I recently read a fascinating article about synthetic biology by Michael Specter, “A Life of its Own,” in the New Yorker of Sept 28, 2009. The article is online here.

As old-timers may remember there was a fad for so-called artificial life in the 1980s. Artificial life was largely about computer programs that emulated living things—such as ant colonies, flocks of birds, or growing plants. You can see my Artificial Life Lab book for more information about old-school A-Life.

Synthetic biology is different, it’s about building slippery wetware entities that might live in the real world.

Just for my own convenience, I’ll begin by posting some links to things mentioned in Specter’s article. He talks about MIT researcher Tom Knight’s BioBricks project, which involves developing a kind of open source wetware protocol so that people can fairly easily “snap together” DNA molecules of their own designs.

Knight has also posted some of his stuff on the startling site, OpenWetWare, a vast, loose, and baggy site whose 10,000+ webpages are collaboratively maintained by some 6,000+ people involved in, or interested in biotech , genomics, synthetic biology, wetware engineering, or whatever you want to call it. The idea is, I think, that it’s actually safer and more socially useful to have wetware engineering tools be open to all than to entrust them to secretive government groups.

Drew Endy, formerly at MIT but now at Stanford, is another player in the open source new goo thang. Here’s a Wikipdia page on Endy with lots more links. Specter bagged some good quotes from Endy. “My guess is that our ultimate solution to the crisis of health-care costs will be to redesign ourselves so that we don’t have so many problems to deal with.”

This reminds me of a story by Samuel Delany where people readily eat food they find on the ground—as their bodies are bioengineered to resist invasive viruses and bacteria. Actually, I don’t think this could ever work. As I’ll discuss some more below, Nature is an endlessly cunning and resourceful hive mind, and no matter how we might amp up our immune defenses, those seething critters out there will find a way to zap us. Like spammers getting around spam filters.

This said, it’s obviously the case that we ought to be able to ameliorate certain kinds of medical problems with gene tweaks.

And of course cosmetic changes will be huge. “Do these new genes make my butt look too fat?”

One of the big carrots which the synthetic biologists hold out is that we ought to be able to design some kind of microorganism that eats inexpensive crud and generates energy in some usable form or another. This does seem more feasible and less risky than nuclear fusion. Specter quotes the genomic businessman Juan Enriquez : “We’re going to start domesticating bacteria to process stuff inside enclosed reactors to produce energy in a far more clean and efficient manner. This is just the beginning of being able to program life.”

In May 31st, 2007, I wrote a light-hearted sidebar essay for the online Newsweek magazine about synthetic biology. I can’t find that essay online anymore, so I’ll just reprint it here, with this notice regarding the text (but not the images): Copyright 2007 by Newsweek, Inc. All rights reserved. Reprinted by permission.

The illustrations I’m including are drawings of mine that appeared in my novel, Saucer Wisdom, which also includes some discussion of synthetic biology.

The synthetic biology approach is onto something big—a new version of nanotechnology, which is the craft of manufacturing things at the molecular scale. Synthetic biology’s plan is to capitalize on the fact that biology is already doing molecular fabrication all the time. What might happen if we repurpose biology to our own ends?

One big worry is what nanotechnologists call the “gray-goo problem.” What’s to stop a particularly virulent synthetic organism from eating everything on earth? My guess is that this could never happen. Every existing plant, animal, fungus and protozoan already aspires to world domination. There’s nothing more ruthless than viruses and bacteria—and they’ve been practicing for a very long time.

The fact that the synthetic organisms are likely to have simplified Tinkertoy DNA doesn’t necessarily mean they’re going to be faster and better. It’s more likely that they’ll be dumber and less adaptable. I have a mental image of germ-size MIT nerds putting on gangsta clothes and venturing into alleys to try some rough stuff. And then they meet up with the homies who’ve been keeping it real for a billion years or so.

Now let’s look at the upside. Donning the funhouse spectacles of science fiction, I envision a wide range of biotech goodies.

Every child is likely to want a pet dinosaur, and this will be easily managed once the online Phido Pet Construction Kit is up and running. Of course, if you prefer something cuddly, you can design a special dog with red polka dots.

