Category: Book Preview

Discovering my microbiome: "You, my friend, are a wonderland"

By Carl Zimmer | June 27, 2011 11:09 am

Some people get a thrill from getting their genome sequenced and poring through the details of their genes. I’m a bit off-kilter, I guess, because I’m more curious about the genomes of the things living in my belly button. And let me tell you: it’s a jungle in there.

I first became curious about my navel in January. I was in Durham, North Carolina, to attend a meeting, and as I walked out of a conference room I noticed a cluster of people in the lobby handing out swabs. They were asking volunteers to stick the swabs in their belly button for the sake of science. Our bodies are covered with microbes, and scientists are discovering weirdly complex patterns to their biodiversity. From fingers to elbows to chin to forehead, different regions of our skin are dominated by different combinations of species. But the bellybutton remained terra incognita.

I happily donated my microbiome to the study, which is being conducted by Jiri Hulcr and Andrea Lucky, two post-doctoral researchers in the laboratory of Rob Dunn at North Carolina State University. After a few weeks, Hulcr sent me a photo of a Petri dish in which some of the bacteria from my bellybutton were thriving. Then Hulcr and Lucky got down to the serious work of identifying the species in the navels of their volunteers (90 and counting).

Yesterday, Dunn sent me a spreadsheet detailing my own results. “You, my friend, are a wonderland,” he wrote.

To catalog the biodiversity of bellybuttons, Hulcr and Lucky are extracting the genetic material from their collection of swabs. They then compare these fragments of DNA to the millions of sequences that are stored in public databases. (They limited themselves to DNA from bacteria, so for now they’re not cataloging the fungi, viruses, and other creatures that may be lurking in our navels.)

Some fragments of navel DNA precisely match the DNA of a known species of bacteria. In other cases, they’re close enough to a species for Hulcr and Lucky to assign them to a genus, a family, a class, or  some higher unit of classification. In a few cases, the bacterial DNA is so exotic that all they can say for sure at this point is that it is bacteria.

Hulcr, Lucky, and Dunn had lots of questions about the things that dwell in the human omphalos. Are they different from the species that live in other parts of the skin? Do they differ from one person to the next? Is there a core set of species found in all navels? To address these kinds of questions, they tallied up the number of volunteers who carried each species, and investigated how each species makes a living.

All told, I now discover, my belly button harbors at least 53 species of bacteria. This, Dunn informs me, is a “whopping” number.

I’m not sure whether to feel good or bad about this revelation. On the good side, I know that diversity can make ecosystems work better. One of the most important services that our microbial ecosystem performs for us is protecting us from pathogens. They can outcompete invaders, kill them with poisons, and otherwise ward them off. Scientists have run experiments to test the effect of diversity on infections. They manipulated mice so that some had no resident bacteria, and others had low levels of diversity. The researchers found that pathogens did a better job of invading low-diversity mice than high-diversity ones.

So perhaps my belly button is especially well-defended. Still, I can’t help but wonder if I ought to scrub it with some steel wool. There are some very exotic things in there. Only a small fraction of my belly button bacteria were common among the other 89 volunteers. The microbes I share with most other volunteers tend to be ordinary skin dwellers that are typically harmless (although sometimes they can turn nasty and cause problems ranging from acne to staph infections).

But out of 53 species, 35 were present in only 10 or fewer other volunteers. And 17 species in my navel didn’t show up in anyone else. In the column for notes in Dunn’s spreadsheet, he’s annotated these species with scientific descriptions like “weird one” and “totally crazy.”

Several species I’ve got, such as Marimonas, have only been found in the ocean before. I am particular baffled that I carry a species called Georgenia. Before me, scientists had only found it living in the soil.

In Japan.

When I learned this, I emailed Dunn to let him know I’ve never been to Japan.

“It has apparently been to you,” he replied.

