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11 Ways the Government Shutdown Affects Science

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When the federal government shut down early last week, many of the people and projects that explore the universe, cure disease, figure out things we didn’t know before, and generally make our lives and our world better were deemed inessential. More than 95 percent of the staff at the National Science Foundation and NASA have been furloughed, along with three-quarters of the staff at the National Institutes of Health and around half of the staff at the National Oceanic and Atmospheric Administration. Experiments are being halted. Grant applications are sitting in empty offices unread. Sick patients are being turned away at laboratory doors. Publicly funded data is locked up on websites that won’t function. Time, money, and effort are being wasted and the world will be a worse place for it. Here are 11 ways scientists have been feeling the shutdown’s effects, some big and some small.

1. Lab mice across the country are going to be killed

The NIH and other federal research centers use hundreds of thousands of mice as animal models to investigate diseases like Alzheimer’s and cancer. Barred from their labs and unable to work or care for their mice colonies, many researchers will have to euthanize the mice to keep them from overbreeding, overcrowding their cages and starving to death. Some of these animals are genetically altered for research. A single transgenic mouse can cost thousands of dollars, but data it might have provided may be irreplaceable.

2. Antarctic research is abandoned

The entire U.S. Antarctic research program has been canceled, and most of the staff at the three bases will have to be sent home. Depending on how long the shutdown lasts, the researchers may miss most or all of the summer research season. One of the projects affected is NASA’s IceBridge, which tracks yearly changes in Antarctica’s ice sheets and monitors how ice on land and in the sea responds to climate change. Interrupting annual data gathering like this leaves gaps in the data record and affects the accuracy of the analyses that scientists are able to make and the inferences and predictions they can draw from it.

3. Sick people are turned away

The NIH and other federal labs run clinical trials for new disease treatments, but reduced staffs can’t handle additional patients, and new enrollments in the trials have slowed to a crawl. In a typical week the NIH might have taken on 200 new patients, but in the first week of the shutdown only 12 patients, in imminent danger of dying, were enrolled.

4. No one’s tracking the flu

Flu prevention isn’t a problem so much as flu surveillance is, says Maryn McKenna. Many local health organizations already have their stocks of flu vaccines and can distribute them as normal, but with two thirds of the staff at the Centers for Disease Control and Prevention (CDC) on furlough, programs that track disease outbreaks, and share that data with state and municipal health agencies around the country, are shutting down. That will create blind spots in what we know about this year’s flu strains. We won’t know how bad they are, where infections are concentrated, how to direct the limited resources the CDC has, or how to prepare next year’s vaccines.

5. …Or other health problems

The Food and Drug Administration has also furloughed almost half of its staff, curbing its ability to monitor and combat food-borne illnesses and inspect food facilities. In a memo about shutdown staffing, the Department of Health and Human Services admits that the “FDA will be unable to support the majority of its food safety, nutrition, and cosmetics activities. FDA will also have to cease safety activities such as routine establishment inspections, some compliance and enforcement activities, monitoring of imports, notification programs (e.g., food contact substances, infant formula), and the majority of the laboratory research necessary to inform public health decision-making.”

While the FDA’s hands are tied, an outbreak of Salmonella Heidelberg has erupted, making hundreds of people sick in 18 states. Depending on how long the shutdown lasts, this could be the first of many such outbreaks. As CDC director Tom Frieden said on Twitter the other day, Microbes/other threats didn't shut down. We are less safe.”

6. Hawaii gets left in a sticky situation

Remember when a few hundred thousand gallons of molasses spilled into Honolulu Harbor in September? Federal agencies who were helping clean up the mess, restore and repair affected ecosystems, and investigate the failures that led to the spill have all had to stand down with much of their work left unfinished. State and local agencies will continue working, but progress will be much slower without the additional money and manpower.

7. Other researchers get left in the cold 

It’s not just scientists working directly for the government who are affected by the shutdown. Plenty of other researchers who work at private institutions and independent organizations fund their work partly or fully through federal research grants. With no new grant applications being reviewed, and some grants approved but not fulfilled, even non-government researchers may have to discontinue some experiments or give up on starting others if they were expecting federal money. Delays in grant approval and funding will delay many projects and could keep some from beginning at all.

8. Publishing of new work will be derailed

Even research that’s completed isn’t safe from the shutdown if hasn’t cleared the various huddles to getting published in a scientific journal. If a researcher hasn’t sent their new paper off to a journal for review or submitted revisions on an accepted paper, and they can’t use their email or conduct other work activities during the shutdown, they’re just going to have to wait. On the journal side, some of the editors and peer reviewers (those scientists that review papers for journals to safeguard against errors and flaws in research’s methods and conclusions, and other serious problems like plagiarism) may be government-employed or affiliated and unable to fulfill their duties for the journal. Instead of being shared with other researchers and the public, completed research that’s ready for the world will collect dust instead.

9. Science journalists have fewer resources to work with

If you’re a science writer working on a story about a federally funded research project, or need to talk to a federally funded researcher about their work or get an outside comment on other scientists’ work or even just check some numbers or a fact on a government website (say, census numbers, or polio infection rates), you’re kind of out of luck, especially if you’ve already put money into a reporting trip. Of course, this means less science news for the public to consume.

