Category: Biology

Synthetic life is much in the news these days. In the last month there has been a Discover article on simulated evolution, a Popular Science article (Life Built to Order) on the synthetic life efforts of Steen Rasmussen and his colleagues in Los Alamos, and a cover story in New Scientist on artificial life. The articles are thoughtful and the work is credible. How surprised will you be if one of these teams pulls it off? What do you suppose the Vatican will have to say about it?

If, as some biologists speculate, life evolved on Earth within 50,000 years of cooling down, I don’t doubt we’ll be able to coax the same trick into happening within our lifetime.

If you are occasionally dragged down by the thought that religious conservatives are pushing creationism into the science curriculum of our public schools, it may provide some (mostly comic) relief to hear about religion masquerading as science in countries far away from our own. In the recent Wired News story Cattle, the Research Catalyst, we learn that Hindu fundamentalists have been busy researching the miraculous properties of cow waste. For example, “tests have shown that distemper made out of cow dung and spread over walls and roofs can block nuclear radiation.” Another researcher concludes that “cows’ urine can cure cancer, renal failure, arthritis and a lot of other ailments.”

I mention this not to laugh so much as shrug. It’s the same all over the world. The oldest stories are slowest to change because they are old. We would twist the world into a pretzel to make it match our convictions rather than see what is in front of us. The Cobb County biology book stickers say “This material should be approached with an open mind.” Open eyes help too.

EE Times – Experts worry that synthetic biology may spawn biohackers

I’m off for a vacation this week, but here’s a good parting shot: EETimes (that is, Electrical Engineering Times) covered a biology conference last week. That must be a first. What conference was it? Synthetic Biology 1.0. Why does EETimes care? Here’s what they have to say.

A small group of about 300 attended the Synthetic Biology 1.0 conference here on the edge of the Massachussets Institute of Technology’s campus. Biologists from a variety of subdisciplines mixed with AI experts, circuit designers and chemical engineers along with a small clutch of researchers from the biotech industry. It seemed remarkable that this group has a common language, and one that an uninitiated EE would find strangely familiar.

Here’s the full article: Conference kicks off synthetic bio revolution. The electrical engineers and biologists are dancing together… the penultimate convergence is upon us. The last convergence will be when the poets, priests, and philosophers join in.

There’s more good information at http://syntheticbiology.org/.

I’ve talked about synthetic biology here before, but only in the context of adding new functionality to organisms that are already alive. Science writer Carl Zimmer has written an article for the June 2004 issue of Discover magazine that addresses a far more ambitious approach to synthetic biology: synthesizing a new life form altogether. See
“What Came Before DNA?” at CarlZimmer.com.

Improbable as it sounds, researchers are attempting to bootstrap life using as a roadmap our best guess as to how life got started in the first place. The idea is that, before DNA was used to store genetic information, and before proteins were used to perform their enzymatic magic, RNA was able to fill both roles. This means that instead of having to account for the mysterious arrival of three different cooperating types of molecules (DNA, RNA, proteins), we have only to account for the mysterious arrival of RNA. This latter scenario is preferred by William of Ockham.

Starting with this concept, researchers have been systematically evolving RNA molecules to fill various roles required in a living organism, and they’re having remarkable success. Transfer RNA (tRNA) already has my vote as coolest molecule of all time. Add to that microRNA, siRNA, RNAi, and others and it’s a safe bet that a lot of biology in the next few years is going to revolve around this remarkable molecule. There’s a lot of life in the old girl yet.

Synthetic biology is the subject of a feature story in Scientific American. Happily, it’s being made available for free on their website: Synthetic Life. They get up close and personal with synthetic biology rock stars Ron Weiss (Princeton) and Drew Endy (MIT). The article has a good summary quote about synthetic biology.

This nascent field has three major goals: One, learn about life by building it, rather than by tearing it apart. Two, make genetic engineering worthy of its name–a discipline that continuously improves by standardizing its previous creations and recombining them to make new and more sophisticated systems. And three, stretch the boundaries of life and of machines until the two overlap to yield truly programmable organisms.

If you want to see what synthetic biology “looks like”, look at this project page for one of the MIT classes that’s designing an organism. It looks like a science fiction mishmash of electrical engineering and biology, but it’s a real DNA “circuit”.

I find this extremely exciting, but it doesn’t surprise me that it gives a lot of people the creeps. However you feel about it now, you’re going to have to get used to it, because it’s the leading edge of something really big. Sophocles once said that nothing vast enters the life of mortals without a curse. But he’s been dead for 2400 years, so how smart could he be?

Lenticulars, also known as “winkies”, are those goofy quasi-3D plastic gimcracks that are good for two-step animations showing things like Jesus looking up to heaven or dancing girls wiggling their hips. I never thought they’d be useful for anything but cheesy gimmicks. But they turn out to have numerous cheese-free applications in the modern world. For one thing, you can now buy a Sharp laptop with a three dimensional lenticular display. And then there’s this nifty lenticular map of Manhattan in which three different maps come together in one virtuous unit: Urban Mapping. Make sure and run the Flash demo to see how it works.

Sure you sequenced the human genome, Craig Venter, but what have you done for us lately? Plenty, as it turns out. Venter (and some of his close friends) have figured out how to assemble (relatively) long sequences of wholly synthesized DNA, enough to make a complete virus, in fact. This is one step closer to the “DNA Printer” where you just specify the sequence and squirt out a chromosome. Here is the story in New Scientist. This somewhat more technical version from GNN is more revealing: Synthetic Genome Has Potential Value for Energy and Environment.

The article talks about energy because Venter’s plan is to make a kind of wacky tobacky that can spew hydrogen gas. Which is pretty nifty stuff so far as it goes, but you don’t have to be too clever to see this has other implications: “If we can get them little bugs to make hydrogen gas, I wonder what else we can make ’em do?”

Still, it’s fascinating stuff, and the ride is just starting. A living cell is already a sophisticated information processing system. Once we figure out how to communicate with it (through techniques like the ones Venter is working on), it will cough up its secrets with amazing speed.

In my last entry, I mentioned that you can print out DNA for viruses and genetic programs. You can, for example, order genes printed to your specifications at Blue Heron Biotechnology. But you can also print out large 3-D models of molecules, avoiding the hassle of those crappy kits from organic chemistry class. Through the magic of rapid prototyping 3-d printing capability, you can make models of an ever-increasing array of interesting molecules.

This is a picture of my favorite molecule: transfer RNA. I like it so much, I had the people at 3-D Molecular Designs custom-build me a model. You can get your own for $30 these days. I paid a lot more than that because (A) I got mine last year and (B) because I asked for a particular molecule: 1yfg yeast initiator tRNA. You can read what David Goodsell said about tRNA in his Molecule of the Month column. But if you’re interested in understanding the meaning of life and how it relates to tRNA, read my new essay on the topic: The pen of Thoth and the meaning of life.