Category: Synthetic Biology

Yammerings: San Diego, New York, and TV

By Carl Zimmer | May 22, 2010 10:29 am

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 who are designing solar panels for camels, cook stoves that could save millions of lives, and other important inventions.

I may be asked to moderate other panels; if so, I’ll update this post accordingly. I will definitely be going to some other sessions as an audience member: the line-up looks great.

Thursday June 3, 8 pm and 10 pm: The Science Channel is airing, “Creating Synthetic Life,” a show about Craig Venter’s new hand-made cell. The producers asked me to talk about the research Craig Venter and his team have been carrying out for the past fifteen years on the path to creating artificial life. At the time they interviewed me (a few weeks ago), I knew there was some big news coming down the pike, but wasn’t able to talk about the particulars. So I expect that I’ll turn up on the show speaking in hazy generalities set in the future tense. Feel free to set your TV on mute when I show up. But based on the previews, I think the rest of the show is worth checking out.

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

By Carl Zimmer | May 21, 2010 1:51 pm

jamesjoyceThis 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, these watermarks cannot disrupt any essential protein-coding genes or stretches of DNA that are vital for switching genes on and off.

It turns out that the genome of the synthetic cell is not identical to its original, even if you ignore the watermarks. Mutations slipped into its sequence during its synthesis. Yet those mutations caused no harm to the microbe, presumably because they didn’t disrupt an essential function encoded in its DNA. Once the synthetic cell came to life and began to grow and divide, it copied its entire DNA, including Joyce’s words. But as lovely as those words may be, and as important as they may have been to the scientists during their experiment, they mean nothing to the microbe. Every time an organism replicates, each spot in its DNA has a tiny chance of mutating.

In the growing colony of synthetic cells, now numbering in the billions, it’s almost certain that Joyce’s watermark has already been defaced by a mutation. The bacteria that carry these degraded versions of Joyce presumably do not suffer from these mutations, since the watermarks don’t matter to them anyway. So they can keep replicating.By contrast, the DNA in the really useful parts of their genome is changing very little over the generations, thanks to selection.

Inserting Joyce into the first synthetic cell was certainly a kind gesture, but not a timeless memorial. It would be fascinating to go back to the synthetic cell colony in a few years and sequence Joyce’s line again. I’d bet that it won’t even be recognizable anymore.

The fate of Joyce’s DNA points up something important about this project. There have been lots of headlines over the past day about how the scientists who made this cell were playing God. Yet our power, even over synthetic cells, is limited. Once this new cell came into existence, it started changing through evolution, slipping away from its original form. In fact, evolution is the great enemy of all scientists who want to use synthetic biology to supply us with medicine, fuel, and other valuable things. Once they engineer a microbe, they start to lose control of their handiwork. Life takes its own course from there. It is life, ultimately, that recreates life from life.

CATEGORIZED UNDER: Evolution, Synthetic Biology

Synthetic Genome+Natural Cell=New Life?

By Carl Zimmer | May 20, 2010 12:55 pm

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 Venter

Update: The scientists are in a live press conference that started a 1 pm.

Infecting Big Think

By Carl Zimmer | January 25, 2010 12:48 am

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)

By Carl Zimmer | July 24, 2009 2:13 pm

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

The Worry of Biohacking: Closet Frankensteins or Kafkaesque Government?

By Carl Zimmer | May 12, 2009 1:15 pm

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

By Carl Zimmer | April 4, 2009 11:19 am

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?

By Carl Zimmer | January 17, 2009 12:19 pm

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

By Carl Zimmer | January 13, 2009 4:19 pm

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, will be figuring out how to design feedstock plants that would grow using fewer energy inputs and prove more robust in the field. The program’s also investigating pretreatments for plant-based cellulosic feedstocks. Their goal: to facilitate the ability of single-cell organisms to break these materials down by separating out and discarding the molecules that plants make to protect themselves from attack by microbes and fungi.

Such a multi-pronged approach looks to optimize all phases of biofuels production with no preconceived idea of which area is likely to offer the biggest payoff. And that, Chu said, “is why I’m so optimistic some real progress can be made.” And rapidly.

I expected this. Unfortunately, nobody asked Chu to estimate how much land would be required in Alabama and elsewhere to grow enough food to allow these hungry little bugs to make a significant contribution to our energy needs. Nor did anyone ask Chu to comment on the potential environmental impacts of harvesting so much plant matter, a topic I brought up recently in an article on the environmental effects of synthetic biology.

But, then again, I wonder how many senators even know what synthetic biology is. Perhaps it’s time they find out.

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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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