The Loom » Microcosm: The Book

2011: A Letter from the Loom

Carl Zimmer — Sat, 31 Dec 2011 06:19:38 +0000

In 2011, the Loom reached its eighth birthday. Thanks to everyone who’s paid a visit or become a loyal reader in that time. With the year coming to a close, I spent a little time this week perusing the Loom’s archive, reflecting on the things that obsessed me during 2011.

More than many years, this one reminded me just how huge science is. Even if you limited yourself to the most important stories of this past year, there was just too much to keep up with. (Here’s Discover’s top 100 picks.) As a science writer, my focus is biology, but that didn’t ease my year-long case of head-spinning. The anchors that kept me from spinning away completely were the very small and the very complicated.

At the small end of the spectrum were, among other things, the bacteria that call us home. Like every year, 2011 saw outbreaks, such as the E. coli that sickened thousands in Germany. But now that we can read the genomes of these killers, as I noted in Newsweek, we can see how chillingly fast new pathogens can evolve.

But the good germs also ...

Do you own your germs? My new piece for the New York Times on micro-bioethics

Carl Zimmer — Sun, 04 Dec 2011 15:20:35 +0000

There are 100 trillion microbes that live in your body. Do you own them? Do they deserve the same protections as your own genes and cells? If someone genetically alters a microbe and claims that if you swallow it, it will let you lose weight, should that living germ be regulated as a drug?

These are a few of the questions I mull in a piece that appears in the Sunday Review section of today’s New York Times. I’ve been writing a lot about the microbial world for a few years now, but only recently did I encounter a group of bioethicists who are now pondering what sort of ground rules we should set up to govern science and medicine as we gain understanding and power over the microbiome. Check it out.

If you’re interested in reading more about all this, here are a few new papers (some free, some behind paywalls).

The Human Microbiome Project: lessons from human genomics: Trends in Microbiology (in press)

The folks at Wired recently asked me to put together a guide to the human ecosystem. You can get it in the October issue as a centerfold–the kind of centerfold that shows someone who took off the clothes, and then took off the skin. Bugs in your eyes, in your ears, in your gut, influencing your mind and health–they’re all there. Check it out.

Bellybutton biodiversity update: Wonderlands upon wonderlands

Carl Zimmer — Sat, 30 Jul 2011 14:31:59 +0000

Last month I contemplated the staggering diversity of microbes in my bellybutton–an experience made possible by my participation in a survey of microbiome diversity carried out by scientists at North Carolina State University. At the time, I thought I was quite the host. I was informed there were 53 species living in my navel, some of which had never been seen on skin before and some of which were altogether new to science. I was even informed that I was a “wonderland.”

Well, the project is moving forward at quite a clip, and the scientists are starting to push more of their data online. Here you can see the species from the first 60 volunteers they’ve studied. The lists are coded by number–I’m B944. I appear to have lost a species so I’m down to 52. And 52 is, I’m seeing, nothing to blog home about. So far, the diversity champion is the anonymous owner of bellybutton B1288. 107 species! Now that’s a wonderland….

Goodbye, E. coli?

Carl Zimmer — Fri, 08 Jul 2011 14:18:25 +0000

Lucas Brouwers, one of the new bloggers at Scientific American’s snazzy new blog network, takes a look at an intriguing paper (free pdf). The authors of the paper in examined many different strains of E. coli and come to a remarkable conclusion: they’ve been splitting apart so far that they may soon no longer be a single species. Check it out. (And, if you have a lot of time to spare, check out the rest of Scientific American’s fine line-up of bloggers.)

Last year: Arsenic life. This year: Chlorine life?

