The Loom » Synthetic Biology

Flu Fighters

Carl Zimmer — Fri, 03 Feb 2012 07:26:23 +0000

Michael Osterholm, his face a pink-cheeked scowl, looked out across the table, beyond the packed room at the New York Academy of Sciences, and out through the windows. The New York Academy of Sciences is housed on the fortieth floor of 7 World Trade Center, and their endless bank of windows affords a staggering view of Manhattan, Brooklyn, and New Jersey. One reason that its view is so magnificent is that there’s a huge gap in the skyline–and a huge gouge in the ground–where the Twin Towers once stood.

Osterholm had come here from Minnesota, where he runs a research center for infections diseases and terrorism, to talk Thursday night about the threat of a new kind of flu sitting in labs in the Netherlands and Wisconsin. In nature, it’s a flu that spreads easily between birds but doesn’t travel well from human to human. The Dutch and Wisconsin scientists had found ways to get this bird flu, known as H5N1, to move between ferrets. For Osterholm, ferrets were uncomfortably close to humans on the evolutionary tree. And so he, along with other members of an advisory board, issued a recommendation in December that key information in the papers about ...

Life with a capital L? (Like Zimmer with a capital Z?)

Carl Zimmer — Wed, 11 Jan 2012 19:39:42 +0000

Over on Facebook, David Hillis, an evolutionary biologist at the University of Texas, took up my question as to whether anyone can define life in three words. His short answer was no, but his long answer, which I’ve stitched together here from a series of comments he wrote, was very interesting (links are mine):

Like all historical entities (including other biological taxa), it is only sensible to “define” Life ostensively (by pointing to it, noting when and where it began, and following its lineages from there) rather than intensionally (using a list of characteristics). This applies to the taxon we call Life (hence capitalized, as a formal name). You could define a class concept called life (not a formal taxon), but then that concept would clearly differ from person to person (whereas it is much less problematic to note examples of the taxon Life). So, I’d say that I can point to and circumscribe Life, and that it the appropriate way to “define” any biological taxon. A list of its unique characteristics is then a diagnosis, rather than a definition. So, I’d argue that any ...

Can you define life in three words?

Carl Zimmer — Wed, 11 Jan 2012 14:59:38 +0000

We are all sure we know what life is, but if you try to actually define it, things get tricky fast. I wrote a feature about the scientific struggle to define life in 2007 for Seed, and I’ve been keeping tabs on the evolution of this metaphysical quandary ever since. I was particularly intrigued to discover recently that one scientist thinks he can define life–and do so in just three words. I’ve written an essay about his short and sweet definition for the web magazine Txchnologist. Check it out.

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 ...

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.

Copyright law meets synthetic life meets James Joyce

Carl Zimmer — Tue, 15 Mar 2011 17:37:53 +0000

Last year I wrote about how Craig Venter and his colleagues had inscribed a passage from James Joyce into the genome of a synthetic microbe. The line, “To live, to err, to fall, to triumph, to recreate life out of life,” was certainly apropos, but it was also ironic, since it is now being defaced as Venter’s microbes multiply and mutate.

Turns out there’s an even weirder twist on this story. Reporting from SXSW, David Ewalt writes about a talk Venter just gave. Venter recounted how, after the news of the synthetic microbe hit, he got a cease-and-desist letter from the Joyce estate. Apparently, the estate claimed he should have asked permission before copying the language. Venter claimed fair use.

Man, do I wish this would go to court! Imagine the legal arguments. I wonder what would happen if the court found in the Joyce estate’s favor. Would Venter have to pay for every time his microbes multiplied? Millions of little acts of copyright infringement?

[Update: Looks like it wasn't actually a cease-and-desist letter the Joyce estate sent--more an expression of disappointment. Ah, life's grand game of telephone. Joyce would have loved it. ...

DIY Tumors

Carl Zimmer — Sun, 19 Dec 2010 17:51:27 +0000

Last month I wrote a piece for the New York Times about what ten scientists are looking forward to in 2011. One of the scientists, Rob Carlson, saw garage stem-cell research in our near future:

“It seems pretty likely within this year someone will show how to go from an adult peripheral blood draw to pluripotent stem cells. It means anyone who wants to try to make stem cells will be able to give it a whirl.”

Carlson took to his own blog to write at more length about what exactly he meant. For one thing, stem cell biohackers may want to think twice before sticking stem cells in their own bodies. They could end up with what Carlson calls DIY tumors. Check it out.

Up for Discussion: Neanderthals and Synthetic Genomes

Carl Zimmer — Sat, 29 May 2010 14:47:22 +0000

Two of my favorite bloggers, John Hawks and Christina Agapakis, talk about the big genome news of recent weeks on Bloggingheads. Gets technical, but in a good way!

Yammerings: San Diego, New York, and TV

Carl Zimmer — Sat, 22 May 2010 14:29:55 +0000

I’ve got some public face time coming up:

Tuesday, May 25, 5:30 pm: In San Diego, I’ll be talking at the American Society for Microbiology. I was asked to speak at the President’s Forum, “Tell the Story of Science.” My own talk is, “Newspapers, Blogs, And Other Vectors: Infecting Minds With Science In the Age of New Media.”

Random House will be kindly providing copies of Microcosm for sale at the meeting. I will spend some time signing them all when I get to the conference Monday. The books will be available at the American Society for Microbiology Press Booth. (I’ll update this post when I know exactly where the booth is located.)

I’ll also plan on hanging out at the booth at some point on Wednesday, hoping that I can meet face to face with some of the Loom’s microbiologist readers. (Again, I’ll update this post about exactly when I’ll be there once I get to the meeting.)