10. The Mars rover is basically a really expensive paperweight 

11. Plus, so much more

Follow  on Twitter for tons of personal stories and news from reseachers whose research and careers are in limbo for the time being. 

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iStock // Ekaterina Minaeva
Man Buys Two Metric Tons of LEGO Bricks; Sorts Them Via Machine Learning
May 21, 2017
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iStock // Ekaterina Minaeva

Jacques Mattheij made a small, but awesome, mistake. He went on eBay one evening and bid on a bunch of bulk LEGO brick auctions, then went to sleep. Upon waking, he discovered that he was the high bidder on many, and was now the proud owner of two tons of LEGO bricks. (This is about 4400 pounds.) He wrote, "[L]esson 1: if you win almost all bids you are bidding too high."

Mattheij had noticed that bulk, unsorted bricks sell for something like €10/kilogram, whereas sets are roughly €40/kg and rare parts go for up to €100/kg. Much of the value of the bricks is in their sorting. If he could reduce the entropy of these bins of unsorted bricks, he could make a tidy profit. While many people do this work by hand, the problem is enormous—just the kind of challenge for a computer. Mattheij writes:

There are 38000+ shapes and there are 100+ possible shades of color (you can roughly tell how old someone is by asking them what lego colors they remember from their youth).

In the following months, Mattheij built a proof-of-concept sorting system using, of course, LEGO. He broke the problem down into a series of sub-problems (including "feeding LEGO reliably from a hopper is surprisingly hard," one of those facts of nature that will stymie even the best system design). After tinkering with the prototype at length, he expanded the system to a surprisingly complex system of conveyer belts (powered by a home treadmill), various pieces of cabinetry, and "copious quantities of crazy glue."

Here's a video showing the current system running at low speed:

The key part of the system was running the bricks past a camera paired with a computer running a neural net-based image classifier. That allows the computer (when sufficiently trained on brick images) to recognize bricks and thus categorize them by color, shape, or other parameters. Remember that as bricks pass by, they can be in any orientation, can be dirty, can even be stuck to other pieces. So having a flexible software system is key to recognizing—in a fraction of a second—what a given brick is, in order to sort it out. When a match is found, a jet of compressed air pops the piece off the conveyer belt and into a waiting bin.

After much experimentation, Mattheij rewrote the software (several times in fact) to accomplish a variety of basic tasks. At its core, the system takes images from a webcam and feeds them to a neural network to do the classification. Of course, the neural net needs to be "trained" by showing it lots of images, and telling it what those images represent. Mattheij's breakthrough was allowing the machine to effectively train itself, with guidance: Running pieces through allows the system to take its own photos, make a guess, and build on that guess. As long as Mattheij corrects the incorrect guesses, he ends up with a decent (and self-reinforcing) corpus of training data. As the machine continues running, it can rack up more training, allowing it to recognize a broad variety of pieces on the fly.

Here's another video, focusing on how the pieces move on conveyer belts (running at slow speed so puny humans can follow). You can also see the air jets in action:

In an email interview, Mattheij told Mental Floss that the system currently sorts LEGO bricks into more than 50 categories. It can also be run in a color-sorting mode to bin the parts across 12 color groups. (Thus at present you'd likely do a two-pass sort on the bricks: once for shape, then a separate pass for color.) He continues to refine the system, with a focus on making its recognition abilities faster. At some point down the line, he plans to make the software portion open source. You're on your own as far as building conveyer belts, bins, and so forth.

Check out Mattheij's writeup in two parts for more information. It starts with an overview of the story, followed up with a deep dive on the software. He's also tweeting about the project (among other things). And if you look around a bit, you'll find bulk LEGO brick auctions online—it's definitely a thing!

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Scientists Think They Know How Whales Got So Big
May 24, 2017
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It can be difficult to understand how enormous the blue whale—the largest animal to ever exist—really is. The mammal can measure up to 105 feet long, have a tongue that can weigh as much as an elephant, and have a massive, golf cart–sized heart powering a 200-ton frame. But while the blue whale might currently be the Andre the Giant of the sea, it wasn’t always so imposing.

For the majority of the 30 million years that baleen whales (the blue whale is one) have occupied the Earth, the mammals usually topped off at roughly 30 feet in length. It wasn’t until about 3 million years ago that the clade of whales experienced an evolutionary growth spurt, tripling in size. And scientists haven’t had any concrete idea why, Wired reports.

A study published in the journal Proceedings of the Royal Society B might help change that. Researchers examined fossil records and studied phylogenetic models (evolutionary relationships) among baleen whales, and found some evidence that climate change may have been the catalyst for turning the large animals into behemoths.

As the ice ages wore on and oceans were receiving nutrient-rich runoff, the whales encountered an increasing number of krill—the small, shrimp-like creatures that provided a food source—resulting from upwelling waters. The more they ate, the more they grew, and their bodies adapted over time. Their mouths grew larger and their fat stores increased, helping them to fuel longer migrations to additional food-enriched areas. Today blue whales eat up to four tons of krill every day.

If climate change set the ancestors of the blue whale on the path to its enormous size today, the study invites the question of what it might do to them in the future. Changes in ocean currents or temperature could alter the amount of available nutrients to whales, cutting off their food supply. With demand for whale oil in the 1900s having already dented their numbers, scientists are hoping that further shifts in their oceanic ecosystem won’t relegate them to history.

[h/t Wired]