Rather than mining for ore, why not let plants use their roots to extract minerals from the ground? Sow a handful of Knife Plant grain over a dumpsite, and before long you’ll have what looks like corn—but with a cob-handled steel knife in each ear.

Why bother building houses when you can get a Giga Gourd seed? The seed is the size of a pizza and grows very fast. Push it into wet, fertile ground and stand back. In a few days you’ll have a big, hollow home with plumbing and wiring grown right into the walls, which come complete with transparent window patches.

Of course, people will want to start tweaking their own bodies. Initially we’ll go for enhanced health, strength and mental stability, perhaps accelerating the pace of evolution in a benign way.

But, feckless creatures that we are, we may cast caution to the winds. Why would starlets settle for breast implants when they can grow supplementary mammaries? Hipsters will install living tattoo colonies of algae under their skin. Punk rockers can get a shocking dog-collar effect by grafting on a spiky necklace of extra fingers with colored nails. Or what about giving one of your fingers a treelike architecture? Work ten two-way branchings into each tapering fingerlet of this special finger, and you’ll have a thousand or so fingertips, with the fine touch of a sea anemone.

It’s easy to imagine grafting an electric eel’s electromagnetic sensitivity into our brains so we can pick up wireless signals. There’d have to be an off switch, of course, but the net effect could be amazing. We’d have true telepathy, and the ability to form group minds.

As the technology of brain-to-brain contact improved, you’d no longer need to send someone every detail of a plan, a memory or a design. Instead you could send something like a mental Web link, allowing those you invite to simply view your thoughts right in your own mind.

The biggest problem with manned spaceflight is the immense mass of the requisite life-support systems and radiation shielding. What if the truly determined astronauts could transform themselves into tough, spindle-shaped pods that could sail endlessly through empty space, nourishing themselves with solar radiation and directing their journey with the exhalations of their ion jets?

One last thought. Suppose it were possible to encode a person’s memory and personality into a single, very large, DNA-like molecule. Now suppose that someone turns himself into a viral disease that other people can catch. If I were you—sneeze—oh, wait, I guess I am. Are we completely agreed?

Today it’s raining hard for the first time in about seven months. What we call a “storm” here in the Bay Area.

So naturally this morning I was on the freeways, driving up to the Executive Briefing Center at HP between Sunnyvale and Palo Alto. I was there to give a talk for the Institute of the Future, who were hosting a meeting on the theme, “When Everything is Programmable.” I’ve written about this line of thought in my book The Lifebox, the Seashell and the Soul—and of course it’s something I’ve discussed in my SF as well.

I had a PowerPoint presentation ready for my talk, with the title, “Everything is a Computation.” You can see the slides as a PDF file online. I’ve learned always to post my slides in advance like this, as so often it’s hard to get your laptop working amid the chaos of the rostrum.

My message was that, yes, it’s useful to think of the world as being made up of a lot of interacting computations: physics, biology, psychology, and society. And, yes, if we see the unfolding stream of events as made of computations we can sometimes get a better grasp on how to tweak what’s coming down. But—and this is, I would say, the key fact—naturally occurring computations are unpredictable.

Natural events are orderly enough not to be random, but they’re unpredictable in the sense that there aren’t any shortcut methods that reliably predict what will happen over any longer period of time.

That’s why weather forecasts are only good for a few days out. That’s why technical analysts don’t always win in the stock market. That’s why the legislatures can’t ever really fix things the way they’d like. And that’s why no product design is effective for more than a couple of years.

This isn’t just my crackpot opinion, by the way, it’s a formal argument from computer science. In a nutshell: natural processes are complex enough to be universal computations, and, due to the unsolvability of the halting problem, we know there’s no simple algorithm to predict the behavior of a universal computation on an arbitrary input.

What to do? Stay alert, remember that you’ll be wrong pretty soon, and be ready to change. Trust your instincts…you’ll always be smarter than your machines.

