Author: gulley

The first synthetic biology company

Codon Devices may be the world’s first true synthetic biology company. What is synthetic biology? Is it artificial life? No. The name is misleading, but it really refers to the idea of bringing a design-based engineering approach to biology: take well-understood biological mechanisms (protein synthesis, biochemical pathways) and bend them to create new desired end products. What differentiates it from earlier biotech approaches is the unprecedented degree of biological understanding. Milk, for example, is economically useful and chemically complex, but milking a cow doesn’t require a degree in molecular biology. We merely harvest what nature presents. Suppose, however, you wanted that cow’s milk to contain large amounts of a specific vaccine. That would mean introducing altogether new biochemical pathways inside the cow: synthetic biology. If you could pull off a trick like that reliably, you’d be onto something big. That big something is what Codon Devices is shooting for. As Drew Endy, one of the founders, observes, “The scope of material I can work with is not limited to the set of things that we inherit from nature.”

Codon Devices has assembled a biotech Who’s Who list for its founders and advisors, along with money from storied venture capital firm Kleiner Perkins Caufield & Byers. So they’re off to a good start. In my googling, I came across this page about Codon from Drew Endy’s lab at MIT which was embedded in a wiki called the Endipedia. In the wiki, you can learn things like how to operate a microfluidic chemostat, and the favorite slogan to describe synthetic biology: “Making life better, one part at a time.” A blog entry from another researcher puts it this way: “Every time I mention my research to lay people I elicit two widely different responses: It’s either ‘Wow, that’s so cool!’ or ‘MY GOD, you’ll kill us all!’.”

Enter the Homogecene Epoch


Out of Eden: An Odyssey of Ecological Invasion

“I have seen the future, and it lives in Miami,” says Alan Burdick of Discover magazine. Burdick, author of the recently released book Out of Eden : An Odyssey of Ecological Invasion, excerpted parts of the book for Discover in May’s The Truth About Invasive Species. Unfortunately the entire article is unavailable online, but here’s the gist: don’t worry so much about the importation of alien species. You can kill off species by killing them (pollution, habitat destruction), but it’s hard to kill them simply by mixing them together. Burdick’s comment about Miami concerns the fact that south Florida is the epicenter of a vast unplanned experiment: what happens when you dump hundreds of exotic plant and animal species into an unsuspecting and perhaps fragile ecosystem? Conventional ecological wisdom has been to predict disaster, but as always, nature surprises.

Man is a very efficient biological mixing agent, churning together everything he touches, sometimes on purpose, sometimes not. The spectacular examples (hordes of hungry rabbits devouring Australia, proliferating Zebra mussels in the Great Lakes, bird-eradicating snakes on Guam) are just a fraction of the biological chaos launched during this great era of human commerce, which some scientist have dubbed the Homogecene. Burdick has two messages for us: there’s no stopping it, and it’s not as disruptive as originally suspected. The ecological chaos of the Homogecene is real, but it’s surprisingly hard to put your finger on what the bad part is.

The intrusion of judgmental, xenophobic language into invasion science is particularly interesting. The whole notion of invasive species and the pristine habitats they ravage is built on the flawed idea of ecological stasis, that there was once a Golden Age in which God’s happy creatures dwelt together in harmony. Burdick deconstructs the loaded language used by some of the scientists: opportunistic aliens attack and destroy hapless natives. Natives? Since when? We all came from somewhere, and we’re all headed someplace else. It’s only a matter of when you baseline your time horizon. I’ve been a native of this chair for a good half hour, but now it’s time for me to go invade the bedroom. Good night.

Medical tourists and stem cells

I recently read an article about the latest stem cell breakthrough in South Korea and it resonated with something I read about some months ago: medical tourism. Medical tourism is the practice of traveling to a cheap country with excellent doctors, typically India, in order to get uninsured medical procedures done. Tech Central Station and Yale Global both have good articles about the topic. The bottom line is that, if you’re uninsured for a given operation, it can cost as much as two thirds less to do it in India even when you take air travel and recuperation time into account. As both wealth and medical expenses continue to mount in the West, medical tourism is bound to take off. The trends all point in the right direction, and besides, isn’t your doctor already Indian? Or maybe she’s Chinese?