While I may be a bit of an outlier in the belly button department, I’m not a freak. Among all 90 belly buttons Dunn and his colleagues have studied so far, they have found 1400 species of bacteria, a number of which have never encountered on human bodies before. These species are probably not so out of place as they may seem, however. The diversity of the world’s microbes is vast–far bigger than the whole animal kingdom combined. For the most of the history of microbiology, scientists have focused most of their attention on bacteria that make humans sick–ignoring the huge number of species that don’t harm us, or that live elsewhere in the world. Many species are turning out to have a much wider range than scientists have previously appreciated. Bacteria have also evolved to leap from one niche to another to another. Take Pantoena–a lineage Hulcr and Lucky have only found in my belly button and that of one other subject. Most species of Pantoena infect plants. But a few lineages have shifted from plants to people. As scientists add more branches to the tree of life, they will probably find more such transitions.

In ancient Greek mythology, Zeus release a pair of eagles to find the center of the world–the “omphalos,” which means belly button in Greek. Several statues, like the one shown above, were built around the Mediterranean to mark the supposed place where the eagles landed. It’s wonderful to be part of an experiment that gives a new meaning to this ancient word. Each of us carries a biological omphalos: a small, lint-clogged center of the microbial world.

(For more information, check out Dunn’s new book, The Wildlife of Our Bodies, for which I happily provided a cover blurb.)

[Image: University of Kentucky]

Great science books for high school students: The hive-mind speaks

By Carl Zimmer | March 28, 2011 5:31 pm

Over the weekend, I was contacted by Melissa Townsend, an Arizona high school teacher, with this question:

Getting ready to assign spring reading to my students. What are your favorite non-fiction science books a HS kid can handle?

It’s an excellent question–there are some books that can open up the mind of a teenager, and leave an impression that lasts a lifetime. But when I got Townsend’s request, I was traveling to Washington to talk on a panel about blogging, so I was a bit scatter-brained. I therefore tossed the question out to the hive mind. When I read the responses, many of them made me think, “Yeah, what she said!”

Here is a selection of the answers. Add your own in the comment thread; I can update the list here accordingly.

The Immortal Life of Henrietta Lacks, by Rebecca Skloot. (This one was mentioned so often Townsend decided to go with it.)

Wonderful Life: The Burgess Shale and the Nature of History, by Stephen Jay Gould

The Diversity of Life, by Edward O. Wilson

Under a Lucky Star, by Roy Chapman Andrews

The Double Helix: A Personal Account of the Discovery of the Structure of DNA, by James Watson

E=mc2: A Biography of the World’s Most Famous Equation, by David Bodanis

A Short History of Nearly Everything, by Bill Bryson

A Primate’s Memoir: A Neuroscientist’s Unconventional Life Among the Baboons, by Robert Sapolsky

Microbe Hunters, by Paul deKruif

The Ghost Map: The Story of London’s Most Terrifying Epidemic–and How It Changed Science, Cities, and the Modern World, by Steven Johnson

The Hot Zone: A Terrifying True Story, by Richard Preston

Musicophilia: Tales of Music and the Brain, Revised and Expanded Edition, by Oliver Sacks

Uncle Tungsten: Memories of a Chemical Boyhood, by Oliver Sacks

The Story of Science: Aristotle Leads the Way>, by Joy Hakim (follow the link to the other two books in the series, too)

The Meaning of It All: Thoughts of a Citizen-Scientist, Richard Feynman

Why Evolution Is True, by Jerry Coyne

CATEGORIZED UNDER: Book Preview, Link Love, Teaching

Henrietta Lacks and the Future of Science Books

By Carl Zimmer | February 2, 2010 12:32 am

The Immortal Life of Henrietta Lacks CoverI first met the writer Rebecca Skloot about eight years ago. She had been working on a book for a couple years and running late. The idea was brilliant, though, so I hoped she’d be able to get it done before too long. Many scientists who study human cell biology use a special line of cells known as HeLa. It came from a woman named Henrietta Lacks, who died of cervical cancer in 1951. Skloot was writing about Lacks, her family, and the way her body became dispersed around the world.

When I would see Skloot again, I’d ask how the book was going. Still going. After a while, I stopped asking, because I know how irritating that question can get when the answer hasn’t budged for a while. When the book was done, it would be done.

