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Can Computing Keep up With the Neuroscience Data Deluge?

human os iconToday's neuroscientists have some magnificent tools at their disposal. They can, for example, examine the entire brain of a live zebrafish larva and record the activation patterns of nearly all of its 100,000 neurons in a process that takes only 1.5 seconds. The only problem: One such imaging run yields about 1 terabyte of data, making analysis the real bottleneck as researchers seek to understand the brain.

To address this issue, scientists at Janelia Farm Research Campus have come up with a set of analytical tools designed for neuroscience and built on a distributed computing platform called Apache Spark. In their paper in Nature Methods, they demonstrate their system's capabilities by making sense of several enormous data sets. (The image above shows the whole-brain neural activity of a zebrafish larva when it was exposed to a moving visual stimulus; the different colors indicate which neurons activated in response to a movement to the left or right.)

The researchers argue that the Apache Spark platform offers an improvement over a more popular distributed computing model known as Hadoop MapReduce, which was originally based on Google's search engine technology. Here's how Spectrum described these conventional systems in an article on "DNA and the Data Deluge":

While Hadoop and MapReduce are simple by design, their ability to coordinate the activity of many computers makes them powerful. Essentially, they divide a large computational task into small pieces that are distributed to many computers across the network. Those computers perform their jobs (the “map” step), and then communicate with each other to aggregate the results (the “reduce” step). This process can be repeated many times over, and the repetition of computation and aggregation steps quickly produces results.

But the Janelia Farm researchers note that with MapReduce, data has to be loaded from disk for each operation. The Apache Spark advantage lies in its ability to cache data sets and intermediate results in the memory of many computers across the network, allowing for much faster iterative computations. This caching is particularly useful for neural data, which can be analyzed in many different ways, each offering a new view into the brain's structure and function.

The researchers have made their library of analytic tools, which they call Thunder, available to the neuroscience community at large. With U.S. government money pouring into neuroscience research for the new BRAIN Initiative, which emphasizes recording from the brain in unprecedented detail, this computing advance comes just in the nick of time.

Madrid Begins Electric Bike Sharing

For something that took years to arrive, Madrid’s public bicycles sure get off to a fast start. Pedal once and the 36-volt, 10-ampere, electric motors will give you a sudden boost. Going up one of Madrid’s many hills, it is a welcome aid. Downhill, the burst jars. But riders can disable the boost by not pedaling, and moderate it with electric controls on the handlebars. With a little practice, the bikes begin to feel like underpowered motor scooters. “Our major goal is to move journeys that are now done by car to the bicycles,” says Elisa Barahona, Madrid’s director of sustainability and environment.

During the program’s first week, however, almost nobody could sign up through the touchscreen UNIX computers at the bike docking stations. While first approved years ago in an effort to combat air pollution, economic concerns and then logistical problems delayed the launch by years, building up attention and demand. After the program finally launched, online attacks to the payment system blocked registration. In the first two weeks, the company’s information technology engineers racked up a 20 gigabyte log from Internet attacks, says Miguel Vital, director of Bonopark, the contractor operating the system on behalf of the city of Madrid. Other attacks were less sophisticated: Bonopark left some of the docking station computers' screen resolutions at the wrong size, allowing at least one naughty user to access a web browser and leave pornography visible in the place of the user registration screen (The Local).

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World War I: The War of the Inventors

Illustration: Alamy

Big Gun: Germany's “Paris Gun” had an astounding range of 130 kilometers, it wasn’t terribly accurate, and so the effect it had was mainly psychological.

One hundred years ago, as the international conflict that became known as World War I began, most Europeans were predicting a quick victory. Within a few months, it became clear their optimism was unrealistic. As the fighting spread and grew more deadly, the role of engineering and invention took on new urgency. Eventually, the Great War became known in certain circles as an “inventor’s war.” To be sure, many of the inventions people now associate with World War I—submarines, torpedoes, fighter and bomber aircraft—had actually been conceived earlier. However, the pressures of war pushed their advancement. Here are four such technologies that still influence our world today.


