From the text of John Holdren’s recent congressional testimony on the science budget (also available here):

All told, this Budget proposes $66.8 billion for civilian research and development, an increase of $4.1 billion or 6.5 percent over the 2010 funding level in this category. But the Administration is committed to reducing the deficit even as we prime the pump of discovery and innovation. Accordingly, our proposed investments in R&D, STEM education, and infrastructure fit within an overall non-security discretionary budget that would be frozen at 2010 levels for the second year in a row. The Budget reflects strategic decisions to focus resources on those areas where the payoff for the American people is likely to be highest.

This is similar to what I argued with Meryl Comer in the Los Angeles Times in December–tough economic times are the times to invest in science, not cut it.

Holdren concludes:

Let me reiterate, in closing, the guiding principle underlying this Budget: America’s strength, prosperity, and global leadership depend directly on the investments we’re willing to make in R&D, in STEM education, and in infrastructure.

Investments in these domains are the ultimate act of hope, the source of the most important legacy we can leave. Only by sustaining them can we assure future generations of Americans a society and place in the world worthy of the history of this great Nation, which has been building its prosperity and global leadership on a foundation of science, technology, and innovation since the days of Jefferson and Franklin.

In hard times, you don’t give up on vision. You knuckle down, sure, but you also look ahead. (Meanwhile, Paul Krugman reminds us today that the budget debate is deeply mis-aligned because we’re so focused on cutting the smallest part of the budget, when the real issues are healthcare costs and tax revenue.)

The anti-laser—a tech with such a cool name it doesn’t need an obvious application—first came to our attention last year when Yale’s A. Douglas Stone proposed the idea. Now Stone is back with the real thing. His new paper in Science documents the world’s first anti-laser.

Conventional lasers create intense beams of light by stimulating atoms to spit out a coherent beam of light in which all the light waves march in lockstep. The crests of one wave match the crests of all the others, and troughs match up with troughs. The anti-laser does the reverse: Two perfect beams of laser light go in, and are completely absorbed. [Wired]

Anti-lasers are a bit of a funny concept, because anybody who has worn black on an August afternoon knows that absorbing light and turning it into heat isn’t a problem. But creating a device that matches the concentrated beam of a laser and traps more than 99 percent of it—essentially reversing a laser—is an engineering feat.

Whereas a laser uses mirrors to bounce light back and forth through an ...

It turns out that the news reporter who suddenly began speaking gibberish as she covered the Grammy Awards wasn’t suffering from a stroke–doctors conclude that a migraine is to blame.

Serene Branson, a reporter for KCBS-TV, began speaking incoherently during her coverage of the annual music awards ceremony. “As soon as I opened my mouth I knew something was wrong,” Branson told MSNBC. “I was having trouble remembering the word for Grammy…. I knew what I wanted to say but I didn’t have the words to say it.”

Many internet viewers thought she was stricken by an on-air stroke, but physicians from the University of California at Los Angeles scanned her head and tested her blood, and discovered that she was simply the victim of a migraine. It all started with a strong headache, Branson told MSNBC, but then it escalated:

“At around 10 o’clock that night I was sitting in the live truck with my field producer and the photographer and I was starting to look at some of my notes,” she said. “I started to think, the words on the page are blurry and I could notice that my thoughts ...

On March 17, just a month from now, NASA’s MESSENGER probe is scheduled to enter orbit around Mercury, the smallest planet in the solar system. No other mission from Earth has ever done this, and for the first time we’ll get high-resolution maps of the entire globe.

On its way down, the spacecraft was commanded to turn around and look outward, toward space. It took a series of images of what it saw… this astonishing family portrait of the solar system:

Click it to ensolarsystemate it and see it in more detail. When you do you’ll see the five classical planets in our system, as well as the Earth and Moon. Uranus and Neptune are there, but too faint to see, unfortunately, but still, this is an interesting picture. In November 2010, when these pictures were taken, Mercury was still nothing more than a dot. In fact, all the planets as barely more than dots, a reminder that this probe is well away from home and nowhere near any solid ground.

I like very much the images of Venus and the ...

