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The interplay of biology and information technology is transforming how and why computing is done.
October 1, 2003

Advances in information technology usually boil down to a few classic story lines. There’s the story of Moore’s Law, in which computers steadily gain performance, use less power, and fall in price. Then there is the story of how the exchange of data between far-flung computers gets easier every day. Look at this year’s TR100 innovators in computing, which spans both hardware and software, and you’ll see evidence of these trends at every scale, from tiny, single-electron transistors to computer grids that gird the globe. But look again and you’ll also see a bold new story emerging: the increasingly productive interplay between computing and biology. 

More and more biological processes are being understood by viewing them in terms of information processing. And computer models are increasingly helping biologists design new experiments and gain insights into the workings of complex biological systems. In turn, computer scientists are looking at living organisms as the ultimate models for new approaches in decentralized computing. All in all, it’s a cross-fertilization that was practically unheard of until a few years ago.

Perhaps nowhere are advances in computing helping biology more than in the field of genomics. Consider, for example, the genome-parsing programs that Serafim Batzoglou has developed at Stanford University. The software takes full advantage of all the cheap computing power and memory hitting the market. “Now, we can easily hold the entire human genome in main memory,” Batzoglou says. With “small clusters of cheap Pentium machines,” he adds, it has become possible to rapidly search that data for specific DNA sequences. Comparable to scanning volumes of the Encyclopedia Britannica to locate a specific string of 10 words, this search is crucial to understanding genetic differences between individuals and between species. The biggest speedups in the search process, Batzoglou says, have come from “designing clever algorithms.”

In another example of the infotech-biology convergence, startup Sana Security in San Mateo, CA, is building a computer security scheme that is rooted in the study of how organisms protect themselves from biological intruders. Steven Hofmeyr, Sana’s founder and chief scientist, explains that studying immune systems through the lens of digital information processing has yielded several powerful algorithms that help protect banks of computer servers from hackers and computer viruses. Biology has taught researchers that software distributed across many machines that can teach itself the difference between benign activities and malicious attacks, for instance, may provide better security than centrally managed, hard-coded approaches. Information systems are getting too complex for humans to manage effectively, Hofmeyr says, so it’s important to build software that can learn and take care of itself.

While researchers like Hofmeyr are inspired by the workings of biological systems, others are inspired by the human body itself. Cynthia Breazeal at MIT’s Media Laboratory has built robots whose mechanical faces appear to express human emotions in response to the gestures and facial expressions of people they encounter. She’s using her robot called Leonardo to explore how people and robots might one day communicate. NaturalMotion cofounder and CEO Torsten Reil and MIT’s Jovan Popovic have each developed software to generate realistic animations of the human body in action, with an eye toward applications in video games and filmmaking. Reil’s programs model the physics, musculature, and behavior of human bodies as they run, jump, or balance on wires. Popovic’s code serves as an artist-in-a-box, instantly creating sequences of drawings as an animator drags a digital object with a computer mouse.

For some, nature is not only an inspiration but a collaborator. It has long been known, for instance, that certain molecules naturally assemble themselves into highly regular, periodic structures when deposited on flat surfaces. If researchers could figure out how to control this process, it could provide a simple way to make novel nanoscale hardware devices and materials for ultradense storage. At the University of Toronto, Ted Sargent has figured out how to apply electric fields to assemblies of molecules as they self-organize, prompting them to form nanostructures of a specific design. His methods could yield a way to mass-produce photonic crystals used to more precisely route light, a feat that could revolutionize optical communications.

In most areas of computing, however, it’s still sheer human brainpower-not inspiration from biology-that is driving innovation. Vipul Ved Prakash, founder of the anti-spam company Cloudmark, has come up with a way for-potentially-millions of people to jointly decide which mass e-mails are junk. He first released his online voting mechanism, called Vipul’s Razor, as open-source software that’s free to use and that anyone can inspect and modify. Once the program gained a substantial following, he founded Cloudmark to produce a commercial version. “Open source gives people an outlet to publish their stuff, get lots of users quickly, and prove their product,” says Prakash. “Then they have a better chance of getting [venture capitalists] to take a look and invest.”

Whether the TR100 are working to bring about the convergence of biology and information technology or are worried about more mundane matters, such as spam, their work shares a goal: to expand the impact of computing. In the next few pages, you will read how they are adding to the classic story lines of information technology.

TR100 Startups in Hardware and Software
Geoffrey Barrows Centeye (Washington, DC) Visual sensors that use neural-like circuits to detect obstacles and guide unmanned aircraft
Ian Clarke Cematics (Santa Monica, CA) Software for distributed secure networking and artificial intelligence
Uprizer (Santa Monica, CA) Peer-to-peer software that distributes content within large organizations; raised $4 million in 2001
Andrew Heafitz TacShot (Cambridge, MA) Method for snapping aerial photos from small rockets and sending them wirelessly to a laptop computer
Steven Hofmeyr Sana Security (San Mateo, CA) Software, modeled on the immune system, that enables computers to defend against viruses and hackers; $10 million in funding
Mike Horton Crossbow Technology (San Jose, CA) Microelectromechanical sensors, a.k.a. “smart dust,” that self-assemble into wireless networks; has taken in $13 million from Intel Capital and other investments
Kevin Lee LNL Technologies (Cambridge, MA) Integrated photonic and optoelectronic microchips for communications and computing;
has raised at least $7.1 million in seed funding
Desmond Lim LNL Technologies (Cambridge, MA) See above
Michael O’Connor IntegriNautics (Menlo Park, CA) Hands-free, Global Positioning System-based apparatus for automatically steering tractors and other heavy equipment; has raised $18 million from venture capitalists and institutional investors
Joe Pompei Holosonics (Watertown, MA) Narrowly focused beams of high-quality audio for use in consumer products
Vipul Ved Prakash Cloudmark (San Francisco, CA) Spam-filtering software for use by individuals and corporations; raised $4 million in venture funding in July 2003
Torsten Reil NaturalMotion (Oxford, England) Software that generates lifelike, 3-D animations of human characters for computer games and films; technology will be used in Troy, a forthcoming movie starring Brad Pitt
Tim Sibley StreamSage (Washington, DC) Software for searching and managing audio and video files that recognizes sequences
of spoken words
Lorraine Wheeler Botzam (North Billerica, MA) Utility software for Palm-OS-based personal digital assistants

TR100 Computing Honorees

Barrows, Geoffrey
Batzoglou, Serafim
Breazeal, Cynthia
Clarke, Ian
DeHon, Andr
Gottesman, Daniel
Guarini, Kathryn
Gundrota, Vic
Heafitz, Andrew
Hofmeyr, Steven
Horton, Mike
Howard, Ayanna
Lee, Kevin
Lim, Desmond
O’Connor, Michael
Pompei, Joe
Popovic, Jovan
Prakash, Vipul Ved
Reardon, Thomas
Reil, Torsten
Riel, Heike
Riesenhuber, Maximilian
Rottenberg, Linda
Sargent, Ted
Sibley, Tim
Vasilescu, Alex
Wheeler, Lorraine
Yamamoto, Tsuyoshi

What is the TR100?

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