SONAR: Making the Sea Safe for Democracy

Illustration: Imperial War Museum
U-Boat Casualty: On 5 September 1914, a German torpedo sank the British cruiser HMS Pathfinder. Technology to detect U-boats eventually led to the development of SONAR.


Photo: NOAA
Sea Sounds: Canadian radio pioneer Reginald Fessenden conceived his electric oscillator in response to the sinking of the Titanic. The acoustic device receive echoes from the ocean’ bottom as well as from any obstructions in the water.

In the years leading up to the war, navies that had submarines used them mainly for coastal defense. Germany changed that by developing its U-boats into long-range offensive weapons. That shift in military strategy compelled the Allies to 1) also begin using submarines offensively and 2) develop countermeasures to protect cross-Atlantic shipping.

The work of Reginald Fessenden proved crucial. After an iceberg sank the RMS Titanic in 1912, the Canadian radio pioneer began conducting underwater acoustic experiments in search of a way to protect ships from submerged obstacles. This led him to invent an electro-mechanical oscillator, a device carried aboard a ship that would transmit sound through the water at a specified frequency and then listen for reflections from any objects in the vicinity. He developed the technology first as a means of communicating with (friendly) submarines and later as a warning device that could be attached to navigation buoys to alert approaching ships of shoals and other hazards. In October 1914, the British Navy purchased Fessenden oscillator sets for underwater signaling, and in November 1915 decided to equip all of its submarines with them.

French physicist Paul Langevin designed an electronic version of Fessenden’s device that was much better at detecting moving objects. It included a quartz transmitter and receiver, which greatly improved the range and clarity of the signal. In February of 1918, he achieved a transmission range of 8 kilometers and clear echoes from a submarine.

The Fesseden oscillators continued to be used as late as World War II for detecting stationary objects such as mines. And Fessenden’s and Langevin’s inventions laid the foundations for what would become SONAR (Sound Navigation and Ranging). For more on Fessenden’s oscillator, see the IEEE Global History Network’s “Inventors’ Responses to the Sinking of the RMS Titanic.”]


The Superheterodyne Receiver: Better Tuning for Radio

Image: RCA
Peacetime Receiver: RCA’s Radiola AR-812 radio, the first commercially produced superheterodyne radio receiver, was introduced in 1924. The invention of the superheterodyne during World War I made it much easier to tune a radio and to pick up distant signals.

Radio technology existed before the war, but two wartime inventors greatly improved them. In 1917 and 1918, respectively, a French officer named Lucien Lévy and an American officer named Edwin H. Armstrong independently came up with what would become known as the superheterodyne receiver—a way to tune radios and to allow them to pick up distant signals. The receiver basically superimposed one radio wave on another and greatly amplified and filtered the resulting intermediate frequency, which was then demodulated to generate an audio signal, which was in turn amplified for output to loudspeakers or earphones.

Initially, Lévy sought a way to increase the secrecy of radio transmissions. He had been working at the Eiffel Tower—which the French military began using for radio experiments when the war broke out. Lévy had the idea that a supersonic wave could be superimposed upon a radio frequency carrier wave, which would itself be modulated by an acoustic wave. He refined that idea, producing the supersonic wave in the receiver and then heterodyning the received signal against a local oscillator. He applied for a French patent on 4 August 1917.

Armstrong was made a captain in the U.S. Army Signal Corps shortly before he was sent to France in 1917 to work on Allied radio communications. By then, he was already famous in the radio world for his regenerative feedback circuit (a device that greatly amplified a signal), for which he received the first Medal of Honor from the Institute of Radio Engineers. While in Paris in early 1918, Armstrong witnessed a German bombing raid. He thought that the accuracy of the antiaircraft guns could be improved if there were a way of detecting the extremely short electrical wavelengths emitted by the ignition systems of the aircraft engines. That led him to invent his superheterodyne receiver, for which he filed a French patent application on 30 December 1918.

After the war, Armstrong’s and Lévy’s competing claims on the superheterodyne receiver did not prevent it from being used widely, helping transform the radio into a hugely popular consumer product. [For more on Lévy, Armstrong, and the controversy surrounding their inventions, see Alan Douglas’s “Who Invented the Superheterodyne?”]