What struck me recently is how therapeutic stem cell research fits perfectly into this picture. You might travel to another country simply because a procedure is cheaper there, but you might do it because it is illegal and considered morally reprehensible where you come from. That is, if you have the means to save your child’s life through the magic of stem cells, then you you will fly to find them wherever they can be found.

House Republican leader Tom DeLay has made his position on stem cells clear. “An embryo,” he said, “is a person, a distinct internally directed, self-integrating human organism.” Korean researchers, however, don’t give a goddamn about Tom Delay’s opinion on stem cell research (aside from perhaps being grateful for the extra business he sends their way). And when, years from now, you need stem cells to treat your withering Parkinsonism, it will be cheap and pleasant to fly to Korea to get them. Think of all the morally upright American institutions you’ll fly over to get there. And I wouldn’t be at all surprised if, while you’re over there, you see an aging and palsied Tom Delay getting a stem cell boost of his own.

My handy Sudoku-solving applet

What is a Sudoku? A Sudoku (as explained here in the Wikipedia) is a number/logic puzzle that involves placing the numbers 1 through 9 on a 9-by-9 grid such that no number appears twice on the same row, column, or specially marked 3-by-3 box. Perhaps the real puzzle is why it should have become such a pop sensation in places from Hong Kong to New Zealand to the UK. Here is some coverage of the story from the BBC and Guardian. Nevertheless, a phenomenon it certainly is, and I am not one to shrink from hopping on the bandwagon.

I have been interested in brushing up on my Java skills, and this Sudoku craze has given something good to chew on. With that in mind, I have created Sudoku Satori, the Sudoku solving assistant. Try it out and let me know what you think. It’s in a pretty rudimentary state right now, but it sure works when it comes to solving these puzzles. It’s a simple matter to have the computer solve the puzzle for you. What this tool does is help you see the patterns so you can understand and solve the puzzle (hence the satori part).

Opportunity rover is free at last

For those of you who missed the recent drama on Mars, for something like a month, the rover named Opportunity has been stuck in the mud, or rather in a fine powdery rover-swallowing dust. So for five weeks it’s been sending back picture after pathetic picture like this. Fortunately it had already been on the planet for more than a year, so the mainstream press paid it almost no attention. But imagine what a drag it would have been to roll off the lander straight into soupy quicksand. At last, however, it’s out of the sand trap and on the move once more.

One of the entertaining things about the Mars rovers is that the latest pictures are posted immediately, so you can put together the story even before the JPL press release. So I had been going to the rover site regularly to see if they were making progress. Similarly, I was watching a few months ago as the Spirit rover struggled up a mountain looking for a view of the far side (also known as the view from Larry’s Lookout). Why did the bear go over the mountain? To see this. It’s not the most gorgeous picture, but it’s the first one that offered a glimpse of the world on the far side of the range. Every bear that went over a mountain knows that thrill. It was exciting to watch over the laboring rover’s shoulder, undistracted by public relations staff. We were given a virtual version of what cavers call “booty scooping”, which is to say, being the first to lay eyes on territory never before beheld by man.

Before we leave Mars for the day, take a look at this picture.
From orbit you can actually see the tracks left behind by Spirit as it climbs. Think about this: right now, there are two robots built by humans crawling around on the surface of Mars. Robots. On Mars.

That thought makes me happy.

Shirky’s ontology speech

Clay Shirky has posted the full text of his Ontology is Overrated talk. I mentioned this before, but now that the full text is up (including the illustrations from the PowerPoint presentation), it’s worth a read. Here is an example he brings out from the old Dewey Decimal System, which I sure remember from my school libraries growing up.

