Tuesday, August 5, 2014

Physicists eye neural fly data, find formula for Zipf's law

The Zipf's law mechanism was verified with neural data of blowflies reacting to changes in visual signals.

By Carol Clark

Physicists have identified a mechanism that may help explain Zipf’s law – a unique pattern of behavior found in disparate systems, including complex biological ones. The journal Physical Review Letters is publishing their mathematical models, which demonstrate how Zipf’s law naturally arises when a sufficient number of units react to a hidden variable in a system.

“We’ve discovered a method that produces Zipf’s law without fine-tuning and with very few assumptions,” says Ilya Nemenman, a biophysicist at Emory University and one of the authors of the research.

The paper’s co-authors include biophysicists David Schwab of Princeton and Pankaj Mehta of Boston University. “I don’t think any one of us would have made this insight alone,” Nemenman says. “We were trying to solve an unrelated problem when we hit upon it. It was serendipity and the combination of all our varied experience and knowledge.”

Their findings, verified with neural data of blowflies reacting to changes in visual signals, may have universal applications. “It’s a simple mechanism,” Nemenman says. “If a system has some hidden variable, and many units, such as 40 or 50 neurons, are adapted and responding to the variable, then Zipf’s law will kick in.”

That insight could aid in the understanding of how biological systems process stimuli. For instance, in order to pinpoint a malfunction in neural activity, it would be useful to know what data recorded from a normally functioning brain would be expected to look like. “If you observed a deviation from the Zipf’s law mechanism that we’ve identified, that would likely be a good place to investigate,” Nemenman says.

“Letters and words in language are sequences that encode a description of something that is changing over time, like the plot line in a story,” Nemenman says.

Zipf’s law is a mysterious mathematical principle that was noticed as far back as the 19th century, but was named for 20th-century linguist George Zipf. He found that if you rank words in a language in order of their popularity, a strange pattern emerges: The most popular word is used twice as often as the second most popular, and three times as much as the third-ranked word, and so on. This same rank vs. frequency rule was also found to apply to many other social systems, including income distribution among individuals and the size of cities, with a few exceptions.

More recently, laboratory experiments suggest that Zipf’s power-law structure also applies to a range of natural systems, from the protein sequences of immune receptors in cells to the intensity of solar flares from the sun.

“It’s interesting when you see the same phenomenon in systems that are so diverse. It makes you wonder,” Nemenman says.

Scientists have pondered the mystery of Zipf’s law for decades. Some studies have managed to reveal how a feature of a particular system makes it Zipfian, while others have come up with broad mechanisms that generate similar power laws but need some fine-tuning to generate the exact Zipf’s law.

“Our method is the only one that I know of that covers both of these areas,” Nemenman says. “It’s broad enough to cover many different systems and you don’t have to fine tune it: It doesn’t require you to set some parameters at exactly the right value.”

Neurons turn visual stimuli into units of information.

The blowfly data came from experiments led by biophysicist Rob de Ruyter that Nemenman worked on as a graduate student. Flies were turned on a rotor as they watched the world go by, hundreds of times. The moving scenes that the flies repeatedly experienced simulated their natural flight patterns. The researchers recorded when neurons associated with vision spiked, or fired. All sets of the data largely matched within a few hundred microseconds, showing that the flies’ neurons were not randomly spiking, but instead operating like precise coding machines.

If you think of a neuron firing as a “1” and a neuron not firing as a “0,” then the neural activity can be thought of as words, made up of 1s and 0s. When these “words,” or units, are strung together over time, they become “sentences.”

The neurons are turning visual stimuli into units of information, Nemenman explains. “The data is a way for us to read the sentences the fly’s vision neurons are conveying to the rest of the brain.”

Nemenman and his co-authors took a fresh look at this fly data for the new paper in Physical Review Letters. “We were trying to understand if there is a relationship between ideas of universality, or criticality, in physical systems and neural examples of how animals learn,” he says.

The physicists are now researching whether they can bring their work full circle, by showing that the mechanism they identified applies to Zipf’s law in language.

In order to navigate in flight, the flies’ visual neurons adapt to changes in the visual signal, such as velocity. When the world moves faster in front of a fly, these sensitive neurons adapt and rescale. These adaptions enable the flies to adjust to new environments, just as our own eyes adapt and rescale when we move from a darkened theater to a brightly lit room.

“We showed mathematically that the system becomes Zipfian when you’re recording the activity of many units, such as neurons, and all of the units are responding to the same variable,” Nemenman says. “The fact that Zipf’s law will occur in a system with just 40 or 50 such units shows that biological units are in some sense special – they must be adapted to the outside world.”

The researchers provide mathematical simulations to back up their theory. “Not only can we predict that Zipf’s law is going to emerge in any system which consists of many units responding to variable outside signals,” Nemenman says, “we can also tell you how many units you need to develop Zipf’s law, given how variable the response is of a single unit.”

They are now researching whether they can bring their work full circle, by showing that the mechanism they identified applies to Zipf’s law in language.