Air-to-Ground Communication: Radiotelephony Takes to the Skies

Photo: AT&T Archives and History Center

Voices on High: AT&T employees (some of whom had joined the U.S. Army Signal Corps during World War I) listen in on an early trial of air-to-ground voice communication.

As early as 1910, experimenters demonstrated wireless transmissions between aircraft and the ground. These trials all involved the pilot tapping out Morse code on a transmitter held in his lap. There were a few problems, however. Engine noise tended to drown out any received messages. And pilots were usually far too busy to be operating a code key.

Clearly, voice radio would be necessary for wireless communication to become practical in the air. But voice transmissions required higher frequencies than did Morse code, and the radios and their power sources were too big and heavy to fit into the aircraft of the time.

Engineers on both sides of the conflict succeeded in making those improvements. In 1916 the French successfully tested air-to-ground voice communication during the battle of Verdun; one year later, they demonstrated air-to-air voice communication at Villacoublay. Transmitters became standard aboard German aircraft in 1916 and, by the end of that year, so were receivers. On 17 May 1918 a U.S. airplane squadron was successfully commanded by voice from the air for the first time. [For more on early airborne radio, see George Larson’s “Moments and Milestones: Can You Hear Me Now?”]


Analog Fire-Control Calculators: Precursors to Digital Computing

As the range of large caliber guns increased, aiming them became more difficult. The World War I naval engagements of Coronel (off the coast of Chile) and Dogger Bank and Jutland (both in the North Sea) saw gunnery ranges from 13,000 to 15,000 meters. To hit another ship from those distances required precise calculations of the target ship’s range, course, and speed, as well as the wind's speed and direction, which in turn were used to determine the gun’s elevation and direction, the wind’s effect on the shell in flight, and any corrections for the motion of the ship doing the firing.

Illustration: Admiralty Library
Point and Shoot: The British Navy’s Dreyer Tables were mechanical calculators used to determine the range and deflection of artillery guns. Such analog machines gave rise to the first electrical computers, like the ENIAC.

In 1912, the British Royal Navy pioneered a system in which all the guns on a ship were directed from a single position (usually the highest part of the ship). The fire-control officer and rangetakers used a T-shaped optical rangefinder containing prisms to ascertain the distance, bearing, and change-of-bearing to the target by means of triangulation. The fire-control officer then communicated—usually via telephone, but with voice tubes as backup—this information to the sailors in the control center deep in the ship. They in turn moved cranks and levers to input the information into large mechanical calculators (some the size of three or four refrigerators), which used this constantly changing data to plot firing solutions for the guns. The guns would then be fired in salvoes, with a slightly different trajectory from each gun, thereby increasing the chance of hitting the target.

During the course of the war, the navies of the Allies and the Entente made significant improvements to these fire-control calculators, and there is still scholarly debate as to which navy had the most advanced system. The British Navy’s Dreyer Tables were probably the best documented of these devices, while the German battlecruiser SMS Derfflinger was widely regarded for the accuracy of its gunnery at sea. Derfflinger was scuttled at Scapa Flow in 1919, and what is known about its fire-control system emerged mostly through Allied intelligence interviews with its gunnery officers.

The range of land artillery also increased significantly during World War I. By the end of the war, for instance, the Germans were bombarding Paris with a massive gun mounted on a railroad car. Known as the Paris Gun or the Kaiser Wilhelm Geschütz, it had a range of 130 kilometers. Although it was not very accurate, it could hit something the size of a city, and so its effect was primarily psychological.

The analog mechanical calculators used to target artillery guns led directly to electronic computers. In fact, one of the most famous of the early electronic computers, ENIAC, did essentially the same tasks during World War II as the analog fire-control calculators of World War I.

About the author: Robert Colburn is the Research Coordinator at the IEEE History Center

Mimicking the Super Hearing of a Cricket-Hunting Fly

Ormia ochracea is a little, yellow fly of the American south whose breeding strategy has an outsize ick factor. It deposits its larvae on the bodies of male crickets. The larvae then eat their way into their unwilling hosts, and devour them from the inside.

