Congress was unable to pass the funding bill before the deadline, and as of midnight tonight the US government has begun shutting down.

The US government is headed for a shutdown as of this writing, after members of Congress were unable to reach a compromise on the federal budget. They have until midnight tonight to pass a new funding bill in time for the start of fiscal year 2014. If they can’t make it in time, about 800,000 civilian workers, about 40 percent of the entire US federal government’s civilian workforce, will be required not to work. Many of them will be furloughed without pay.

It’s unclear just how long the great shutdown of 2013 would last, but if history is any indication, it could be a while. The US government has closed its doors 17 times previously, and the last time was also the longest — back in 1995, Congressional Republicans and the Clinton administration managed to keep the government dark for 21 days. The impending shutdown this year is also largely the result of party politics, with the Republican-led House trying to defund the healthcare reform law backed by the president (nicknamed "Obamacare"), which goes into effect tomorrow.

largely the result of party politics

But looking beyond the questions of the moment and the political fight that’s holding America’s finances hostage, it’s already clear that the most severe consequences of the shutdown will be felt by those government agencies specializing in science, technology, health, and the environment. Here’s a rundown of what to expect:

NASA

The National Aeronautics and Space Administration will see over 90 percent of its civilian workforce immediately furloughed: 17,701 out of 18,250 total employees, according to the shutdown plan the agency filed last week. As President Obama put it in an emergency address last night, "NASA will shut down almost entirely, but Mission Control will remain open to support the astronauts serving on the Space Station."

"NASA will shut down almost entirely."

NASA notes that there’s a crew of six astronauts aboard the station now that it can’t abandon, and that operating the ISS requires ground controllers on duty 24 hours a day, 7 days a week, who send about 1,000 commands to the station every day. If the shutdown drags on, NASA also points out that employees will be needed to help launch crew and cargo to the station aboard Russian Soyuz spacecraft, and to return crew from orbit. The next mission to carry crew to the station is scheduled for November 6th.

In Florida, NASA’s historic Kennedy Space Center is likely to see most of its 2,085 civilian employees and another 4,384 private contractors asked to stay home. Not surprisingly, government officials are worried about the effects of an extended shutdown on the economy, especially coming on the heels of the closure of the space shuttle program in 2011, in which thousands of jobs were shed.

"suddenly the shutdown of NASA starts affecting the whole community."

"A good chunk of the population work out at Kennedy Space Center," says Don Walker, communications director of the Brevard County, Florida, government. "If they don’t get paid, or aren’t working, they’re not going to be going out to restaurants or the movies, and suddenly the shutdown of NASA starts affecting the whole community." He continues: "We barely kept our head above water just long enough to get through the end of the space shuttle program, this could be a double whammy."

Environmental Protection Agency (EPA)

The EPA, by its own count, has about 16,200 people on the payroll. But only 1,069 or about 6.5 percent, of those are staying on — either because they're doing vital work or because another fund is paying their bills, according to the agency’s shutdown plan. The former category is essentially a reminder of all the things we depend on the government to do. Would you like someone to keep managing the sites where toxic waste is being cleaned up (so-called "Superfunds")? The EPA has you covered.

As the shutdown plan explains: "For example, if ceasing the operation of an acid mine drainage treatment plan would cause a release to a stream that provided drinking water to a community, the agency would consider that situation to pose an imminent threat."

"the agency would consider that situation to pose an imminent threat."

Not all Superfund work is dependent on the bill being debated, which also helps employees stay at work. Like other agencies, the EPA is taaking employees with maintaining important facilities: some people will stay behind to stop lab animals from dying and make sure long-running tests can keep going. A skeleton crew will still be around should an environmental disaster occur, and attorneys and law enforcement will be able to prosecute cases and enforce rules.

This still doesn't mean business will be going on as usual. If your work is absolutely necessary, you can still only show up for the time it takes to complete it: if you have to spend an hour a day managing something, you'll spend that hour and not a minute more. So when EPA head Gina McCarthy said a few days ago that a furlough would mean that her agency "effectively shuts down," she wasn’t exaggerating.

Health and Human Services (HHS)

The US Department of Health and Human Services is a sprawling agency that includes everything from the Food and Drug Administration to the Centers for Disease Control and Prevention to the National Institutes of Health. And yet, about half of the organization’s 78,686 staff members — some 40,512 employees — would be asked to stay home during the shutdown, according to its shutdown plan.

The HHS says that most of the agencies to keep staff will be those with a "substantial direct service component," such as health care clinics, child support and foster care, services for the elderly and those with disabilities, and yes, care for lab animals. Tragically, at the National Institutes of Health, clinical trials of new, potentially life-saving treatments will also be halted, including those affecting about 30 child patients, The Wall Street Journal reports. Most of them are reportedly suffering from cancer.

"significantly reduced capacity to respond to outbreak investigations."

Other programs being paused for the shutdown should give Americans pause: the seasonal flu vaccine program, for example, won’t run during the shutdown. And let’s hope there’s no deadly outbreak of disease while the government is down, as the CDC will have "a significantly reduced capacity to respond to outbreak investigations," and won’t be able to provide updating disease treatment information. Perhaps most worrisome of all HHS notes that "the preparation to respond to H7N9 influenza or MERS incident" — two lethal, emergent diseases — "could be delayed." CDC will maintain its 24 / 7 emergency hotline, though.

The Food and Drug Administration will also continue to "handle emergencies, high-risk recalls, civil and criminal investigations," but will stop food and drug inspections, as well as cease the "majority of the laboratory research necessary to inform public health decision-making."

Ironically, one HHS program at the center of the shutdown conflict in Washington — the health insurance exchanges set up under the health care reform bill — will go ahead as planned on October 1st, the first day of the shutdown itself.

However long the shutdown lasts, the government’s science, technology and health arms will be taking the biggest hits. It follows that the people who depend on them will be out of luck, too.

Updated to add information about the National Institutes of Health clinical trials.

Adi Robertson contributed to this report