Carl Zimmer — Wed, 06 Jul 2011 18:17:27 +0000

[Note: Some folks don't like the phrase "chlorine-based life." I welcome suggestions in the comments for a better shorthand descriptor]

Last year, a team of NASA-funded scientists claimed to have found bacteria that could use arsenic to build their DNA, making them unlike any form of life known on Earth. That didn’t go over so well. (See my two pieces for Slate for a quick recap: #1, #2.) One unfortunate side-effect of the hullabaloo over arsenic life was that people were distracted from all the other research that’s going on these days into weird biochemistry. Derek Lowe, a pharmaceutical chemist who writes the excellent blog In the Pipeline, draws our attention today to one such experiment, in which E. coli is evolving into a chlorine-based form of life.

As I wrote in Microcosm, scientists have been contorting E. coli in all sorts of ways for years now to figure out what the limits of life are. Some researchers have rewritten its genetic code, for example, so that its DNA can encode proteins that include amino acids that are not used by any known organism.

Others have been tinkering ...

Discovering my microbiome: “You, my friend, are a wonderland”

Carl Zimmer — Mon, 27 Jun 2011 15:09:59 +0000

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 ...

The two faces of E. coli: my article in Newsweek and interview with the BBC

Carl Zimmer — Mon, 06 Jun 2011 13:30:21 +0000

On Friday, as the E. coli outbreak gained horrific speed in Germany, Newsweek asked me to write about how this epidemic came to be. Scientists still have a lot to figure out about it, but some things are clear–in particular, that the bacteria have great scope for evolution into new deadly strains, thanks in part to the shuttling of viruses between them. (In my book Microcosm, I explain how this is true not just for E. coli, but for much of life.) My piece appears in the new issue of Newsweek, which you can read online here. (One late-breaking piece of news that didn’t make it in, by the way, is the finding yesterday that the new outbreak appears to have come from bean sprouts.)

While I was working on my Newsweek piece, a reporter for the BBC called me up for an article on the good side of E. coli. I explained how much of how we understand about life itself came out of research on this typically harmless bug, and that the biotechnology industry was build upon its biology. That piece came out over the weekend. Check ...

Another purge sale: autographed copies of the UK hardback edition of Microcosm

Carl Zimmer — Tue, 24 May 2011 14:06:43 +0000

Last week I announced that I had 17 autographed copies of the US hardback edition of Microcosm, and in 85 minutes you folks cleared me out. There were a few cries of “Arg!” later on Facebook and Twitter, to which I responded that I still needed to deal with more books in advance of our house renovation. And so (voice turning crazy), here’s the next deal: we’ve got 8 autographed copies of the British hardback edition of Microcosm: E. coli and the New Science of Life. It’s out of print, but between now and next Tuesday, it’s available for ten dollars from my Amazon store.

Again, here’s a quick description of Microcosm: In the book, I tilt at one of my favorite windmills–the definition of life. But rather than try to take on all of life on Earth, I chose one species–the one that we know best of all. That would be our gastrointestinal lodger, Escherichia coli, the little bug that helped build modern biology and launch the entire biotechnology industry. In my biography of this scrutinized germ, I explore the origin of life, our inner ecology, and ...

We purge, you save! Get an autographed hardcover copy of Microcosm

Carl Zimmer — Thu, 19 May 2011 17:35:58 +0000

As I wrote on Monday, we’re boxing up books in preparation for some house renovations. You were kind enough to take 21 autographed paperback copies of At the Water’s Edge off our hands–in about three hours.

Well, we have even more books that we’d rather sell than pack.

Here’s our new deal: we’ve got 17 autographed copies of the American hardback edition of Microcosm: E. coli and the New Science of Life. The hardback edition is out of print, but between now and next Thursday, you can buy them for the low, low price of ten dollars from my Amazon store. (Cue Crazy Eddie again!)

In Microcosm, I tilt at one of my favorite windmills: the definition of life. But rather than try to take on all of life on Earth, I chose one species–the one that we know best of all. That would be our gastrointestinal lodger, Escherichia coli, the little bug that helped build modern biology and launch the entire biotechnology industry. In my biography of this scrutinized germ, I explore the origin of life, our inner ecology, and the search for life on other planets. You ...

