Stanford Researchers Discover The 'Anternet'

The Behavior Of Harvester Ants As They Forage For Food Mirrors The Protocols That Control Traffic On The Internet.

Deborah Gordon, a biology professor at Stanford, has been studying ants for more than 20 years. When she figured out how the harvester ant colonies she had been observing in Arizona decided when to send out more ants to get food, she called across campus to Balaji Prabhakar, a professor of computer science at Stanford and an expert on how files are transferred on a computer network. At first he didn’t see any overlap between his and Gordon’s work, but inspiration would strike soon.

“The next day it occurred to me, ‘Oh wait, this is almost the same as how [Internet] protocols discover how much bandwidth is available for transferring a file!’” Prabhakar says. ”The algorithm the ants were using to discover how much food there is available is essentially the same as that used in the Transmission Control Protocol.”

Transmission Control Protocol, or TCP, is an algorithm that manages data congestion on the Internet, and as such was integral in allowing the early web to scale up from a few dozen nodes to the billions in use today. Here’s how it works: As a source, A, transfers a file to a destination, B, the file is broken into numbered packets. When B receives each packet, it sends an acknowledgment, or an ant, to A, that the packet arrived.

This feedback loop allows TCP to run congestion avoidance: If ants return at a slower rate than the data was sent out, that indicates that there is little bandwidth available, and the source throttles data transmission down accordingly. If ants return quickly, the source boosts its transmission speed. The process determines how much bandwidth is available and throttles data transmission accordingly.

It turns out that harvester ants (Pogonomyrmex barbatus) behave nearly the same way when searching for food. Gordon has found that the rate at which harvester ants—which forage for seeds as individuals—leave the nest to search for food corresponds to food availability.

A forager won’t return to the nest until it finds food. If seeds are plentiful, foragers return faster, and more ants leave the nest to forage. If, however, ants begin returning empty handed, the search is slowed, and perhaps called off.

Prabhakar wrote an ant algorithm to predict foraging behavior depending on the amount of food—i.e., bandwidth—available. Gordon’s experiments manipulate the rate of forager return. Working with Stanford student Katie Dektar, they found that the TCP-influenced algorithm almost exactly matched the ant behavior found in Gordon’s experiments.

“Ants have discovered an algorithm that we know well, and they’ve been doing it for millions of years,” Prabhakar says.

They also found that the ants followed two other phases of TCP. One phase is known as slow start, which describes how a source sends out a large wave of packets at the beginning of a transmission to gauge bandwidth; similarly, when the harvester ants begin foraging, they send out foragers to scope out food availability before scaling up or down the rate of outgoing foragers.

Another protocol, called time-out, occurs when a data transfer link breaks or is disrupted, and the source stops sending packets. Similarly, when foragers are prevented from returning to the nest for more than 20 minutes, no more foragers leave the nest.

Prabhakar says that had this discovery been made in the 1970s, before TCP was written, harvester ants very well could have influenced the design of the Internet.

Gordon thinks that scientists have just scratched the surface for how ant colony behavior could help us in the design of networked systems.

There are 11,000 species of ants, living in every habitat and dealing with every type of ecological problem, Gordon says. “Ants have evolved ways of doing things that we haven’t thought up, but could apply in computer systems. Computationally speaking, each ant has limited capabilities, but the collective can perform complex tasks.

“So ant algorithms have to be simple, distributed, and scalable—the very qualities that we need in large engineered distributed systems,” she says. “I think as we start understanding more about how species of ants regulate their behavior, we’ll find many more useful applications for network algorithms.”

The work is published in the Aug. 23 issue of PLoS Computational Biology.

Via: "Stanford University"

Introducing 'Bi-Fi' - The Biological 'Internet'

The researchers, Monica Ortiz, a doctoral candidate in bioengineering, and Drew Endy, PhD, an assistant professor of bioengineering, have parasitized the parasite and harnessed M13's key attributes -- its non-lethality and its ability to package and broadcast arbitrary DNA strands -- to create what might be termed the biological Internet, or "Bi-Fi." Their findings were published online Sept. 7 in the Journal of Biological Engineering.

Using the virus, Ortiz and Endy have created a biological mechanism to send genetic messages from cell to cell. The system greatly increases the complexity and amount of data that can be communicated between cells and could lead to greater control of biological functions within cell communities. The advance could prove a boon to bioengineers looking to create complex, multicellular communities that work in concert to accomplish important biological functions.

Medium and Message

M13 is a packager of genetic messages. It reproduces within its host, taking strands of DNA -- strands that engineers can control -- wrapping them up one by one and sending them out encapsulated within proteins produced by M13 that can infect other cells. Once inside the new hosts, they release the packaged DNA message.

The M13-based system is essentially a communication channel. It acts like a wireless Internet connection that enables cells to send or receive messages, but it does not care what secrets the transmitted messages contain.

"Effectively, we've separated the message from the channel. We can now send any DNA message we want to specific cells within a complex microbial community," said Ortiz, the first author of the study.

It is well-known that cells naturally use various mechanisms, including chemicals, to communicate, but such messaging can be extremely limited in both complexity and bandwidth. Simple chemical signals are typically both message and messenger -- two functions that cannot be separated.

"If your network connection is based on sugar then your messages are limited to 'more sugar,' 'less sugar,' or 'no sugar'" explained Endy.

Cells engineered with M13 can be programmed to communicate in much more complex, powerful ways than ever before. The possible messages are limited only by what can be encoded in DNA and thus can include any sort of genetic instruction: start growing, stop growing, come closer, swim away, produce insulin and so forth.

Rates and Ranges

In harnessing DNA for cell-cell messaging the researchers have also greatly increased the amount of data they can transmit at any one time. In digital terms, they have increased the bit rate of their system. The largest DNA strand M13 is known to have packaged includes more than 40,000 base pairs. Base pairs, like 1s and 0s in digital encoding, are the basic building blocks of genetic data. Most genetic messages of interest in bioengineering range from several hundred to many thousand base pairs.

Ortiz was even able to broadcast her genetic messages between cells separated by a gelatinous medium at a distance of greater than 7 centimeters.

"That's very long-range communication, cellularly speaking," she said.

Down the road, the biological Internet could lead to biosynthetic factories in which huge masses of microbes collaborate to make more complicated fuels, pharmaceuticals and other useful chemicals. With improvements, the engineers say, their cell-cell communication platform might someday allow more complex three-dimensional programming of cellular systems, including the regeneration of tissue or organs.

"The ability to communicate 'arbitrary' messages is a fundamental leap -- from just a signal-and-response relationship to a true language of interaction," said Radhika Nagpal, professor of computer science at the Wyss Institute for Biologically Inspired Engineering at Harvard University, who was not involved in the research. "Orchestrating the cooperation of cells to form artificial tissues, or even artificial organisms is just one possibility. This opens a door to new biological systems and solving problems that have no direct analog in nature."

Ortiz added: "The biological Internet is in its very earliest stages. When the information Internet was first introduced in the 1970s, it would have been hard to imagine the myriad uses it sees today, so there's no telling all the places this new work might lead."

Via: "Science Daily"