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Article: Writing Life

You've learned a lot about how computing power gives us new perspectives on biology. At the center of it all is a component more advanced than any silicon chip inside a computer processor. It's the human brain. Biologists, engineers, physicists, computer scientists, epidemiologists, geneticists, and even writers and artists have brought their brainpower to the table to solve these old and new problems.

»  Time for Computation
»  Excerpts from an Internship
»  Programming Biology
»  Think You Want to Compute Life?

“As an undergrad, I actually majored in physiology, but had spent some time doing research in a genetics lab where I learned to appreciate the computer as a tool for doing biological research.”
— Eric Lee, an M.D./Ph.D. candidate at the University of Illinois at Urbana-Champaign who creates molecular simulations of biological processes

Time for Computation
By Jilliene Mitchell

Ryan Harrison. Many scientists have mistaken Harrison for a college or graduate student!
Credit: Stephen Spartana

Going from Mom's or Dad's savory home cooking to the campus cafeteria's "mystery meat" can be a big adjustment for any college freshman. But for Ryan Harrison, a sophomore biomedical engineering and economics major at Johns Hopkins University in Baltimore, Maryland, it wasn't a big deal.

While most of his high school friends took it easy their last year to fully enjoy "senioritis," Harrison spent his downtime at Hopkins, where he worked in the chemical and biomolecular engineering lab of professor Jeff Gray. Harrison got the chance through his high school, which offers a program that pairs students with researchers.

Harrison had been writing his own computer programs since the 4th grade. So when his high school biology teacher introduced him to Gray, everything fell into place. "He was into computational biology and we immediately hit it off!" says Harrison.

While in the Gray lab, Harrison improved the Rosetta computer program that predicts how proteins fold and attach to other biological molecules.

Before he had even graduated from high school, Harrison had presented his research to scientists older than his parents and received numerous awards, including a top prize in the 2005 Intel Science Talent Search—the nation's oldest and most prestigious high school science competition.

As a Hopkins student carrying a full load of courses, Harrison still finds time to work on the program. These days, he's mostly fixing its bugs.

Don't be fooled, though. Just because he was an award-winning researcher at age 17 doesn't mean he's a whiz at everything! When he started losing the battle in a high-level algebra course, he says he knew it was time to visit the math help room, where students could work with tutors. The effort paid off. Harrison finished the class with a B-, which, considering how tough the class was, he says felt more like an A+.

"I study a lot," admits Harrison. "But I still make time to do things that I enjoy."

Among his hobbies: directing a one-act play, experimenting with light and sound for student theater productions, and playing his favorite computer game, Civilization© III. And he teaches disadvantaged kids in Baltimore how to play chess, explaining, "It's also really good practice for me!"

With so many interests, one of Harrison's biggest challenges in college is finding time for all of his activities—and deciding what he ultimately wants to do professionally. As he wrote in his online diary (see excerpts below), "I have more questions now about my future than ever before. But, I guess that's...a normal part of growing up."

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Excerpts from an Internship

Ryan Harrison spent his first summer off from college in New York City, where he did a 10-week internship at Weill Medical College of Cornell University.

Instead of working in a computer lab, he worked in a "wet lab," complete with live organisms, chemicals, and petri dishes. He studied how a particular protein affects the life cycle of the parasite that causes malaria.

Harrison wrote about his summer experience in his blog, "Verdant Force: Discoveries in Life and Proteomics."

6/29/06 Thursday 8:37pm
"I've been in New York City for almost a month now. Settling in well to my new lab environment and even forgetting that I'm in NYC occasionally . . . . Wish I could work a little more independently, but I understand that I just don't have the proper laboratory background/experience to handle my own independent project. I guess I was expecting a Gray lab type arrangement—where I work at my own pace at a problem I selected and I am the only one responsible for the outcome (good or bad) . . . . Whatever I decide to do, I think it will combine computational with "wet lab" work. Since I haven't the slightest idea how my life is going to unfold, I am just going to do what I enjoy."

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Programming Biology

Drew Endy likes taking things apart and putting them back together—bikes, cars, lawn mowers. He essentially does the same thing when he tries to understand biology. A professor at the Massachusetts Institute of Technology in cambridge, Endy assembles and programs living machines. I asked him a few questions about his work and why he likes it.—DB

What got you interested in science?
I'm curious. It bothers me when I don't understand how things work.

You're trained as an engineer. How does that influence your approach to biology?
If you ask engineers what they want to do in their heart, they want to make something. My interest is to be able to routinely, reliably, quickly, easily, and cheaply put together the bits and pieces of biology to make new and useful things

With the help of a Hollywood illustrator and others, Endy created a comic book called Adventures in Synthetic Biology. He hopes to use it as a teaching tool.
Credit: Drew Endy

You're in a new field called synthetic biology. What's the goal of this field?
It's to make routine the engineering—the programming—of living organisms.

Why do you want to do this?
I started to think about why it's been so hard to understand biology. The conclusion I've come to is that the biological systems we find in nature aren’t easy to understand. I figure that if I want to have biology that I understand, I'd be better off building it myself.

What makes the field so hot right now?
Seventy years ago, physicists came into biology and really shook things up. I suspect that what's happening now is that the engineers are coming into biology, and they're going to shake things up.

Describe your typical day.
I feel like I'm an enzyme, helping stuff happen. I teach two courses on synthetic biology, and I supervise the research in my lab. Every now and then I get a little bit of time to think.

What have you thought about lately?
Are we discovering biology faster or slower than nature is inventing new biology? I did some back-of-the-envelope calculations, and this number could be completely wrong, but sometime between the year 2085 and 2105 we should be able to sequence all the DNA on the planet in a month.

What do you like most about your job?
The people in research are some of the coolest, [most] interesting, [and] nicest people you're ever going to meet. It's just a great experience.

What do you think makes for a successful scientist?
The best, most fun-loving, happy scientists I've seen are the people who recognize when an idea isn't working and abandon it for a better idea without feeling too bad.

Do you think you'll always be a scientist?
I'm doing what I want to be doing, and if I wasn't, I would change it. If at some point in the future, I'd rather be raising pheasants in southern France, or northern France, or wherever they raise pheasants in France, I presume I would go do that. Of course, I'd have to learn French.

Last words?
People express great wonderment, excitement, and almost a magical relationship with the living world. But I think over the coming years—faster than most expect—we'll see a transition in biology where it becomes much simpler and easier to engineer living systems. We don't actually know how to do that right now, but there are lessons buried in the lore and wisdom of other engineering disciplines.

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Think You Want to Compute Life?

"When I was in high school, I never thought there was a field that combined all my interests."
— Christina Mills, a Harvard Medical School student who models infectious diseases

People with many different talents can join in computing life. If you're interested, ask yourself what aspects of the research featured here you find exciting. Do the projects blend many of your academic interests? Are there particular biological problems you'd like to solve?

Here are a few tips on how to get started looking into computing life as a career.

• Ask your science teacher or guidance counselor about opportunities to work with a researcher at a nearby college or other institution.
• Search the Web for scientists working at the crossroads of biology and computation.
• E-mail scientists at your local college or university for more information.
• Enter a science fair to get experience presenting research results.

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