Blood type, meet bug type: my new story for the New York Times

Carl Zimmer — Thu, 21 Apr 2011 01:40:17 +0000

For some time now I’ve been bewitched by the microbiome–those 100 trillion passengers that make our bodies their vessel (here’s a piece from the New York Times last year, and a long essay from last month). But I was especially intrigued by a paper that came out today in Nature. Scientists found they could sort people into just three distinct gut microbiomes, much like they can sort people into four blood types. Here’s my story in the Times, which will appear in tomorrow’s edition.

One thing that you won’t find in the article is some intriguing speculation I indulged in with the scientists I interviewed. Researchers have clearly demonstrated that microbes can influence their host’s behavior. They release molecules in the gut that travel into the blood and then into the brain. The bacteria that live in obese mice can make ordinary mice voracious. My fellow Discover blogger Ed Yong has written about how the microbiome can steer the development of mice to become more or less anxious as adults. In an upcoming review called “The Mind-Body-Microbial Continuum,” a team of microbiome experts ponder how our microbes might play ...

Tomorrow: Synthetic Biology lecture in Manchester, Connecticut

Carl Zimmer — Wed, 13 Apr 2011 03:07:44 +0000

If you live in central Connecticut, please consider coming to my public lecture tomorrow (Wednesday 4/12). It’s entitled, “Synthetic Biology: Playing God or Harnessing Nature?” The talk is sponsored by the Connecticut Association of Biology Teachers, the Connecticut Valley Branch of the American Society for Microbiology, and Manchester Community College.

Here are the details:

Where: Manchester Community College, Great Path Academy Building, Community Commons. (Here are directions and maps.)

When: 5:30 pm, Wednesday, April 12

More information here.

The Human Lake

Carl Zimmer — Thu, 31 Mar 2011 16:25:04 +0000

I went recently to San Francisco to give a talk to a conference of scientists. The scientists were experts in gathering together mountains of biological data—genome sequences, results of experiments and clinical trials—and figuring out how to make them useful: turning them into new diagnostic tests, for example, or a drug for cancer. The invitation was an honor, but a nerve-wracking one. As a journalist, I had no genome scan to offer the audience.

We science writers do have one ace in the hole, though. Instead of being lashed to a lab bench for years, carrying out experiments to illuminate one particular fold in one particular protein, we get to play the field. We travel between different departments, different universities, different countries, and—most important of all—different disciplines. And sometimes we see links between different kinds of science that scientists themselves have missed. Which is why, when I arrived in San Francisco, walked up to the podium, and switched on my computer, I presented my audience with this photograph of a lake.

For the next hour, I tried to convince them that their bodies are a lot like that lake, and ...

Evolvability: My story in today’s NY Times

Carl Zimmer — Tue, 22 Mar 2011 03:17:17 +0000

Today I’ve got a story about some new research into evolvability–the potential to reach new adaptations. Scientists have explored the possibility of evolvability for some time now, but mostly through analyzing mathematical equations. Now a new study offers a fine-grained picture of evolvability in action. Richard Lenski of Michigan State and his colleagues have watch evolvability help one line of bacteria beat out another one. It’s a Darwinian story of the tortoise and the hare. Check it out.

(For more on evolvability, check out this review by Massimo Pigliucci [pdf])

[Image: Wikipedia]

Dive into your inner lake: My keynote lecture on the microbiome (slides and audio)

Carl Zimmer — Mon, 21 Mar 2011 03:46:20 +0000

Earlier this month I was invited to deliver a keynote address at the Joint Summit on Translational Science in San Francisco. The meeting brings together scientists who seek to master the rising tide of biological data, in order to find new medical treatments. I urged them to think like ecologists, and treat the human body like an ecosystem of thousands of species.

I recorded my talk on my trusty iPhone, and I’ve posted the audio below. (You can download it.) It’s also here.

Carl Zimmer Keynote Lecture on the Human Microbiome by Carl Zimmer

And below are the lecture slides (also on Slideshare). (Thanks to everyone who responded to my query about the best way to present my talks. I hope later this week to turn the talk into a written post.) [UPDATE: Here's my essay, "The Human Lake."]