“Letters and words in language are sequences that encode a description of something that is changing over time, like the plot line in a story,” Nemenman says. “I expect to find a pattern similar to how vision neurons fire as a fly moves through the world and the scenery changes.”

Related:
Biology may not be so complex after all 

Photos: iStockphoto.com

Thursday, July 31, 2014

Planting the seeds for healthier communities

"Being a woman of color, born and raised in the South, I want to dedicate my life to improve health in whatever way I can," says Leandra Lacy, an MPH student and intern at an inner-city garden. "I believe knowledge is power, and I want to spread as much knowledge as I can."

By Elaine Justice, Emory Report

The Super Giant Community Garden, run by the Emory Urban Health Initiative, aims to provide Northwest Atlanta with a more nutritious selection of foods. The area is considered a food desert, marked by limited access to grocery stores, fresh foods and convenient transportation.

The community garden is located in the parking lot of the Super Giant Foods grocery store, which is also working to expand healthy offerings. Organizers hope to eventually create a "Healthy Hub" for the area that will include a community kitchen, health clinic, childcare facilities and a laundromat.

"We have several regulars who come in," says DeJa Love, who became involved in the project as an undergraduate intern in Emory's Ethics and Servant Leadership Program. "We connect with them about nutrition and healthy living," Love says. "Being a listening ear, that's what my job has turned into."

"I live less than a mile away from a Kroger and a Publix," says Leandra Lacy, an MPH student working alongside Love at the urban garden. "To be in an area of Northwest Atlanta that's a food desert — besides the Super Giant and the garden in the parking lot, there isn't another grocery store within a 10 mile radius — was hard for me to fathom. I'm just glad that I'm in this place where I can be present and really get to know the people there and help open up access to healthy food." 

More than 30 Emory student interns are working with Atlanta non-profits this year while completing a non-credit ethics course on what it means to be not just a leader, but a servant leader.

Read more in Emory Report.

Thursday, July 24, 2014

Lucy: Debunking the 10 percent brain myth



"It is estimated most human beings use only 10 percent of the brain’s capacity.” Morgan Freeman pronounced it in his God-like voice so it must be true, right?

Definitely not, says Emory neurologist Krish Sathian. The premise of the new sci-fi movie “Lucy,” starring Freeman and Scarlett Johansson, is based on a widespread, lingering myth that we tap into only a tiny fraction of our neurons.

“We are probably using all of our brain much of the time, and much of our brain all of the time,” Sathian says. “Even when you’re engaged in a task, and some neurons are engaged in that task, the rest of your brain is occupied doing other things. That’s why, for example, the solution to a problem can emerge after you haven’t been thinking about it for a while, or after a night’s sleep. That’s because your brain’s constantly active.”

Watch the above video, part of the Emory Looks at Hollywood series, to learn more.

Related:
The science and ethics of X-Men
Nazi eugenics versus the American Dream

Tuberculosis: A rising concern on U.S. southern border



Cases of tuberculosis have been steadily decreasing in the United States – except along the southern border and within the Mexican-born population where cases are on the rise.

“Most alarming is the increase in multi-drug-resistant tuberculosis on both sides of the border,” says Polly Price, an Emory law professor and an expert on immigration. “Multi-drug-resistant tuberculosis is very expensive to treat. It’s a very debilitating disease, many people don’t survive. It’s a problem that needs to be addressed at the national level.”

Tuberculosis requires a long course of treatment, 12 months or more, so continuity of care is the primary issue along the border, Price says. She is developing a guide to U.S. laws pertaining to tuberculosis treatment for states along the border.

“California, Arizona, Mew Mexico and Texas all have slightly different procedures for how to treat tuberculosis, what do to with a non-compliant patient, how to follow that patient and make sure the treatment regimen is followed,” Price says. “So just coordinating laws on the U.S. side is something of a big task.”

Price is also working on a best-practices guide for health care workers dealing with the situation along the border. “The law should help in this situation, it should not hinder in the efforts to provide tuberculosis care,” Price says.

Friday, July 11, 2014

Apes vs. humans: Finding common ground



Is war ever truly inevitable?

That question is central to “Dawn of the Planet of the Apes,” opening this weekend. The movie is the latest in the “Apes” drama series featuring a character named Caesar, an ape raised by humans who leads a simian rebellion against the human race.

Fear and misunderstanding can easily lead to violence, says Emory political scientist Shawn Ramirez, an expert on conflict resolution. In this video, Ramirez considers the plot to “Dawn of the Planet of the Apes” as a mirror to real-life situations.

“I think it’s really hard when one side sees the other as a lesser – a lesser species or a lesser race or a lesser ethnicity or religion,” Ramirez says. “It’s very hard to overcome that.”

What can one side do when they face that issue?

“I think Hollywood captures this, actually,” Ramirez says, “because usually it’s some central characters that move over to the other side and they start communicating to the other side and realize that there is something more valuable there.”

Related:
A wild view of "Planet of the Apes"