I’ve been painting pretty much this week, working on a large (40 by 30 inch) acrylic painting that I started at Four Mile Beach north of Santa Cruz about three weeks ago. That day I trekked down there from the parking lot with my painter friend Vernon and got the canvas covered with a light layer—when I’m en plein air, it’s all about getting the composition blocked out, and finding some of the colors, although often, back home, I’ll dial up the colors to match my memories and my aesthetics, which tend to be brighter and more saturated than reality.

[Click to see a larger version.]

It was kind of a big canvas to carry to the beach. A certain amount of blowing sand got stuck to the paint, which is nice, as it adds physical texture and a you-are-there quality. When my mother painted en plein air, she’d often bring home a little baggie of dirt or sand and mix it in with her paint.

I’m calling this one Surf Pilgrim, because there’s a surfer in the foreground with a determined look about him. As usual, you can find out more about my paintings on my Paintings page.

[This little guy showed up to watch me paint. I think he’s called a stinkbug.]

I think I saw the title phrase “Surf Pilgrims” phrase as a graffito on the sea wall near Ocean Beach in San Francisco about fifteen years ago, maybe it was spelled “Serf Pilgrims” there. And then Marc Laidlaw and I used a variation of the phrase, “Stoke Pilgrims,” as the name of a gang of surfers in an SF surfing story, “Probability Pipeline.”

[Frank’s patio.]

We were in Madison, Wisconsin, recently visiting our daughter Georgia and her family. While we there we toured Taliesin, the farmland estate where Frank Lloyd Wright had a house and a school.

[Bassist at a Madison street festival celebrating the hemp harvest.]

It’s been hard to really get cranking with the writing after the trip—times like that, it’s nice to be able to paint and get away from the computer. I’ve just been chipping away at some little things on Jim and the Flims, like fixes and a nice rewrite of my plot outline. I have a pretty good idea of what happens in the next two chapters. I’m hoping to see the Muse this coming week.

[Frank’s fountain. He had a knack for getting a nice standing wave pattern going, you see the same thing in his “Martian Embassy” building in Marin County. He died broke, having spent a lot of money on Asian art.]

I’m not sure if Surf Pilgrim has anything to do with Jim and the Flims—but you never know. I do have some scenes with surfers in the planned “Surf Zombies” chapter that’s coming up later on. And Jim might possibly encounter some beings like surfers when he sets out across the Helaven Sea. The Buddha on a standing wave…

Man, when was the last time I saw a good movie in the theaters? We do like to get out, and there’s a movie house within walking distance from our house, so we hit the theater fairly often. It’s potentially more fun than watching a rental at home.

But…Matt Damon in Informant! — ugh! I’ve always found the Matt to be physically repellent, and to see him play an unbalanced, lying sleaze-bag, wearing a kids-Halloween-costume mustache, in a seemingly endless series of scenes set in beige plastic corporate offices — ugh! The movie is so repetetive and slowly paced that, while watching it, I started wondering if my watch had stopped.

Was that movie with the stupid title even worse? I think so. 100 days of {Dullness}? Oh, wait (500) Days of Summer. Take a not-quite-love story between two completely uninteresting people and shuffle the order of the scenes. Who cares? Over and over the screenwriters have the opportunity to convey some personality and spark during this couple’s conversations—over and over they don’t even bother to try.

But, ah, wait, a ray of joy — District 9. (Are we in a period where most movies will have numbers in the titles?) The best SF movie I’ve seen since Terminator 1. (Well, make that “The best SF movie that my deliquescing brain can remember, off the cuff, after ten seconds thought, having seen since T1.” Maybe Blade Runner was better, except for the dull and gratiuitous violence at the end, so contrary to the spirit of Phil Dick. But I digress.)

The weapons in District 9 kick butt, it’s great how grotty the guns are, with those wild fractal sparks, and that you need a funky alien hand to shoot one. And, as John Shirley remarked to me, it’s quite a feat for a director to get the audience rooting for a gang of aliens who are tearing apart a human and eating him. A sensitive treatment of the difficult topic of prejudice! The main actor is great too, so weaselly and frantic and nervous and, in the end, courageous. Wonderful giant UFO, too. And the Nigerian gangsters are a trip. Bring on District 10!