The Human Jungle: Exploring the Microbiome

View more presentations from cwzimmer

The ultimate case of TMI: Behold my bellybutton’s microbiome

Carl Zimmer — Tue, 25 Jan 2011 14:00:32 +0000

Why is ScienceOnline a meeting like no other? Because it’s the sort of meeting where a biologist named Rob Dunn can set up shop in the lobby to ask for samples of bellybutton shmutz that he can analyze for biological diversity. Not only is it a place where such a person will not be hustled out by security, but it’s a place where a whole bunch of people respond by grabbing Q-tips to do their part for science. And you can bet every last bit of your bellybutton lint that I was right up near the front of the line.

Ten days later, my sample is now thriving nicely on a Petri dish, awaiting a more detailed analysis of its DNA. And here are the rest of the samples from the meeting.

All I can say is, #974, what is going on in there?

Synthetic biology documentary in the making

Carl Zimmer — Wed, 19 Jan 2011 18:50:36 +0000

I don’t usually make pleas on the Loom. It doesn’t suit my journalistic nature, and if I make a plug for one cause, it may seem like I am cruelly indifferent to all the other good causes out there. In this case, I’ll just fall back on self-interest! A few weeks back two young film-makers, Sam Gaty and George Costakis, stopped by my house to interview me about synthetic biology for a documentary they’re making on the subject. They’ve been filming across the country for the movie, but it won’t finished in time for next year’s Sundance unless they can raise a little scratch to get them through the summer. Over at the fund-raising site Kickstarter, Gaty makes the case–and offers a clip about goats making spider silk. If this movie doesn’t get made, I end up on the cutting room floor. Oh, the humanity! (Actually, I think the film would be pretty cool without me–but judge for yourself.)

Losing our germs: My last podcast

Carl Zimmer — Thu, 30 Dec 2010 14:02:25 +0000

On my new podcast, I talk to Martin Blaser of New York University about Helicobacter pylori, best known as the microbe that causes ulcers. It’s also an ancient passenger in our stomachs, and has evolved a delicate balance with its human hosts. In fact, Blaser is worried by the disappearance of H. pylori from the modern world, thanks to antibiotics and hygiene. We may have to pay a price for its extinction, in the form of higher rates of asthma, esophageal cancer, and perhaps even obsesity. Check it out.

With this episode, the American Society for Microbiology is bringing the Meet the Scientist podcast series to a close. In the coming year, they’re going to be focusing their online efforts on some new projects you can look forward to on the Microbe World web site. (And they’ll be keeping all the episodes of Meet the Scientist on the site.) I’ve had a wonderful time over the past year hosting the podcast, and I’d like to thank all the scientists who shared their work with me and all the people at ASM who made this experience possible.

Of arsenic and aliens: What the critics said

Carl Zimmer — Wed, 08 Dec 2010 21:57:21 +0000

A lot of people are interested in my Slate story yesterday on the arsenic aliens. It’s still the most-read story of the site at the moment, Slashdot and others have linked to it, and I’m doing some more radio and maybe other media (details to come).

I think that what has gotten so much attention to the story is just how many scientists had such critical things to say. The verdict was not unanimous, but the majority was large. I was only able to quote a tiny bit from just a few of the scientists I communicated with, so I thought, for those who’d like to delve more deeply into this, that I’d post a list of everyone I spoke to, and, when possible, post their reactions. A lot of scientists replied to me by email or even attached word files where they went on at length. I put together a similar dossier for another biological controversy–the search for soft tissue in dinosaur fossils–and I think (or at least hope) that this sort of exercise can help further discussion.

Of course, as I and others have reported, the authors of the new paper claim that all this is entirely ...

Of Arsenic and Aliens

Carl Zimmer — Thu, 02 Dec 2010 19:00:15 +0000

Rumors have been swirling this week about a press conference NASA is starting right now. Some people have speculated that they’re going to announce evidence for life on another planet.