In New Zealand, there’s a running joke that the sheep outnumber the people. What’s not funny is the consequence of all those woolly creatures: poop. Piles and piles of it. To reduce this overflowing cornucopia of crap, the government is calling in reinforcements in the form of 11 Australian dung beetle species.

The country’s excess poo not only finds it way into water reservoirs, it also releases nitrous oxide into the atmosphere–and to put that in perspective, cow crap alone accounts for 14 percent of New Zealand’s greenhouse gas emissions. “One of the big things basically is the accumulation of dung on pasture surfaces,” Landcare New Zealand research scientist Shaun Forgie told the Australian Broadcasting Corporation. It’s bad for cattle because more dung increases the “zone of repugnance, which means there’s an area around dung which is basically offensive to grazing livestock…. They don’t want to eat around that, so unless you break feed, you’re losing that surface area to graze on.”

Dung beetles cut the crap by feasting on it: adults lay eggs in manure, and the baby beetles feed on the scrumptious scat, ...

The Hudson River has been one of the most polluted in America, but because of that pollution, it’s now the site of evolution happening at a breakneck pace.

The furiously evolving species is the bottom-feeding Atlantic tomcod, which lives in areas of the Hudson that were contaminated by PCBs through much of the 20th century.

PCBs, or polychlorinated biphenyls, were first introduced in 1929 and were used in hundreds of industrial and commercial applications, mostly as electrical insulators. They were banned 50 years later, but they don’t simply degrade. Partly because of PCB contamination, a 200-mile stretch of the Hudson River is the nation’s largest Superfund site. [National Geographic]

Despite swimming in PCB-polluted waters and accumulating the chemicals in their systems, the tomcods are alive and well in the river. In a study in Science this week, Isaac Wirgin and colleagues show that this is because in the span of just a few dozen generations, the fish have evolved a resistance to PCBs.

The resistance is provided by a variant in a single gene that prevents the chemical from binding ...

Humans and dolphins are inventing a common language together. This is big news!

In all the hoopla over the world ending due to being asteroid-smashed, man becoming immortal thanks to the singularity in 2045, and Watson the trivia-machine winning Jeopardy! the story of budding interspecies communication got under-reported. Denise Herzing and her team with the Wild Dolphin project has begun developing a language to allow humans and dolphins to communicate. If successful, the ability to communicate with dolphins would fundamentally change animal intelligence research, animal rights arguments, and our ability to talk to aliens.

Herzing and her team faced two huge problems when it came to talking to dolphins. The first problem is that the current state of animal language research creates an asymmetrical relationship between humans and the animals with whom they wish to communicate. The second problem is that (save for parrots) animal vocal cords cannot replicate human speech, and visa versa.

Most, if not nearly all, animal language research involves either studying how animals communicate with one another, or teaching them a human language to ...

There’s a fascinating discussion thread at Quora on this question–check it out.

First of all, I am not disputing the premise: This Pew survey, for instance, found that

More than half of the scientists surveyed (55%) say they are Democrats, compared with 35% of the public. Fully 52% of the scientists call themselves liberals; among the public, just 20% describe themselves as liberal.

So, scientists are, in aggregate, more liberal than the rest of America…but why?

I am not going to be satisfied with a “really smart people are liberals” kind of answer. I know too many smart conservatives. Other arguments that I’ve seen in the thread that sound more plausible:

1. Republicans have taken a lot of anti-science positions lately (climate, evolution, etc) and scientists are just responding to that.
2. Academia is a very liberal environment, and that’s where scientists cut their teeth.
3. Smart and talented conservatives don’t hang around for a Ph.D., they want to get out of the ivory tower (which they perceive hostile anyway) and into the business world.

What do others think?

On January 4, 2011, the Moon passed directly in front of the Sun, treating much of Europe, north Africa and western Asia to a total solar eclipse. I saw lots of really interesting pictures from the event, but this has to win for what must be the oddest image:

[Click to penumbranate.]

This was the view using LOFAR, or the LOw Frequency ARray, a radio telescope in the Netherlands. It’s designed to sense radio waves from space in the range of 10 – 250 Megahertz (which encompasses FM radio and TV broadcast signals, interestingly). Lots of astronomical objects emit at this energy. The Sun is not a terribly luminous source, but it happens to be pretty close by, making it bright.