Thursday, June 3, 7 pm: The World Science Festival returns to New York for its third year, and I’m delighted to enter my third year of moderating panels for them. I’ll be part of “Modern MacGyvers,” a gathering of innovative thinkers ...

James Joyce’s Words Come To Life, And Are Promptly Desecrated

Carl Zimmer — Fri, 21 May 2010 17:51:11 +0000

This old English major’s heart is warmed by the news that the new synthetic cell carries a line from James Joyce, inscribed in its DNA: “To live, to err, to fall, to triumph, to recreate life out of life.”

What would Joyce have thought if someone had told him that one day the synthesized genome of a goat pathogen would carry his words? I would hope that whoever told him would make sure that he did not think this moment marked his literary immortality. In fact, his deathless prose is probably being desecrated by the relentless erosion of evolution right now.

The scientists who produced the new synthetic cell copied the genome of a microbe, letter for letter, and then inserted the synthetic version into a host cell. To determine that their experiment worked, they needed a way to tell the genomes of their synthetic cells from the natural genomes that were their model. So they inserted “watermarks” into the artificial genome. These sequences of DNA (which spelled out the work of Joyce and others through the genetic code) sit in non-coding regions of the microbe’s DNA. As a result, ...

Synthetic Genome+Natural Cell=New Life?

Carl Zimmer — Thu, 20 May 2010 16:55:57 +0000

Craig Venter has taken yet another step towards his goal of creating synthetic life forms. He’s synthesized the genome of a microbe and then implanted that piece of DNA into a DNA-free cell of another species. And that…that thing…can grow and divide. It’s hard to say whether this is “life from scratch,” because the boundary between such a thing and ordinary life (and non-life) is actually blurry. For example, you could say that this is still a nature hybrid, because its DNA is based on the sequence of an existing species of bacteria. If Venter made up a sequence from scratch, maybe we’d have crossed to a new terrain.

Anyway–this news just hit the wires thanks to an embargo break, so I don’t have time to go into more detail. Joe Palca at NPR has posted his article on the subject. For background, please check out these stories I’ve written about this general area of research:

Tinker, Tailor: Can Venter Stitch Together A Genome From Scratch?

The Meaning of Life

The Six Most Important Experiments In The World

Artificial Life? Old News.

The High-Tech Search For A Cleaner Biofuel Alternative

On the Origin of Tomorrow

My Bloggingheads interview with ...

Infecting Big Think

Carl Zimmer — Mon, 25 Jan 2010 05:48:15 +0000

Here’s a talk I just gave on Big Think–about viruses, synthetic biology, and tapeworms that carry my name. The sound quality isn’t as good as I’d like, but I hope the words make up for it.

Is There Nothing E. Coli Cannot Do? (Redux)

Carl Zimmer — Fri, 24 Jul 2009 18:13:26 +0000

Scientists tinker with my favorite bug so that it can solve mathematical puzzles.

The Worry of Biohacking: Closet Frankensteins or Kafkaesque Government?

Carl Zimmer — Tue, 12 May 2009 17:15:23 +0000

There’s a piece in the Wall Street Journal today about biohacking: people experimenting with genetically engineered microbes and viruses at home. It tries to inject anxiety into your brain right from the start, with a headline, “In Attics and Closets, ‘Biohackers’ Discover Their Inner Frankenstein–Using Mail-Order DNA and Iguana Heaters, Hobbyists Brew New Life Forms; Is It Risky?”

I was surprised, however, to discover that the reporter does not mention the one time that somebody actually got arrested and charged with biohacking. At last year’s World Science Festival, I moderated a panel with the artist Steven Kurtz, who had just finished navigating a Kafkaesque experience with the FBI for having a PCR machine and some harmless soil bacteria in his house. While we certainly need protection against bioterrorism and risky experiments, we definitely do not need the sort of ignorance of basic biology that was on display in the Kurtz affair.

Eyebeam, the New York gallery that hosted the panel, later posted the talk in several parts on YouTube. I’ve embedded them below. Kurtz has a sad and surreal story to tell.

DNA in the Mail and the Future of Life

Carl Zimmer — Sat, 04 Apr 2009 15:19:37 +0000

Over on bloggingheads, I talk with Rob Carlson, one of the most perceptive thinkers around when it comes to pondering where biotechnology is headed. Until his new book comes out in the fall, this will have to tide us over….

Mooney and Me: The War Is Over?

Carl Zimmer — Sat, 17 Jan 2009 16:19:39 +0000

Over at Bloggingheads, Chris Mooney declares the War on Science over, I foresee different sorts of conflicts, and together we try to predict the future of science in 2009.

Secretary of Synthetic Biology Indeed

Carl Zimmer — Tue, 13 Jan 2009 20:19:53 +0000

Over at Science News, Janet Raloff has a report about Steven Chu’s appearance earlier today before the Senate for his nomination to be Secretary of Energy. It sounds like he really perked up when asked about biofuels from synthetic biology:

Chu explained that the two-year-old program is striving to develop fourth-generation biofuels. To date, researchers at the lab have “trained” bacteria and yeast to take simple sugars and produce “not ethanol, but gasoline-like substitutes, diesel-fuel substitutes and jet [fuel] substitutes.” He says a cadre of “brilliant” scientists who had previously spent most of their careers in basic research is now “very focused on making this technology commercially viable.”

Asked about what type of plant material would be used — since Lincoln was hoping it might be grown in Arkansas — Chu perked up and chuckled: “Now we’re getting to science. I love this!”

Currently, no particular plants are being focused on, but they could include anything from algae and corn stover to grasses and lumber-mill dust and scrap. So Chu reassured Lincoln that her state grows suitable raw materials.

But the real key to making these next-gen biofuels, Chu says, ...