Control theorists have pondered living things for decades, but until recently they lacked the mathematical tools to analyze them as they would a technological system. Doyle and his colleagues have created some of those tools. In keeping with Doyle’s gritty real-world philosophy, he then set out to see how they applied to a common bacterium, Escherichia coli. He soon discovered remarkably precise parallels between living networks and technological ones.
When E. coli is heated to dangerous temperatures, for example, it can rapidly churn out thousands of heat-shock proteins, molecules that help protect the microbe’s workings. When the temperature falls, the heat-shock proteins quickly get dismantled. Doyle demonstrated that this behavior takes place through a series of feedback loops inside the bacterium, akin to the feedback loops that keep an airplane on autopilot steady even as the plane is buffeted by gusts.
Doyle is now tackling a far bigger network of genes in E. coli: the master network responsible for governing its metabolism. He and his team are probing the control systems that allow the microbe to eat many different kinds of sugar and transform them into the thousands of molecules that make up the bacterium. E. coli’s metabolism is nothing if not robust, able to easily withstand significant environmental fluctuations.
The reason the bacterium works so well, Doyle finds, is that it is organized in much the same way as the Internet. Both the Internet and E. coli are conceptually organized like a bow tie, with a broad fan of incoming material flowing into a central knot and then flowing into another broad fan of outgoing material. On the Internet, the incoming fan is made up of data from a huge range of sources— e-mail, YouTube videos, Skype phone calls, and the like. In E. coli, the incoming fan is made up of the many sorts of food it eats. As information and food move into their respective bow ties, they get homogenized: E. coli breaks down its food into a few building blocks, while the Internet breaks down its motley incoming data streams into streams of standardized packets.
From the knot, both bow ties then fan out. E. coli turns its building blocks into DNA, proteins, membrane molecules, and any other special ingredient it needs. On the Internet, data packets reach a computer, where they can be reassembled into the original e-mail, YouTube videos, Skype telephone calls, and the like.
A bow-tie organization allows both the Internet and E. coli to run quickly and efficiently. If E. coli (like all bacteria, indeed like all living things) did not have a bow tie, it would have to use a different set of enzymes to make each of the thousands of different molecules it needs from each type of food. Rather than use such a huge, slow system, E. coli just points all its metabolic pathways into the same bow-tie knot, making everything from the same raw materials. Likewise, the Internet’s bow-tie architecture means that it doesn’t have different ways to handle, say, e-mail traffic and instant-message traffic. Everything passes through as the same types of data packets.
The bow-tie architecture also makes both the Internet and E. coli robust. If the type of incoming material changes rapidly—say, a surge in video traffic in the Internet’s case, or a new food source for the E. coli—the system can process that material without having to retool its entire metabolism to cope.
Another advantage of a bow tie is that it makes feedback control easy. Information travels back from a receiving computer to the sender, which can speed up or slow down its packets in response. E. coli’s metabolism is loaded with analogous feedback loops. Normally E. coli can synthesize all the amino acids it needs for making proteins. But if it can get a certain kind of amino acid from the environment, that information shuts down its own production line.
But as Doyle points out, improving robustness comes with a price. The bow-tie structure opens the door to a vulnerability that could prove very hard to fix. Because of the homogenization that occurs at the heart of the bow tie, it’s difficult to identify and block harmful agents. In the case of the Internet, it takes only a short piece of code to produce a digital virus that can spread quickly to millions of computers and cause billions of dollars of damage. In living organisms, real viruses hijack cells in much the same way.
Doyle thinks the similarity between E. coli and the Internet is no accident. As networks get big and complicated—either through the tinkering of Internet engineers or through millions of years of evolution—they must follow certain rules to stay robust. “There is an inevitable architecture,” Doyle says.
Over dinner, Doyle muses on how to deal with these fundamental vulnerabilities. He hasn’t found a way to improve biological reliability (yet), but he does think he can help address the Internet’s limits.
The current packet-receipt feedback system (known as TCP) has worked wonderfully for years to control the flow of Internet traffic, but it won’t be able to cope with the coming jam, when fridges will scan the RFID chip on a milk carton and send an alert when the expiration date arrives. “Whether we like it or not, [Internet equipment giant] Cisco will network everything. Soon our glasses will tell the kitchen they’re empty,” Doyle says. That vast amount of traffic will make the Internet catastrophically fragile. “We could wake up one morning and nothing works.”
Many Internet experts are also worried, and they’ve launched several projects to save the network, including Steven Low, another Caltech professor. Doyle is working with Low on his project, which is unusual in its simplicity. Their plan to speed up the Internet is to simply do a better job of paying attention to measurements of Internet traffic. Today computers sense Internet congestion by noticing how many packets they lose. That’s like trying to drive down a highway by just looking at what’s 20 feet ahead of you, constantly accelerating and then slamming on the brakes as soon as you see something.
Doyle and his coworkers enable computers to use more information about traffic flow, noting how long it takes for their packets to get to their destination. The less traffic, the shorter the time, and with these traffic reports on hand, their computers make much smarter decisions. The result is a string of victories for high-speed Internet communication competitions. In the last face-off in 2006, they managed to send 17 gigabits—about a full-length movie’s worth—each second across the Internet. Doyle smiles as he describes their success, a flash of the athlete’s spirit in his face. “You’re not just proving theorems,” he says. “It beats anything anyone else can do.”
Last year the Caltech team started operating a company, FastSoft, to market their protocol. In March they started selling a box about the size of a DVD player that you can plug into a server. In one test, a Fortune 500 company was able to speed up its transmissions 30-fold. But Doyle stresses that a real solution to the Internet crisis will require rethinking the control process from the bottom up.
“If someone said, ‘Do a radical redesign,’ I’d say we’re not ready yet,” Doyle confesses. “Going to the moon was trivial compared to dealing with this. We’ve got a research path, but there’s some hard math to be done.”