The images show the partial eclipse at 140 MHz, starting at the upper left as the Moon was already leaving the Sun’s disk. By the last image (lower right) it was all over. I had to laugh: it was cloudy in the Netherlands that day and people missed seeing the eclipse themselves, but clouds are transparent to radio waves. In fact, radio astronomers can, in many ...

1) First, a post from the past: A History of Iran: Empire of the Mind.

2) Weird search query of the week: “pictures of a famous woman drinking alcohol.”

3) Comment of the week, in response to D.I.Y. population structure inference, part 1 of many. I won’t quote it since it has a lot of links, but aesthetic suggestions for bar plots which I’ll probably take to heart.

4) And finally, your weekly fluff fix:

Detecting Some Popular Animals in Online Photos: Learning from Ears and Eyes.

“Robust object detection has many important applications in real-world online photo processing. For example, both Google image search and MSN live image search have integrated human face detector to retrieve face or portrait photos. Inspired by the success of such face filtering approach, in this paper, we focus on another popular online photo category – animal, which is one of top five categories in the MSN live image search query log. As a preliminary attempt, we focus on the problem of animal head detection of a set of relatively large land animals that are popular on the internet, such as cat, tiger, panda, fox, and cheetah. First, we proposed a new set of gradient oriented feature, Haar of Oriented Gradients (HOOG), to effectively capture the shape and texture features on animal head. Then, we proposed two detection algorithms, namely Bruteforce detection and Deformable detection, to effectively exploit the shape feature and texture feature simultaneously. Experiment results on 14,379 well labeled animals images validate the superiority of the proposed approach. Additionally, we apply the animal head detector to improve the image ...

You could be spared the guilt of forgetting your eco-friendly cloth shopping bag on the trip to the grocery: A Japanese inventor has created the first home recycling system that can convert all those extra plastic bags back into oil.

His name is Akinori Ito, and his invention is now for sale through Blest Corporation. According to the website, one model–the Desk-top Waste Plastic Oiling System–weighs a mere 110 pounds. But the best part is that this non-polluting conversion process is also highly efficient: two pounds of plastic can be converted into one quart of oil using a mere kilowatt of power.

It works by capturing the vapors released by heated plastic, and then funneling them through a network of pipes and water chambers, which gradually cool the vapors until they coalesce back into crude oil–where the plastics originally came from.

That process creates oil that can power certain types of stoves and generators–and more refining can turn it into gasoline. But as Clean Technica duly notes:

Of course, the end product of this conversion system is still fuel that must be burned, and thus, it will ...

A hibernating bear might appear to be the perfect metaphor for laziness, laying around half the year in carefree slumber. But in fact, it is a marvel of efficiency. New research in the journal Science shows that bears can drop their metabolic rate all the way down to 25 percent of normal while losing only about 10 degrees in body temperature.

Øivind Tøien and colleagues got lucky when a few black bears came a little too close to residents of Alaska for the Alaskans’ comfort. The state’s Department of Fish and Game intended to remove them as a “nuisance,” so the researchers got their hands on the bears and did a little hibernation experiment. They built artificial dens for the large mammals, complete with cameras and observational equipment including radio transmitters, allowing them to track the bears’ body temperatures and other vitals.

It was thought that, like most animals, the bears would have to drop their body temperatures to put the brakes on metabolism—each 18-degree Fahrenheit (10-degree Celsius) drop in temperature should equal a 50-percent reduction in the chemical activity. [National Geographic]

The ...

This blog has opened several doors for me. It has been a gateway to writing opportunities, speaking engagements and new friendships, and none of these benefits were apparent when I started. Everyone has similar stories of innocuous events that led to greater and unanticipated things. And such stories abound in the narrative of life.

Take the H1N1 flu virus. The drug Tamiflu was generally effective against last year’s H1N1 swine flu pandemic, but it doesn’t work against the seasonal strains that naturally circulate among humans. Ever since 2007, these seasonal strains have evolved to resist the drug thanks to a mutation called H274Y. This genetic tweak prevents Tamiflu from sticking to the virus’s surface, masking the virus from the drug.

