Tech Talk iconTech Talk

Hacking the Cancer Genome

human os iconThese days, cancer is as much a target for researchers with number-crunching skills and their data-mining tools as it is for scientists in biomedical research labs. And one potentially powerful big-data approach to conquering cancer—which involves discovering clever genetic tricks to make cancer cells kill themselves—has moved in a promising new direction this month.

Scottish, Israeli, and American researchers have reported a new discovery that analyzes existing cancer gene databases for clues to combinations of genes that together can kill tumor cells while leaving healthy cells untouched. The idea takes advantage of a phenomenon called synthetic lethality, which in oncology was first explored 17 years ago as a potentially fruitful new line of cancer treatment.

One of the new paper’s coauthors, Eytan Ruppin, director of the University of Maryland’s Center for Bioinformatics and Computational Biology, says cancer cells are like regular cells run amok. They, like regular cells, typically have some 10,000 genes. But in cancer cells, many more of these genes are inactive—meaning that for whatever reasons, those genes don’t produce the proteins that a healthy version of the cell would be producing.

Since the 1920s, it’s been observed that all cells in fact have networks of secret self-destruct switches: When both of a key pair of genes become inactive, the entire cell begins the process of shutdown and cell death.

So, Ruppin says, the hurdle that needs to be overcome in order to make this possible broad-spectrum genetic cancer treatment work is discovering and cataloging as many of these secret “synthetically lethal” (SL) gene pair combinations as nature has provided. Then, when a patient’s cancer is biopsied, and its genome is taken, an oncologist can look to see which genes in the patient’s cancer cells are inactive.

For example, say that the oncologist discovers in an SL database that an inactive gene in a patient’s tumor (call it Gene A) happens to have a corresponding synthetically lethal partner gene (call it Gene B).

In this case, then, a drug that inactivates Gene B will trigger the cell death process in the tumor but not in the person’s healthy cells. (Depending on what Gene B does, there might also be side effects from switching Gene B off. But so long as Gene A remains active throughout the rest of the person’s body, those side-effects should not include cell death.)

Ruppin and his collaborators used a clever data mining technique to discover more than a thousand candidate SL gene combinations. They plumbed the U.S. National Cancer Institute’s Cancer Genome Atlas, which itself contains thousands of genomes of different biopsied tumor samples.

They then ran searches for various inactive genes. So, for the sake of example, say they found some of the cancers in the database with Gene X inactivated. And some of the cancers in the database had Gene Y inactivated. If Genes X and Y don’t form an SL pair, there should then be plenty of examples in the database of cancers where both X and Y were inactive. However, if Genes X and Y do form an SL pair, then there should be almost no examples of tumors in the database where those two genes are both inactive.

“You would have expected them to be inactive together at a certain rate, given their individual inactive frequencies,” Ruppin says. “But when you look at the data, you find that they are never inactive together,” Ruppin adds that this, “is a very strong indication that they are synthetically lethal. Because whenever they were inactive together, they were actually eliminated from the population. Because these cells died.”

Your TV Will Know You Better Than You Do

With satellite, cable, and terrestrial TV stations broadcasting in the hundreds and Internet-based entertainment content companies also competing for viewers’ attention, finding something to watch is, strangely, a growing challenge. To help simplify the task, researchers at Japan’s public TV and radio broadcaster Nippon Hoso Kyokai, better known as NHK, plan to begin testing technology to automatically assess in real time a viewer’s interest in a TV program or video and then suggest other programs to watch based on the results.

Read More

“Twisted” Radio Beams Data at 32 Gigabits per Second

A team led by engineers at the University of Southern California has sent multiple channels of data over a single frequency by twisting them together into a beam resembling a piece of fusilli pasta. By combining several polarized beams carrying information into a single spiraled beam, the team was able to send up to 32 gigabits per second across 2.5 meters of open air, a rate around 30 times as fast as an LTE wireless connection.

Read More

Can Japan Act Like Silicon Valley?

Photo: John Boyd
Stanford professor Richard Dasher.

During the1970s and ‘80s, Japanese electronics manufacturers like Toshiba, NEC, Hitachi, Sony, and Panasonic reigned supreme in memory chips, displays, and consumer electronics. Then along came the Korean chaebols led by Samsung, followed by smaller, nimbler Taiwanese manufacturers, who together toppled the Japanese giants, just as the Japanese had previously dethroned U.S. rivals such as Fairchild, RCA, Zenith, and Motorola.

But whereas the United States’ strength in entrepreneurship has helped it recover and move on to create new game-changing technologies, Japan is still struggling to get out of its stagnant rut.

One way Japanese corporations can do this, suggests Richard Dasher director of Stanford University’s US-Asia Technology Management Center, is to take a leaf out of Silicon Valley’s playbook and adopt more open innovation, rather than continuing to rely on their primarily closed, internal R&D systems.

Dasher, speaking to the foreign press in Tokyo on 11 September, explained that Silicon Valley-style open innovation emerges in an advanced economy after major corporations have consolidated their position at home and overseas. At this stage of economic development, entrepreneurial types become dissatisfied with the opportunities available in a big company and look to work for themselves to bring new products and ideas to market—perhaps disrupting the status quo in the process.

At the same time large companies begin to fear stagnating and losing competitiveness and smart employees. But given that a typical company spends 90 percent of its R&D budget on development, “for the last 25 to 30 years in the U.S., companies have been looking outside to get new ideas that will integrate with what they have in the company in order to improve the pipeline for new ideas,” says Dasher. As a consequence, some 90 percent of successful U.S. start-ups enter the market not via an initial public offering, but rather through acquisition by large corporations.

