Interview: Carl Zimmer, Author of Microcosm

Readers of this column know that from time to time I seed stuff by science writer Carl Zimmer. I discovered his blog, The Loom, a while back and I've been reading his stuff ever since.

When I saw that he had a new book coming out, I asked for an advance review copy and an interview. He kindly granted both requests. The book, Microcosm, comes out tomorrow - check back then for my review. For now, all you need to know is that it's a book that looks at a single life-form - E. coli, that single-celled creature we all associate with really bad food poisoning - and from there takes us from an introduction to molecular genetics to a meditation on the role of life in the universe. It's a completely fascinating read, one part history of science to one part boyish enthusiasm for really cool ideas. But I'll save my enthusiasm for my review tomorrow.

First, to give you a slightly different perspective on what to expect from the book, I'd like to publish a few questions-and-answers with Carl Zimmer about this book and about his work in the life sciences in general.

What made you choose E. coli as a topic for your latest book? Obviously the subject affords a great wealth of information to explore, but so do many others - why work with this one?

CZ: My books usually start out with a lot of connected thoughts drifting around in my head. To turn that thought-cloud into a manuscript, I first have to narrow it down to something that can fit in a few hundred pages, not a few thousand. This time around, I started thinking a lot about life--what it means to be alive, what rules govern life no matter what form it takes. Biologists know so much more today about life than just a few years ago that they can really start to ask these questions in a meaningful way. But I knew I didn't want to write about all 10 million species of life on Earth. So it occurred to me, what if I just choose one species? Which one would I choose? The choice was obvious --E. coli. The story of E. coli is really the story of modern biology, from the 1940s, when scientists struggled to discover what genes are, to today, when they are rebuilding life from scratch.

Obviously you've got a lot of training and expertise in this field, but is there anything really fascinating that you learned specifically in the research for this book that you didn't know before?

CZ: I learned a huge amount of things working on this book. I learned that getting old is an inescapable side-effect of evolution, even for bacteria. I learned that the Internet and the genes in E. coli are organized according to many of the same network rules. I learned that E. coli is being retooled to become an anti-cancer missile. Perhaps the biggest surprise of all was learning how accidental it was that E. coli became science's favorite organism. In the mid-1900s, a handful of scientists were looking for a safe, fast-breeding microbe on which they could do some experiments. Someone handed them some samples of E. coli, and the rest was history.

Getting a bit philosophical here, but: your work in this book seeks to help answer the question "What is life?" Has your research on this book and in biology in general has had any effect on your philosophical outlook on life? If so, would you share it with us?

CZ: One thing that struck me working on this book is that we humans like to build our philosophies and decide what life means based on how we think nature works. But quite often, nature doesn't work that way. So, for example, people on the right and the left object to genetic engineering on moral grounds because--they claim--it is unnatural to break the boundary between species.

But nature itself doesn't respect that boundary. E. coli is a case in point. If you look at the genome of any particular strain of E. coli, it's packed with hundreds of genes that came from distantly related species. They were injected into its genome by viruses--a kind of natural counterpart to genetic engineering. And in the 1970s, scientists started inserting human genes into E. coli to manufacture insulin and other medical drugs. Some people try to dodge this reality by claiming that humans are different. But our own genomes are mosaics as well. We wouldn't even be able to breathe oxygen if not for the DNA inserted into our ancestors by bacteria.

One of my favorite bits in the book is when you describe the way an E. coli moves - it really made the scale of the subject click into place for me. As a sort of teaser for your book, can you take a few sentences and give us a basic summary of that system? It's completely fascinating.

CZ: The way E. coli moves is utterly cool. The microbe builds spiraling tails that trail behind it. Each tail is anchored to a disk-like mass of proteins in its membrane. Those proteins act a bit like a motor. They draw in protons and capture their energy, using it to spin hundreds of times a second. If they spin counter-clockwise, the tails bundle together and drive E. coli forward. It can move twenty body lengths a second, far faster than we can swim. And they're swimming with a serious handicap, because when you're the size of E. coli, water feels like mineral oil. If you stop swimming, you don't coast. You stop instantly.

What's even cooler is how E. coli navigates. Every now and then, E. coli starts spinning its tails in reverse. They fly apart and the microbe goes into a tumble. After a tenth of a second, it switches directions again, the tails come back together, and it begins to move forward. The microbe navigates by changing how long it goes between tumbles. If it encounters something nasty, it tumbles more often so that it moves away. If it senses something tasty, it tumbles less often so that it goes in a straight line. And it can makes these decisions because it has thousands of receptors on its front end that are constantly sniffing the molecules passing by and processing that information like a tiny brain.

In the text you go through study after study that sought to shed light on some small part of the total e. coli picture. How close are scientists to being "done" with E. coli? Is that a feasible goal?

CZ: Despite the hundreds of thousands of experiments scientists have already done on E. coli, there's still so much left to learn about them. For example, out of 4000-odd genes in its genome, scientists still don't know what 600 or so of its genes are for. Francis Crick, the co-discoverer of the structure of DNA, dreamed of the "complete solution" to E. coli, and imagined an entire research institution dedicated to finding it. If scientists could get the complete solution to E. coli, it would be the first time they had found one for any living thing. That would be quite an accomplishment.

Finally, the pitch: I'm a reasonably intelligent individual who likes to dabble in various subjects. I'm interested in learning about new things, but I don't have as much time to read as I'd like. Why should I make time in my schedule for Microcosm?

CZ: If you have ever wondered what it means to be alive, you should read Microcosm. Because by understanding E. coli, you can learn a great deal about life itself.

Edit: I've just published my review of Carl Zimmer's Microcosm - check it out, leave your thoughts!