Scientific Method / Science & Exploration

Ars Book Review: Carl Zimmer’s “Microcosm”

A microcosm is defined as a small item that is representative of a far larger …

Feeling life in the gut

I had the chance to sit down with Carl and ask him about life, gut bacteria, and the public's relationship with science.

Ars: What made you choose E. coli, a gut bacterium, as the topic of an entire book?

Carl: I was actually thinking a lot about life—what is it about living things that makes them different from things that aren't alive, and I was thinking that this should be something that I could write a book about. There's been so much going on recently in terms of looking at life in a fundamentally new way, like looking at all the genes in an organism and figuring out how they're all connected, how they're all working together, and asking "are there any properties they have in common?"

After having written five books I knew that this was probably a recipe for madness, so I thought okay, well, how do I find a way to get my arms around this. And it occurred to me that a lot of the things that I've been reading about—a lot of the most interesting things about life—had to do with E. coli. There were papers on this and you could go again and again and again and again and see it's E. coli that they're looking at. And I thought that would come as a big surprise to a lot of people—why is it that a little microbe that lives in our guts and in some cases makes us really sick—why is it in fact this touchstone for what it means to be alive?

And so I thought that it would be really cool just to do a natural history, or maybe an unnatural history, of E. coli because you end up touching on all of the big issues in life, including remaking life.

Ars: Were there certain things you wanted to cover that you couldn't find a way to link to E. coli?

Carl: There are several ways in which E. coli is not is not the perfect metaphor for all life. It does a really good job. I'd say that 90 percent of the things I wanted to talk about, E. coli would let me, whether it was engineering life in new ways, or whether it was looking at the rules for assembling networks of genes—what are the universal rules, these sorts of things. Ecology—as it turns out, our guts are these wonderful ecosystems. But I guess one place where it came up a little bit short is its social life. It may surprise some people to find out that bacteria have social lives, but they actually can be pretty complicated.

E. coli's social life is, at least as far as scientists understand it, is pretty modest. They'll get together and they'll make these things called biofilms where they are cooperating to survive. You will even have some E. coli that blow themselves up to kill the enemies of their colony. So there's pretty fascinating social stuff there, but if you look at some other bacteria, they are even more social—it's just fascinating. There are some bacteria that will come together and build what looks like a tiny little plant; they create a stalk with a big bulb on the top and those are going to be the spores at the top, and the other bacteria have to basically kill themselves to form that stalk. So you have this kind of collective action that's really complex. E. coli doesn't have that, but it has so many other things—it was a lot of fun.

Ars: What caused you the most trouble? Were there some topics that were just a nightmare for you to come to grips with, or some things that you just couldn't find an easy way to present to general audience?

Carl: There were definitely some things that were very intuitive and then other things that were a real headache, both to understand and to write about. So I was wanting, for example, to talk about the flagella [a tail used for movement], and one of the most fascinating things about the flagella is is that E. coli only makes them but under certain circumstances. They don't just make flagella all the time. That would be crazy—you'd have this ridiculous looking hairy microbe that couldn't do anything else but just keep making flagella. So it has to know when to make flagella and when not.

Sometimes it's good not have a flagella at all—don't waste your energy on it. And if you're building a flagella, it takes a long time, takes a lot of energy. In fact, in the lifetime of one E. coli, it can't be finished. If it has a started making a flagella and it is growing quickly, it divides before it is done, and then its offspring has to continue to make those flagella. I liken it to building a cathedral. E. coli likes to make flagella when times are bad because then it can get out of where it is, it can swim away somewhere.

In order to control all this, it has to use a really impressive network of genes, genes that switch other genes on, switch them off, and they're interacting with each other in this really complicated way. What I find really cool about it is that it works, in a lot of ways, like a noise filter does. So I'm trying to get this across. You've got maybe half a dozen genes that are interacting with each other; some are boosting other genes, some are squelching them. So, I ended up just using a diagram, and I really hope that helps. But you have to do anything you can to get across the beauty of these things. The fact that this little microbe has all these clever little systems in it—I just love it, so I'll just use whatever I can to try to get that across.

Ars: Did you hit any topics where you just gave up?

Carl: There are certainly things I ripped through more quickly than others, things where I said, "if I get into this, it's really going to bog down the book." You figure out how to ratchet the level of description up and down. I wasn't going to get into much of a description of entropy, for example, just get the basics across and then move on.

Ars: When you told the scientists you talked to about the topic of the book, how did they respond?

Carl: They were all very enthusiastic. Some were enthusiastic to talk about their own research, and others about the big ideas they were chasing after. There is also this sort of E. coli community that was very excited that someone was going to write a book about the bacteria, because no one has ever written a book for the public just on E. coli. That sort of surprised me. They're a very interesting group of people because they are dealing with this great history, which can be a blessing and a curse. You have all this research going back decades, but a lot of that work is not in a format that can be exploited today, through datamining and things like that.

So, they're having to bring this E. coli research into the 21st century, and it's a lot of work. I went to a place called the E. coli stock center, which is at Yale. For decades now, they've been collecting these strains of E. coli that have been important in the history of its studies. These are mutant strains that were crucial for the experiments that led to all these Nobel Prizes, and they've got them sitting in the freezers or dried onto little strips of paper. Until recently, the way they kept track of this was a giant notebook, this binder. They opened it up for me, and paging through it, it's like these pedigrees of royalty.

It's a very interesting community, and they were very enthusiastic, as you could imagine. But it's up to me to make sure they're telling me what I need to know. If I need a bit more of a big-picture perspective or to break it down into simpler terms, I just start asking stupid questions, and keep asking until I get what I need. But everyone's been very helpful.

Ars: What level of scientific background do you assume from your readers?

Carl: I generally write assuming a high-school level education. I would like that kids in high school could read something I'm writing and understand it. I don't want to be excluding lots of people. I want as many people as possible to be reading what I'm writing; if I write only for people with a PhD in biophysics, it's going to be a pretty small crowd.

It's tricky figuring out what you can write about. There was a point when I was starting out as a science writer where DNA was still a new enough idea that people were unfamiliar with it to the point where, when you write about it in an article, you might stop and ask yourself, "should I just say DNA, or should I say 'deoxyribonucleic acid, the recipe for life?'" And the answer wasn't entirely clear. Obviously today, you don't have to worry about that—everyone knows what DNA is.

Now, people's understanding has gone to a different level. Now, the question I ask myself is about a word like 'genome.' Someone wrote a book about the genome in the late 90s and, at the time, it was a very weird sounding word, and I think it attracted people's attention because it sounded like gene, but it wasn't gene. And he begins his book by explaining what a genome is. Now, I don't think you need to define it. So people's familiarity with concepts in science change over time, and where you draw that line is a very tricky thing. I should probably get focus groups together to figure out whether I'm doing it right or not.

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