The first viruses with this mutation were discovered in 1999. While they shrugged off Tamiflu, they proved to be otherwise feeble versions of their normal kin. This is a common theme – mutations that bestow resistance to drugs often hobble viruses in some other way. As a result, scientists dismissed the upstart mutation. But they were wrong – flu viruses bearing H274Y soon spread around the world.

Last year, Jesse Bloom from the California Institute of Technology discovered why. He showed that H274Y rose to power thanks to two other “gateway mutations” called V234M and R222Q. These changes did little by themselves, but they helped to compensate for the crippling effects of H274Y. They made it easier for the flu virus to develop resistance to Tamiflu. It’s like giving someone a monitor one year, and then a computer the year later. Both presents are useless on their own, and the value of the first only becomes apparent when you have the second.

When I covered this story last year, I wrote:

“[This] means that some strains of virus are inherently better than others at evolving drug resistance and other important traits. Perhaps some mutations are already out there that could eventually pave the way for more virulent viruses, or ones that could jump the species barrier from other animals. For now, we know of two permissive mutations that allowed H1N1 to pick up Tamiflu resistance. In the future, it would behove us to monitor other lineages of flu – particularly the recent pandemic strains – for these same changes. If resistance crops up, it will most likely do so in these strains.”

Sergey Kryazhimskiy from the University of Pennsylvania is doing exactly that. He thinks it might be possible to predict the evolution of flu viruses by looking for gateway mutations. Kryazshimsky reasoned that certain combinations of mutations would crop up far more often than others. Maybe one of them compensates for the other, just like H274Y and its gateway mutations. Maybe one mutation boosts the beneficial effect of the other. Either way, the whole is much greater than the sum of the parts. This phenomenon is known as epistasis.

Kryazhimskiy looked at over 40 years of flu genomes and measured how quickly mutations appear at one place in the flu genome given another mutation at a second site. If the first mutation acts as a gateway for the second, the latter would turn up quickly after the former, and it would do so independently on many branches of the flu family tree. Kryazhimskiy found hundreds of such pairs.

As expected, in many cases, the first mutation was neutral. It didn’t have any obvious effect and it usually didn’t even change the sequence of amino acids that make up the virus’s proteins. All it did was pave the way for the second mutation, which could crop up at an entirely different part of the protein between three to six years later. The first warns of the arrival of the second.

The initial neutral mutations are often missed or ignored, but they can clearly be very important for the evolution of the virus. Among them were the gateway mutations that allowed H274Y to rise to power, the same ones that Bloom identified did last year. That’s a reassuring result. Better still, Kryazhimskiy found that his statistical technique would have identified the gateway mutations even if he only used data before Tamiflu was introduced.

Kryazhimskiy has developed a crystal ball for the future of flu. We could potentially use his method to look for strains of H1N1 swine flu that have good odds of eventually defying Tamiflu. As new drugs are developed, we could identify the strains that are most primed for resistance. And we could even try to predict the evolution of existing strains to decide which we should target in the next seasonal vaccine.

This ability to predict the path of evolution was the original goal of the study. Joshua Plotkin, who led the study, says, “To be honest, my main interest is in using influenza to address basic questions about molecular evolution. Since the laws of physics and protein folding are universal, we can hope to learn general lessons about protein evolution from studying influenza sequences.”

From goals like these, motivated by pure scientific curiosity, important things often emerge. For example, Plotkin also says, “I’m also working to predict which pairs of sites will be responsible for emergence of Tamiflu resistance in pandemic H1N1. Currently, only seasonal H1N1 is resistant to Tamiflu, but it’s only a matter of time before the new pandemic H1N1 acquires resistance as well. It would be nice to have advance warning of when this will occur.”

Reference: Kryazhimskiy, Dushoff, Bazykin & Plotkin. 2011. Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.1001301

Image by Scherle

More on flu:

• How drug-resistant flu took us by surprise
• Flu viruses take the summer off to go travelling
• Flu and Parkinson’s – how H5N1 bird flu causes neural degeneration in mice
• From Spanish to swine – how H1N1 kicked off a 91-year pandemic era
• Origins of the swine flu pandemic
• Flu survivors still immune after 90 years
• Round peg, square hole – why our bird flu drugs are a fluke
• New flu viruses emerge in tropical Asia before going on one-way world tour

They’re about three and a half feet tall and their origins are mysterious, but an isolated group of Ecuadorians with a genetic mutation causing dwarfism are making news for another reason: They hardly ever get cancer or diabetes. Medical researchers say the villagers’ genetic protection from these diseases could lead to preventative treatments for the general population–and could therefore increase human longevity.