By contrast big Japanese companies tend to look for external partners to fill a particular niche, which is more like outsourcing.

As for hallmark Japanese management characteristics such as the life-time employment system that served so well during the high growth and consolidation years, it now “looks like an inflexible labor market” when you have to move “even faster in an economy where’s there’s much more disruption,” notes Dasher.

There are other hindrances as well, such as the superior status employees of a major company may exhibit towards staff of a small acquisition. Even Japan’s famed customer service can become a problem, “for it can turn the company into something that’s reactive,” says Dasher. “If the customer doesn’t already want it, we won’t bother with it.”

On the other hand, he notes that the Japanese government has been laying the foundations for open innovation for the past two decades. He points to the government-university-industry consortiums, the pressure being put on universities to become more innovative, the changes being made in work regulations and labor policy, and the encouragement of small- and medium-sized business to compete for government contracts. Some Japanese companies have also begun backing venture captial-funded firms, one example being the $300 million investment in World Innovation Lab, which focuses on start-ups both in Japan and in Silicon Valley.

“If Japanese companies get really hungry again and regain their drive … they will be powerhouses,” says Dasher. “There is a lot of good technology. There are a lot of good people—you just have to incentivize them in the right way.”

Unemployment For Engineering PhDs Lower Than National Average

Doctoral degrees are an undertaking. A new NSF report indicates the payoff: PhDs in science and engineering make you much more employable than someone without.

The unemployment rate for those in the United States with engineering doctoral degrees was 1.9% in February 2013. That’s less than a third of the 6.3% unemployment rate of the general population 25 years of age and older.

Read More

NASA Gives All-American Space Taxi Contracts to Boeing, SpaceX

NASA has taken a big step toward restoring U.S. space launch capabilities for human astronauts by awarding a total of $6.8 billion in commercial crew contracts to Boeing and SpaceX. The move comes at a time when some U.S. lawmakers have been urging NASA to reduce its current reliance on Russian rockets to send astronauts to the International Space Station.

Read More

Valencell's Optic Sensors Take Your Pulse From Your Ear

human os icon There are lots of ways to get a sense of how hard you’re working out—wearable pedometers, heart rate monitors built into treadmills, and much more. But getting precise readings from these devices can be difficult. If your treadmill has ever reminded you to hold the handles for heart rate, you’ve gotten a first hand look at how difficult it is to track biometrics during a vigorous workout. North Carolina-based Valencell is using infrared light sensors to measure biometric data with a new degree of accuracy.

Read More

How an iPhone 6 App Puts a Health Coach in Your Pocket

human os iconWith the launch of Apple's new iPhone 6 and the announcement of the forthcoming Apple Watch, the company signaled its intention to play a major role in how we manage our health. Apple has presented the watch as a fancy fitness tracker and has plugged the iPhone's Health app, which serves as a dashboard for all the user's health and fitness data. The company also created the HealthKit API to allow developers to build apps that share data with the phone's health app. 

But all the buzz hasn't answered the real questions: What will consumers do with all that data? What will iPhone-enabled health care look like?

It might look a lot like the forthcoming app RevUp, from the San Diego startup MD Revolution. The company's founder, cardiologist Samir Damani, told Spectrum that the app has the potential to really change people's behavior because it combines the data with personalized coaching. "The data is only as good as what you do with it," he says.

Read More

True Random Numbers From Your Smartphone Camera?

Apple hopes its new iPhone can replace credit cards, but many fear mobile transactions are vulnerable to digital pickpockets. New research now suggests that smartphone cameras could help keep credit card data, phone calls, and email secure with just an app.

The cryptographic systems that help protect digital transactions rely on random numbers, which are used to create "keys" to encrypt and decrypt confidential data. However, "if you want to break these cryptographic systems, the random number generator is one of the weakest links," says lead study author Bruno Sanguinetti, a quantum physicist at the University of Geneva in Switzerland. That’s because computer programs are completely deterministic, designed to do things predictably, and so cannot easily generate truly random numbers by themselves.

One could produce truly random numbers by monitoring intrinsically random quantum phenomena, such as when radioactive atoms decay. Now Sanguinetti and his colleagues reveal that smartphone cameras can serve as the basis of such a quantum random number generator.

Read More

Formula E Opens With A Crash

The first race in the ten-race electric Formula E series ended with a crash this past Saturday in Beijing. e.dams-Renault driver Nico Prost held the lead toward the end of the race, but as he approached the final lap, Venturi driver Nick Heidfeld passed Prost on the inside. Prost bumped Heidfeld, sending the Venturi car into a crash barrier and into the air. After landing upside down, Heidfeld scrambled out of the car and accosted Prost. Audi Sport ABT driver Lucas di Grassi passed the pair and took first place.

Though Formula E cars are heavier than the Formula One cars that inspired them, and much quieter, race organizers are betting that they can put on enough of a show to attract a new generation of race fans (see "Electrifying Formula One" 24 October 2013, IEEE Spectrum). The inaugural race showed that Formula E, in which drivers put single-seat electric race cars through their paces, can deliver much of the same drama as competitions featuring cars with internal combustion engines. Before the final-lap dust-up, other drivers grazed each other, damaging one car. Other cars suffered technical problems, forcing them out of the race.

Read More
Advertisement

Tech Talk

IEEE Spectrum’s general technology blog, featuring news, analysis, and opinions about engineering, consumer electronics, and technology and society, from the editorial staff and freelance contributors.

Newsletter Sign Up

Sign up for the Tech Alert newsletter and receive ground-breaking technology and science news from IEEE Spectrum every Thursday.

Advertisement
Load More