier time points vious constructs, RARED SynHoxA failed to terized RARE still present in this construct. may reveal differences in transcriptional dy- up-regulate the expression of SynHoxa1–5 or namics or output between these constructs. to form a chromatin boundary in response to Discussion The importance of both RAREs and distal RA (Fig. 5, B to D, and figs. S8D and S17C). We developed a “synthetic regulatory recon- enhancers to Hox gene expression was firmly SynHoxa5 was the only gene with any signal, stitution” approach to characterize the rela- established before this work. However, it was potentially due to a poorly characterized RAR tive contributions of distal enhancers and difficult to quantify their relative contributions binding site located between Hoxa5 and intracluster TF binding in specifying dis- to the establishment of transcriptional and Hoxa6 (9, 10). This null phenotype indicates tinct aspects of HoxA regulation. A minimal chromatin domains at the scale of an entire that the behavior of ectopic SynHoxA clusters ectopic cluster lacking distal enhancers in- Hox cluster with previous techniques. Our re- reflects their innate regulatory potential and duced the correct subset of genes in response sults show that an ectopic cluster lacking all to two developmental signals (RA and Wnt). previously described internal RAREs (RARED not the effect of novel interactions formed at The presence of distal enhancers increased SynHoxA) failed to respond to RA both at the the Hprt locus. the transcriptional output from the ectopic transcriptional and chromatin levels. This gene cluster in response to RA, especially at earlier expression phenotype was not fully rescued by This lack of RA response provided the ideal background to measure the independent con- tribution of distal enhancers to HoxA gene regulation. To that end, we built and integ- rated a fourth construct: Enhancers+RARED SynHoxA, with the distal enhancers inserted Pinglay et al., Science 377, eabk2820 (2022) 1 July 2022 5 of 9