Well, not quite. Scientists have found a form of life that they claim bends the rules for life as we know it. But they didn’t need to go to another planet to find it. They just had to go to California.

The search for alien life has long been plagued by a philosophical question: what is life? Why is this so vexing? Well, let’s say that you’re hunting for change under your couch so that your four-year-old son can buy an ice cream cone from a truck that’s pulled up outside your house. Your son offers to help.

“What is change?” he asks.

“It’s…” You trail off, realizing that you’re about to get into a full-blown discussion of economics with a sugar-crazed four-year-old. So, instead, you open up your hand and show him a penny, a nickel, a dime. “It’s things like this.”

“Oh–okay!” your son says. He digs away happily. The two of you find lots of interesting things–paper clips, doll shoes, some sort ...

Is there nothing E. coli cannot do? The Sudoku edition

Carl Zimmer — Tue, 16 Nov 2010 19:44:17 +0000

Every now and then I take a moment at the Loom to marvel anew at the sophistication of a certain microbe. Today, I direct your attention to a report in New Scientist on E. coli that has been engineered to solve Sudoku puzzles. Frank Swain, the author, makes a good point: if E. coli is allowed to spread out the task among millions of individual microbes, it can tackle bigger problems. Let’s just hope that all the E. coli in our guts don’t figure this out on their own…

Time for a Da Vinci Upgrade [The Microbiome Image of the Day]

Carl Zimmer — Sun, 03 Oct 2010 18:42:51 +0000

I’ve been invited to give a few talks in the wake of my article in the New York Times on the microbiome, and so I’m prowling for beautiful images that drive home the fact that we are microbial rain forests, rather than sterile mammals. Below is my favorite image of the day.

It’s from a survey of microbes across people’s bodies, published last year in Science. The inner circle shows the major lineages of bacteria found in all the subjects in each part of the body, while the ring shows the ones found in some people but not others.

This picture was stuffed away in the supplementary materials for the paper, so I missed it the first time around. I’m glad I found it–it’s a new Vitruvian man for our microbiomic age.

Viruses invade the Tech Review 35

Carl Zimmer — Fri, 27 Aug 2010 20:11:02 +0000

I’ve contributed my first article to Technology Review–a short profile of Tim Lu of MIT, one of TR’s 35 innovators under 35. Lu is engineering viruses to attack biofilms–not just the ones that make us sick, but the ones that gum up factories and HVAC systems. Elegant and practical at the same time. Congratulations to all the winners!

The Microbiome Never Ceases to Amaze

Carl Zimmer — Tue, 20 Jul 2010 18:08:42 +0000

While I was away last week on vacation, the New York Times published my feature on the hidden jungle that each of us carries, known as the microbiome. I was very happy to come home to a lot of kind notes, tweets, and various communications about it. Yet I would never claim that my article delivered the Big Scoop on the subject. After all, we’ve known about the microbiome ever since Antonie Philips van Leeuwenhoek scraped his teeth over 300 years ago and discovered wee animacules in the scum. And as I wrote in my book Microcosm, Theodor Escherich discovered his eponymous Escherichia coli over a century ago in a quest to catalog the good microbes in babies’s guts, hoping to thereby identify the ones that were killing the children in droves. Even in the age of molecular biology, the microbiome has been well-chronicled. Jessica Snyder Sachs wrote a book back in 2007 called Good Germs, Bad Germs: Health and Survival in a Bacterial World that I heartily endorsed (and still do).

So why write a story now? That’s a question that science writers have to ponder a lot. Much of ...

Bonnie Bassler on Learning To Speak Microbe

Carl Zimmer — Thu, 01 Jul 2010 15:55:02 +0000

Princeton biologist Bonnie Bassler studies the chemical conversations bacteria use to work together and (sometimes) to make us sick. She joined me for my latest podcast, bringing her trademark enthusiasm and rare skill at telling a good scientific story. Check it out.

And if you crave more, check out her excellent TED lecture last year.