What is most remarkable, though, is that the female fly locates the crickets by sound, homing in on the he-cricket’s stridulations (the chirping that results from the wings rubbing together) with uncanny accuracy. The cricket’s chirp is a smear of sound across the scale from the 5 kilohertz carrier frequency to around 20 kHz. And, as anybody who has tried to evict a passionate cricket from a tent or cabin knows, the sound is maddeningly hard to pinpoint.

With an auditory apparatus—let’s call them ears—only 1.5 millimeter across, ochracea pulls off a major feat of acoustic location; a number of engineering groups are working on devices to duplicate the fly’s sensitivity.

Now, a team at the University of Texas at Austin has built a prototype replica of O. ochracea’s ear. Michael L. Kuntzman and Neal A. Hall, researchers in the school’s electrical and computer engineering department, describe the device and its performance in Applied Physics Letters.

The fly’s ears are very different from those of humans. Human ears are typically separated by about 21 to 22 centimeters—about 625 microseconds apart at the speed of sound (though of course it varies with temperature and humidity). We judge sound direction by assessing ear-to-ear differences in phase and volume. We can distinguish time differences of as little as 10 microseconds, and the phase-difference calculation is useful mainly for lower-frequency sounds—those with wavelengths longer than 21 cm. In this range, we can locate a sound source to within about 1 degree if it is dead ahead, or 15 degrees if it is off to the side.  As frequencies rise above about 1600 Hz (a very sharp G above high C), the wavelength is shorter than the ear-to-ear separation, and we fall back on using the volume difference alone to approximate the source’s position.

The fly’s ear, on the other hand, is 4.3 microseconds wide at the speed of sound, and it can distinguish phase delays much smaller than that in sounds coming in from nearly ahead or behind.

The secret is the physiology of the ochracean ear, whose centerpiece is an elastic plate that pivots on a central support. This structure responds to incoming sound waves by resonating in two distinct modes. You can picture them, albeit on an obviously much larger scale, by standing with your arms outstretched to either side. First, raise one arm while lowering the other, like the ends of a see-saw; that’s the first mode. Now move your hands up and down together, flapping like a bird; that’s the second mode.

In the fly’s ear—and in the Kuntzman-Hall device—each mode responds to a different parameter of the incoming wave. The see-saw action responds only to the x-component of the incoming pressure gradient, indicating, say, a how a high-pressure compression crest at the tips of your fingers shades into a low-pressure trough at your elbow. It tracks the changes only along the one dimension of your arm, though, and reveals nothing about the omnidirectional strength and structure of the wave. The flapping mode, on the other hand, responds only to omnidirectional pressure—the sound volume, for example, or the overall pressure on your body—and reveals nothing about the wave's direction. In the fly's ear, both modes superpose to create a composite displacement of the membrane, so the trick is to break this signal down into its see-saw and flapping components..

The fly can individually quantify the displacements of the right and left sides of its pivoting-beam auditory membrane. Then the fly's neural network subtracts the displacement of the left-side channel from the displacement of the right channel to extract the first-mode see-saw signal; this shows the incident angle of the incoming sound. At the same time, the fly's brain adds the left- and right-channel signals to yield the second-mode flapping displacement. This reveals the omnidirectional sound pressure (a clue to distance).

The UT researchers etched a spring-loaded, 1.5-mm-by-2.5-mm pivoting beam into silicon, with a lead-zirconate-titanate piezoelectric film painted on the supporting springs to sense displacement. In experiments, Kuntzman and Hall have read and analyzed the output just as the fly’s brain does. The prototype can resolve the direction of high-frequency sound sources to within 0.35 degrees for sounds in its directional “sweet spots,” and to within about 6 degrees in its less sensitive zones. (The imprecision, their paper says, is mainly due to some imperfections or asymmetries in the prototype.)

“Synthesizing the special mechanism with piezoelectric readout is a big step forward towards commercialization of the technology," said Hall, an assistant professor. There are sure to be defense applications—after all, the research is funded by the U.S. Department of Defense's Advanced Research Projects Agency (DARPA)—as well as potential for commercial products like hearing aids. 