The villagers’ condition is called Laron syndrome, which is caused by an insensitivity to growth hormone.

Laron syndrome results from a mutation in the gene that codes for growth hormone receptor (GHR), a protein that binds with the human growth hormone and ultimately results in the production of the insulin-like growth factor 1 (IGF1), causing cells to grow and divide. When a person has two of these mutated and non-working genes, they can develop the disease. [LiveScience]

Jaime Guevara-Aguirre, the leader of the study about the Ecuadorians appearing in Science Translational Medicine, has been looking into their condition and extraordinary resistance to age-related diseases for more than two decades, since his serendipitous discovery of the people while riding horseback in ...

It was a stroke of serendipity that may one day help those who hide under comb overs or wear wigs: scientists studying how mice bowels react to a stress-reducing chemical have inadvertently discovered a cure to baldness. But unfortunately, it looks like this cure won’t apply to genetic baldness, which is by far the main cause of most hairless pates. Still, researchers hope the lucky find will eventually be used to battle at least some of the bare heads of humans.

The story begins with mice that were genetically modified to produce too much corticotrophin-releasing factor, or CRF–a type of stress hormone. Normally, as these stressed-out rodents age, their backs lose hair. But a group of researchers from the Veterans Administration and the University of California at Los Angeles didn’t care about hair, they just wanted to study the effects of a chemical on the modified mice.

Researchers at the Salk Institute developed a peptide called “astressin-B”, which blocks the action of CRF, and the teams injected the peptide into the bald mice. They weren’t thinking about baldness at all — they wanted to test whether the ...

Here’s the video of the lecture I gave last week at Stony Brook University, which was the basis of my recent blog post. I’ve uploaded the slides as a pdf here. (You can read the slides online or download them by going to the File drop-down menu.) I’m not sure what the ideal combination of video and slides would be…if anyone has any suggestions, let me know.

NASA’s Solar Dynamics Observatory has a nice video of the solar flare and coronal mass ejection from February 15th which I uploaded to YouTube:

[More formats are available at NASA's SDO site.] Whoa! We’re in no major danger from this event, but wow, that’s cool. So what did you just see?

As I described in an earlier post, Sunspot 1158 is an active region on the Sun, with a lot of magnetic energy stored up. That energy got released with a bang on Tuesday, creating a solar flare — essentially a magnetic bomb on the surface of the Sun — and a coronal mass ejection (CME) — a huge eruption of subatomic particles blasting outward from the Sun.

The flare can be seen as the sudden bright flash just below and to the right of the center of the Sun’s disk. At the same time you can see an expanding circle of light centered on the Sun. That last bit is the CME. We see these launching off the Sun quite often; usually headed off to the side, looking like a big loop or light-bulb shape moving off. When they head straight Earth, though, ...

Was it just me, or was their something faintly bizarre about yesterday’s historical ass whooping of man by machine? Maybe it was Brad Rutter’s increasingly frantic swaying as Watson took his lead and asked for yet another clue in its stilted, strangely mis-timed way. Perhaps it was the effect of the last corporate stiff of the event – in front of a stone wall backdrop that seemed a parody of cheesy corporate décor – telling us where Watson’s winnings will go, all while speaking with a monotone that would make Al Gore jealous. Or maybe it was Alex Trebek’s nonchalance after the historic event as he immediately turned his attention to pitching the next day’s all-teen tournament. Somehow I expected balloons and confetti to descend from the ceiling, maybe with the voice of Hal in the background—“I’m sorry Ken, but you were really improving from your performance yesterday. Would you mind taking out the garbage?” The most important intelligence test of machine versus man in decades sails by with hardly the rattle of a plastic fern.

Besides the very impressive technical achievement of Watson, IBM should be congratulated for ...