A decade passed before the book was done. When Skloot sent me an advance copy of The Immortal Life of Henrietta Lacks a few months ago, I discovered why it had taken so long. She doggedly pursued the story, reconstructing a fifty-year saga intertwining the experience of a family struggling in Baltimore and the rise of modern biology. It was worth the wait, and I happily provided a blurb–

“Rebecca Skloot has written a marvelous book so original that it defies easy description. She traces the surreal journey that a tiny patch of cells belonging to Henrietta Lacks’s body took to the forefront of science. At the same time, she tells the story of Lacks and her family—wrestling the storms of the late twentieth century in America—with rich detail, wit, and humanity. The more we read, the more we realize that these are not two separate stories, but one tapestry. It’s part The Wire, part The Lives of the Cell, and all fascinating.”

Spending a decade working on her book, Skloot became a literary Rip Van Winkle. She started her book back before the rise of blogs, before the annihilation of book reviews in newspapers, before Kindles and Ipads. When Skloot started her book, the book tour was still a relatively common feature of the promotion of a new book. But Skloot discovered that book tours had pretty much evaporated by the time her book was coming out.

As I’ve published books of my own over the past decade, I’ve watched these same changes accrue, book by book. I’ve tried to take more control over the promotion of my work. I look for ways to spread the word about my books online, not just when they come out, but long afterwards. I am grateful to readers who spread the word further on their own blogs and tweets. But I have to say that publishing books gets more and more nerve-wracking as time goes on. Writing books is a slow process, but the publishing industry is changing fast. I feel as if I am at an archery contest. I take a long, long time to aim at a target, but by the time I let the arrow fly, someone’s moved the target away.

So I was curious to see how Skloot would contend with the challenge of publishing a book in 2010. Fortunately, she has comet it with great creativity and verve. One of the thing’s she’s done is crowd-source a book tour. She has sent out a call to everyone she knows for help in lining up talks across the US and beyond. I don’t quite know how the whole thing came together, but she is now starting a zillion-city, multi-month tour.

I offered my help for the Elm City leg of the tour, so let me just take a moment to send out a call to everyone in and around New Haven, Connecticut. Skloot will be talking on Monday, 2/8, at 4 pm at a Morse College Master’s Tea at Yale. Morse College is under renovation this year, so the students are staying at Yale’s Swing Space at 100 Tower Parkway (Map).

Skloot has also been lining up lots of other opportunities to talk about the book. Today (2/2) is the official date of publication, and the book is #11 on Amazon. That’s a great thing to see (even if Amazon’s on my blacklist at the moment because of their ongoing book-disappearing act). It may be too early to pass final judgment on the book’s commercial success, but I’m impressed so far.

I think Skloot’s experiences are worth studying, although they are no guarantee for every writer insane enough to write a book about science. For one thing, Skloot has an exceptional subject, which she has written about exceptionally well. What’s more, the odds are getting tougher for all authors. With more and more book titles in competition for the shrinking amount of time people spend reading books, a lot of disappointment is inevitable. Still, it’s a good idea for writers not to become recluses. Sure, spend time in the monastic solitude that books require, but then emerge and engage. You don’t have to tweet with Skloot’s hurricane-scale intensity, but do forge the relationships in which you can support fellow writers, and they can support you.

CATEGORIZED UNDER: Book Preview, Meta

Congratulations to the Age of Wonder [Book Preview]

By Carl Zimmer | September 16, 2009 12:49 pm

The Age of Wonder: How the Romantic Generation Discovered the Beauty and Terror of Science, by Richard Holmes, has won the Royal Society Prize for Science Books. I haven’t read it, nor is its galleys sitting atop a stack of books I hope to get to. But it does look awfully good, and the Royal Society obviously agrees…Any Loom readers have a review to offer?

Update: I should really have entitled this, Congratulations, Richard Holmes. Books don’t appreciate good wishes very much.

CATEGORIZED UNDER: Book Preview

Book [P]review: For The Scientist

By Carl Zimmer | August 11, 2009 12:44 am

On August 11, 1999–ten years ago tomorrow–the State Board of Education in Kansas voted to take evolution out of the state’s science curriculum.

