By Gwyneth Dickey Zakaib of Nature magazine

Cancer patients desperate to get into government run clinical trials will be sidelined. Researchers maintaining stem cell lines will lose precious weeks as experiments are abandoned. Oceanographers counting on expeditions to service remote probes will instead risk long gaps in data gathering. And thousands of scientists who work in government labs as well as administrators who keep funds flowing to researchers at universities and institutes across the U.S. will simply be asked to go home, unplugged and unpaid.

Throughout the U.S. government, scientists are bracing themselves in different ways for a possible shutdown at midnight on April 8 if Congress fails to pass either a budget for the remainder of the 2011 fiscal year or another stopgap resolution to maintain government spending.

Rarely has so much uncertainly beset the Washington, D.C., area, where most federal activities are headquartered, including the roughly two dozen departments and agencies that engage in and support scientific research. If a last-minute deal is reached, the government may not shut down at all, and even if it does, it may not be for very long. But even a short shutdown could have wide-reaching implications for the thousands of scientists who would not be allowed to continue their work during mandatory furloughs that would begin Saturday.

"One day is tolerable, three days is a killer," says an intramural scientist who works with stem cells at the National Institutes of Health (NIH) and who spoke to Nature on condition of anonymity. "Most stem cell scientists come in every day to take care of their cells. If you shut down an experiment in the middle, you lose all the time and the money that was invested in that experiment, plus it takes many weeks to get back to where you were before," he says, adding that the cost of a shutdown in his lab could be in the range of $10,000 per person.

His lab has been preparing for a shutdown for more than a week by freezing any cells that have reached an appropriate stage, and by not starting any new projects. He says a big problem at NIH has been a lack of clarity about what the plan will be if a shutdown occurs. A letter from Secretary of Health and Human Services Kathleen Sebelius to NIH managers says that those who care for human patients and animals, as well as people protecting federal property, will be excepted from furloughs. However, the letter does not specify if scientists will be allowed to maintain cell cultures.

In addition, the NIH clinical center would stop enrolling new patients and any extramural funds that require personnel for dispersal "will likely cease," according to a memo from an officer at the Association of American Medical Colleges.

Even for researchers not dealing with patients or live cultures, a short shutdown could have long-lasting effects. Mike McPhaden, an oceanographer at the Pacific Marine Environmental Laboratory in Seattle, Wash., an affiliate of the National Oceanic and Atmospheric Administration, says his team makes plans months in advance to board cruises and conduct routine maintenance on floating ocean sensors collecting data about El Nino, La Nina and other kinds of climate phenomena.

"If the government shuts down, we will literally miss the boat on some of these cruises," says McPhaden. There could be gaps in data if some sensors don't get their yearly service and go out of commission. "It's not like getting in your car and driving down the street. If you miss a cruise, you may not get back for many months, and you may lose data until the next time you can get there."

At NASA, researchers will not be allowed to continue their work but operations staff will maintain and protect essential equipment and tend to astronauts and missions without disruption. One exception is NASA's Stratospheric Observatory for Infrared Astronomy (SOFIA), which flies at high altitude to access parts of the infrared spectrum not easily observed from the ground. SOFIA currently has at least one flight scheduled for next week out of the NASA Dryden Aircraft Operations Facility in Palmdale, Calif. A shutdown would cancel that flight, a NASA spokeswoman said, with no subsequent flights scheduled until the summer.

Other agencies may have less to fear from a brief shutdown. The Department of Energy has funds to maintain normal operations for a few days at least, and would not immediately furlough employees at the beginning of next week, according to an e-mail from Secretary of Energy Steven Chu to employees. Unlike most other federal agencies, the Department has access to funds that remain available until expended, Chu wrote. "This would allow us to continue operating for a limited time."

The Department of Energy's Fermilab in Batavia, Ill., for example, could continue operations for four weeks, according to lab director Pier Oddone. "From the financial point of view, for the government shutdown to affect us directly, it would have to be a long shutdown." But in the event that it lasted longer than a month, virtually no projects would continue, he says.

Long-term repercussions

Many scientists are worried more about the long-term effects of being caught in Congress's partisan crossfire. Uncertainty of funding and tight budgets are discouraging some young scientists from pursuing a research career, says Wolf Frommer, a biologist who studies transport in plants at the Carnegie Institution for Science at Stanford in California. "This is affecting science in America in a very dramatic way which most people aren't aware of."

Others say that the funding debate is hurting science's long-term planning process.

"Going from week to week or month to month is not a way to run a research program," says Howard Garrison, director of the Office of Public Affairs for the Federation of American Societies for Experimental Biology (FASEB) in Bethesda, Md. "The real effect is we've lost the dialogue on how to chart our course for long-term investment, and that is likely to have long-term repercussions."

Even if the imminent shutdown is averted, policy experts and politicians warn that the ongoing budget clash between the White House and Republicans in the House of Representatives will certainly have an effect on science funding in the current year, and possibly a far greater one in the following, 2012 fiscal year. At present, a series of continuing resolutions has kept government spending flat-lined at 2010 budget levels. However, President Barack Obama and Democrats, who hold a majority in the Senate, have already agreed to a budget deal that is least $33 billion below that line, which Republicans have rejected. Any agreement that emerges from eleventh-hour negotiations may involve still further reductions.

At a briefing on Capitol Hill today, organized by the American Association for the Advancement of Science, Democratic Rep. Rush Holt of New Jersey told participants that "there will be a change" in the way government business proceeds following the current impasse. "Further deep cuts" to the budget are not in doubt, he added.

This article is reproduced with permission from the magazine Nature. The article was first published on April 7, 2011