Dewey, 200: Religion
210 Natural theology
220 Bible
230 Christian theology
240 Christian moral & devotional theology
250 Christian orders & local church
260 Christian social theology
270 Christian church history
280 Christian sects & denominations
290 Other religions

The one sentence summary of the talk is the title of part two of his talk: “The Only Group That Can Categorize Everything Is Everybody.”

Nabeel’s Geoogle: where are your results?

Some blogs just go on and on about stuff that other people create, but occasionally you find a blog, like my friend Nabeel’s, where he doesn’t say too much, but every now and then he actually makes something. As it happens, Nabeel has stitched together a few services (most notably Google Maps) so that he can show you where the information you’re looking for is found. He calls it Geoogle. He starts with Yahoo to find a list of sites that match your search, then uses reverse domain lookup to find the servers address, followed by a web service that resolves addresses into latitude and longitude, which he can finally pour onto a lovely Google map. Got that? Not surprisingly, all the Boston hits are based in Boston. The string “Nabeel”, however, doesn’t return any pointing to the author of the site. His site may become so popular that he claims the top Nabeel spot after a while.

Well done, Nabeel!

Keyhole becomes Google Earth

Because I am a registered user of Keyhole‘s “Ultimate Interface to the Planet”, also known as Keyhole 2 LT, I was invited to beta test the upcoming release of Google Earth (Keyhole was purchased by Google last October). Damn, is it good! The new Google Earth is pretty much like the old Keyhole application, but it’s a little cleaner, it’s got some Google search and directions capability built into it, and most importantly, it’s got a vastly improved picture database. As a result it’s the most incredible atlas or map reference ever. Ever ever. You can fly around the Grand Canyon, zoom over the Cascades, or hover over your neighbor’s swimming pool. I have lost many hours of useful sleep playing with this insanely addictive program. Here are some ways to blow through the time:

  • Visit every place you ever lived.
  • Visit every place you ever went on vacation.
  • Visit places that you want to go on vacation or are simply curious about (Norwegian fjords, Victoria Falls, Sugarloaf Mountain).
  • Follow the paths of explorers like Lewis and Clark.

If you are the least bit of a map-o-phile, please beware: this is strong medicine. Your productivity is at risk. It is also more evidence of how quickly the world is changing. Encyclopedias bound as books are lost causes, but now atlases are equally doomed. Google Earth is far beyond anything else remotely like it. A description of the functionality is simple enough: Fly over the surface of the entire Earth in three dimensions at (almost) any altitude. But the experience defies description until you see it.

In case you were wondering about the name Keyhole, it was the name of a secret US satellite surveillance program. It’s easy to see why the whole enterprise is being re-branded Google Earth. First of all, they had to stick the Google name on it. But as a close second, who wants to be reminded just how much privacy they’ve already lost as peeping Tom satellites lift their latches and finger their blinds? My advice is to look up and smile from time to time, and for God’s sake don’t do anything incriminating out-of-doors.

Postcard secrets

My brother-in-law sent me this one today: PostSecret. The idea is to send an unsigned postcard with a secret on it. It’s an art project, and the cards the artist has put up so far are impressive little pieces of art in themselves. I have to guess he’s filtering out all the boring postcards on which someone has scrawled “I never flush public toilets.” In fact, the cards are so nice in some cases I start to wonder if the secrets are somewhat manufactured for effect. Still, there are some nice ones that have the ring of truth. I like the one that says

I miss feeling close to God.

… sounds like someone should consider moving back home to that Red State they grew up in. All this is reminiscent of the Apology Project, an installation by artist Allan Bridge that started in 1980 as an answering machine and an ad that encouraged people to call in and apologize for something bad they had done. That project grew and flourished for 15 years before the Bridge died. Here are some sample calls, including this dandy tit-for-tat tale from a Vietnam vet.

We all need to be absolved from time to time. Even so, nobody believes in the old cultural mechanisms that used to carry the load. These days, how many people would trust a priest with their secrets? It’s good to see innovation at work on the guilt frontier.