WikiMusical Travels the Web through Song

Twenty years ago only a quarter of U.S. homes had a PC and the biggest media decision facing a child was Sega Genesis or Super Nintendo. Now, media and the Internet are experienced in a million different ways by a million different people—but can you sum up its essence? Blake Harris thinks he can: with musical theatre.

Harris, author of the video game history Console Wars, grapples with defining the Internet experience and its ever-changing landscapes in a new show called WikiMusical, playing until Saturday as part of the 2014 New York Musical Theatre Festival. Harris wrote the lyrics and book for the musical, which is a meandering journey through the sites, memes, and trends that make up the Web. It’s silly and surreal, and hidden inside is an exploration of the ways we’re making the Internet our home.

“For musical theatre, there’s something that’s almost communal about the experience,” says Harris, “and the story of the tech age is such an interconnected story. It touches upon a lot of different threads—one of the great things about the Internet is that there’s a seemingly infinite number of rabbit holes you can go down. The story is an attempt to make a narrative out of all of it.”

The show starts in a simpler time, with siblings based on Harris and his brother getting a Gateway computer from an eccentric Santa Claus. It quickly jumps to the present: the grown brothers are pulled bodily into the modern Internet where they must defeat the sinister and seductive Spam King to save the Web and return home, mending their relationship along the way. On their journey they meet a blogger on a quest and a cast of unlikely online characters—including the cats that (evidently) invented the Internet,  Mario and Luigi, and Morgan Freeman.

The show has strong acting and the songs are often catchy, although the narrative thread can sometimes get lost among the different encounters and gags. In fact, narrative is one of the challenges this show takes on: how to pull the universal tropes of a hero’s journey from the nebulous, multi-faceted, constantly evolving Internet.

According to Harris: “We live in such a niche age, whether it is websites or television channels, that having flagship websites or central hubs is more important than ever to have those shared communal experiences.” Using these well-known sites along with familiar memes and web personalities as landmarks, Harris takes the audience on a State of the Internet tour: an attempt to capture the zeitgeist of what we all experience when we experience the Internet, and the communities we’ve created.

The show is at its strongest when it explores the Internet’s collaborative nature and makes us stop and think about what we’re building. Harris sees Wikipedia as a window into that world under construction, which is why he kept the title even as the plot ballooned beyond just the editable encyclopedia.

“Wikipedia is basically this giant Ouija board that we all put our hands on and try to create an information network together,” he says. “It represents the best and worst of the technological age.”

Camera-Filled Dome Recreates Full 3-D Motion Scenes

Those thrilling moments when a soccer player kicks home the winning goal in the World Cup final or Beyonce debuts new dance choreography in concert might someday be recreated in full 3-D motion down to the smallest piece of confetti and played back from almost any angle. Such a possibility comes from a new motion-capture technique capable of reconstructing scenes captured by more than 500 video cameras mounted inside a two-story geodesic dome.

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Bitcoin Gets Its Own TV Network

This September, if all goes according to plan, the Bitcoin blockchain will take to the radio waves in Finland. The project is called Kryptoradio. It's the result of a partnership between Koodilehto, a Finnish co-op specializing in open technology development, and another group that was responsible for developing and encouraging the adoption of the alternative digital currency known as FIMKrypto.

Together they have secured the rights to transmit updates to the Bitcoin blockchain across digital terrestrial television in Finland. To do so, they will use Digita, a Finnish network that provides coverage for approximately five million people—95 percent of the population, according to their estimates. The transmissions are scheduled to continue for two months as part of a pilot program, and longer if they can find the funding for it.

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Leaked British Spy Catalog Reveals Tools to Manipulate Online Information

No online communication is for your eyes only in the age of Internet surveillance by government spy agencies. But a leaked British spy catalog has revealed a wide array of online tools designed to also control online communication by doing everything from hacking online polls to artificially boosting online traffic to a particular website.

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UK: Let's Make a Spaceport!

In a bid for rapid-fire relevance in the emerging private spaceplane industry, the UK government announced its intent to open a commercial passenger spaceport within four years. Eight airfields have been singled out as the British Isles’ answer to New Mexico's “Spaceport America” — one each in England and Wales, with the remaining six in Scotland. 

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