This came as quite a shock to a lot of biologists I spoke to at the time. A lot of them couldn’t understand how it have happened. Some decided to get together to plan what to do in response. With lightning-fast reflexes, a meeting was arranged over a year later. Representatives from major scientific societies gathered to make a plan. They invited a number of other people to join them. I was one. And, frankly, I felt like I was observing a meeting of representatives of tribes from some New Guinea highland forest, who were following rules and speaking a language that I could not begin to understand. At the end of the meeting, these dozens of scientists made a momentous decision. They would…wait for it…go back to their societies and suggest that they post on their web site a statement that evolution is good science.

I sat there, gob-smacked, wondering exactly how many people actually visit, say, the American Phytopathological Society. And yet everyone at the meeting seemed so happy, so excited that they had really done something–that they had let the public know just where they stand.

The experience was a stunning lesson for me about what scientists think is effective communication. And while some of that spirit still survives today, a lot has changed–at least based on my highly non-scientific intuition. Many scientists have been thinking about what they can do in their interactions with the media to get a better sense of their science across. Many, fed up with what they consider to be a sadly broken media machine, have taken matters into their own hands with blogs.

Three books are coming out this year directed at these scientists. Unscientific America: How Scientific Illiteracy Threatens our Future, by my fellow Discobloggers Sheril Kirshenbaum and Chris Mooney, was the first. I talked to Chris about the book in this Bloggingheads talk. Cornelia Dean of the New York Times is publishing another, called Am I Making Myself Clear?: A Scientist’s Guide to Talking to the Public. It’s a lean, straightforward tour of the media landscape, led by a journalist who has written about science for many years.

The third is by a scientists–but it’s called Don’t Be Such a Scientist: Talking Substance in an Age of Style. The author is Randy Olson, a biologist who headed to Hollywood. Back in 2006, I wrote about his documentary, Flock of Dodos–which was his own response to the events in Kansas. Rather than post a statement on a web site, Olson made a funny movie that not only demonstrated the flim-flammery of creationists, but also showed how dismally evolutionary biologists communicated to those beyond their guild.

In his book, Olson draws on his own experience making movies to offer some advice to his fellow scientists on how to tell their story, and to get that story heard. Olson doesn’t want scientists to stop being scientists, but he does urge them to pay more attention to what they say and how they can say it best:

By now you may be thinking, “What’s this guy got against intellectuals? He’s calling them brainiacs and eggheads.” Well, I spent six wonderful years at Harvard University completing my doctorate, and I’ll take the intellectuals any day. But still, it would be nice if they could just take a little bit of the edge off their more extreme characteristics. It’s like asking football players not to wear their cleats in the house. You’re not asking them not to be football players, only to use their specific skills in the right place.

You can find out more at the book’s web site.

CATEGORIZED UNDER: Book Preview

Book (P)review #1: Life Ascending, The Ten Great Inventions of Evolution

By Carl Zimmer | June 24, 2009 9:54 am

life-ascending-cover440.jpgLast month, I asked you how to handle the ever-growing pile of science books I receive (before I donate most of them to the library, of course). A plurality of you voted in favor of frequent thumbnail descriptions, rather than alternatives like the less frequent all-out review. That’s a relief, because that was my own preference. So let me pull off the top book from the pile,  Life Ascending: The Ten Great Inventions of Evolution by Nick Lane.

The reason it’s on the top is that it happened to be very useful to me right now with an article I’m working on (more on that next month). Lane has selected a handful of key features of the natural world, from DNA to sex to warm-bloodedness to consciousness, and has written a chapter about each, explaining what we understand about it and how it evolved. The list is, as Lane himself admits, a bit arbitrary, and on first inspection it may give off a whiff of Scala Naturae, arranging life on a ladder from lower to higher. But once you delve into Lane’s writing, those minor qualms will evaporate. Lane, the author of two previous books about biology, writes about tricky topics like the chemistry of photosynthesis with grace and ease. On the topics I’m familiar with, I can vouch that he has picked good studies to showcase. Lane is also a scientist himself, and he not only reports on the latest research on each topic but also sometimes steps in with intriguing ideas of his own.

As with future posts of this ilk, this is not a full-blown book review. Call it a book (p)review: a heads-up about a book that has grabbed my attention. While I started reading Life Ascending for work, I look forward to finishing it for my own enjoyment.

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.
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