Carl Zimmer Ponders Unseen Ecosystems Teeming Within Us

Carl Zimmer
Carl Zimmer Courtesy of Carl Zimmer

If ever you feel alone in the universe, perhaps you can take comfort in the knowledge that in fact, you are never without the company of the thousands of microbial species residing in your body’s every crevice. Collectively, they operate like an invisible organ, and they are essential to our health. As Carl Zimmer masterfully shows, the human microbiome is a metabolic engine whose power and complexity scientists are only beginning to appreciate. “How Microbes Defend and Define Us” appeared in The New York Times on July 12, 2010.

Here, Zimmer tells TON co-founder Siri Carpenter the story behind the story. (This interview has been edited for length and clarity.)


What made you decide to write the microbiome story?

This is kind of a strange story for me because it wasn’t as if one paper suddenly came out and I discovered something I didn’t know anything about before.  I don’t know how young I was—I was a kid, I’m sure—when somebody told me that we have all these bacteria living inside of us, and we need them. I was fascinated by that. Then maybe 15 years ago, they really started to develop this way of identifying bacteria without culture. There would be people who would be off in Yellowstone, getting bacteria out of hot springs that no one thought could support life, and other people doing the same thing in the human body. I thought that was really interesting.

When I was writing my book Microcosm, which came out in 2008, I had an opportunity to write a bit about the microbiome and learn how far things had gotten. [Researchers] would just go and sample hundreds of people, or they would say, “Do people leave bacteria on their keyboards?  And are they distinctive?” Or “What do identical twins look like?” Or “What happens when a woman gives birth by C-section?” The cost for that kind of research started to become so negligible that the real choke point was just creativity.

The bacterium Enterococcus faecalis, which lives in the human gut. USDA

What made you decide to do the story when you did?

I wanted to write about it, but it’s not like there was this moment where the gong goes off, and you say, “Now you’re allowed to write about it.” A couple of years ago, NIH had put a lot of money into the microbiome. I generally don’t like to write about the giving of a lot of money to projects—I feel like the real news would be if you find anything interesting with that money. So I try to hold off. But then a paper came out in Science, where they did an analysis on 178 reference genomes they had sequenced from the human body. That was the hook for me. So I called up Jim Gorman, my editor at The Times, and said I wanted to do the microbiome now, and he said, “Do it.”

How did you go about the reporting for this piece?

I spoke to ten or so people for the story, either on the phone or by email. I also heard some lectures on new data, and I even spent a couple hours late at night at a bar in San Diego shouting over drinks with two microbiologists. I didn’t quote them from that “interview.”

How did you find the patient for the lede?

That was very fortunate. When Jim and I agreed I would do the story, I was already planning on going to the American Society for Microbiology meeting in San Diego. There were a ton of microbiome talks; it was like they had heard that I was working on it, and they had lined up all their best stuff—and I just thought, “Thank you.” There was a microbial ecologist named Janet Jansson, from Lawrence Berkeley Lab who was talking about the methods you use and some of the results that you get when you’re fishing for microbes in different ecosystems, and then she starts describing this “fecal transplant” treatment with this patient who had this terrible C. difficile infection. She flashes a couple of slides, says the patient was cured; then she just moved on. For her, it was just another data point. But I was just stunned. I just thought, “You’re kidding. This really happened? And it worked?”

Then I saw at the bottom of the slide that this was in press, I think, at the Journal of Clinical Gastroenterology. When you’re looking for newsiness, you can’t ask for something better than that. I knew I wanted it in the article, or at least I wanted to pursue it. I called one of the authors and told her that I wanted to know about this case, and she told me I should talk to Dr. Khoruts, the gastroenterologist. Fortunately, he was very willing to describe the case. When he got to the point where he basically said, “You know, I’d just run out of options. This woman was going to die. I had to try something,” and then he tried this and saved her life, I said, “Okay. Not only is this going to be in the article—that’s the lede.”

Did you talk with the patient?

I deliberated about that, and I decided not to because I had all the information I needed for an article of this length, and because I had a hard time seeing how, in this format, I wouldn’t end up being exploitative. If this was a 6,000-word magazine feature, then I definitely would have tried to talk to her, and instead of talking about Khoruts I would have started with her, and gone back to when she was healthy, and how she got a lung infection and took antibiotics for it, and how that opened up the opportunity for infection, and what it was like…I mean, she was in hell. But to bring her into it, you have to do it right. And this wasn’t the place to do it. I would be just looking for one quote from her, and I would feel like I was treating her like she was in a sideshow.

This is such a sprawling subject. Was it difficult to decide what to include and to make it coherent?

That was definitely the big challenge, because you could talk to hundreds of people, and they would each tell you something a bit different and interesting. There comes a point where you just say, “I’ve just got to stop talking to people.” In terms of what to include, I wanted to give a sense of the full scope of research going on today, with vivid examples of how it tells us something about ourselves and can potentially lead to better medicine.

Moving away from this particular article, I’d like to learn more about how you manage to be so prolific. What’s your secret?

It’s not like I have some sort of rational system, and I do sometimes spread myself too thin—there are times when I have to say, “Whoa.” The thing is, as a freelancer you have a hard time saying no, because you’re not entirely sure what the next thing is that’s going to come down your way. But if you say yes too many times, then you’re up at two o’clock in the morning, trying to get that story done so that you can get to the other story that’s also due tomorrow. So part of it is just that I say yes to too many things. Also, my wife does the lion’s share of taking care of [the kids], so that has allowed me to just drill down into my work.

How do you divvy up your time between writing articles and books, teaching, blogging, and tweeting?

I find working on anything just non-stop, unless I’m really fired up about it, can get kind of exhausting. So I’ll work for a little while on a newspaper article, and then I might just skim around on the Internet, and if I see something interesting, maybe I’ll just post something on Twitter, just because I want to share it with people.

You don’t do that on any kind of schedule?

No. I don’t think that Twitter or blogging should adhere to any schedule. That’s my philosophy—I just think that Twitter and blogs are the most fun when they’re spontaneous.

Do you ever use material that you have left over from a story in your blog?

Yeah. Actually, that is a great way to make more use of your time. I wrote a piece for The Times a few months ago about consciousness, and there’s this one scientist who has this very innovative kind of approach to consciousness. He thinks that you could actually measure the quality of conscious experiences, and then compare it in different species, just by doing electrode readings, which is very cool. But just to get the basics of his stuff, I was up to 2,000 words, so I said, “Well, forget that.” But then when I wrote a blog post, I put that out there, and put links to the papers where he talks about the quality of consciousness work. That inspired a very heated debate in my comment thread. Without the blog, that portion of my work would have just withered away—there’d be no place for it.

Who did you want to model yourself after when you were getting started in science writing?

When I was starting, I read a lot of John McPhee. I think one reason was just because here was somebody who could just throw himself into a scientific subject that didn’t seem to have a lot of poetry to it, like geology. And yet he could just see it, and he could make you see it too. People like him are kind of like constellations you can navigate by. You might not ever write anything as good as that. You might not really have the opportunity to write in that kind of way—you know, some 10,000-word feature. But it’s good to just remind yourself of how good science writing can be.

A glimpse behind the scenes:


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