Rental movies: Attack of the 50 Foot Woman! Memorably cheap special effects that are nothing like the famous poster for this film. The errant husband is hanging out in a back lot saloon with a wonderfully nasty girlfriend (Yvette Vickers, in the role of her life), and a woman’s offscreen voice yells hubby’s name very loud, “Harry!” The saloon’s doors swing open, and in slides—a stuffed cloth hand the size of a cow. “It’s your wife, Harry!” cries Yvette.

It’s so early a movie that they didn’t even have the words “flying saucer” or “UFO.” They keep talking about “the satellite”.

And now for some books…

I recently finished reading Charles Stross’s Saturn’s Children. I read slowly at first, rationing it, but wolfed down the second half in one late-running session of bedtime reading. What a feast! Really the most enjoyable SF novel I’ve read since…I don’t know, since Stross’s Accelerando—which set me on the path to writing my novel Postsingular.

I guess to some extent I’m a pre-selected audience for Saturn’s Children, in that I grew up reading Heinlein and Asimov, and Saturn’s Children is in some ways a take-off on that mode, carried out very wittily and consciously, so that, for me, the book felt like a nut-filled holiday cake stuffed with funny twists and jokes and references.

There’s a joke about the robots believing that the “Creators” (the now extinct humans) lived with Tyrannosaur dinosaurs during the “antediluvian” times—they’re getting their historical info from fundamentalist tracts they’ve unearthed.

The statue of the Maltese falcon appears, described as a “model of an extinct airborne replicator that preyed on other similar avioforms.” And the robots wonder about public bathrooms: “I keep moving, looking for an unoccupied shrine—one of those curious rooms of repose that our Creators installed in all public places.”

There’s some beautiful prose in there, too. “Jupiter is a gibbous streaky horror…while the sun, a shrunken glaring button…”

In recent years, I’d almost forgotten about the old-school SF notion of Earth spawning a civilization that spans our solar system. Stross has his his robot lead character move her physical body around with rocket ship rides, and she carries around her ancestors’ personalities in a “graveyard” box of chips. How quaint that now seems! I guess this is what they call Space Opera.

Obviously the author of Accelerando knows that it might be more plausible that robots would simply email their personalities from world to world, and store their data in a Cloud. But, given that the game is to stay in the mental mode of a Heinlein or Asimov novel, the science makes perfect sense, and I was exhilarated to swim around in it once again. Real machines you can get your hands on!

Wanting more Stross now, I’ve been reading The Jennifer Morgue this week, but it’s tweaked into a different channel—it’s a parody James Bond novel in which Lovecraftian magic plays a role. For the Strossian metahumor, the characters are aware that it’s a James Bond novel, in fact some of them have [spoiler alert] cast a spell so as to force the main character to walk the Hero’s Path of being like good old 007. And there’s yet another level…the book itself is a spell that magicks the reader into being James Bond.

The Jennifer Morgue doesn’t quite scratch my itch in the same way that Saturn’s Children did—but it’s hypnotic fun. Like in Saturn’s Children, the plot is wonderfully intricate. It’s always a joy to find out more about Lovecraft’s monsters. Like reading juicy pop gossip about your favorite stars. “Brad Leaves Angela!” “Chthonian Bones Deep One!”

I have to say that the ending of The Jennifer Morgue is a freaking blast, an insane rising arc of action…like taking off in an ejector seat at Mach 3…a final rush which was, I now recall, characteristic of the Bond novels. And, actually there IS a literal ejector involved here, only it ejects a whole car. Carefully the bonfire wood is stacked…and then WHOOOMP! Stross is a demon, an evil genius, a wicked man.

He has an interesting essay about the cultural meaning of James Bond at the back of the book, and he points out that, truth be told, SPECTRE has won out in the modern world. The biggest criminals of all are never brought to justice—they escape by controlling legislatures, by being “too big to fail,” and by manipulating the financial markets…just like Stavros Blofield might have wanted to do.

On the high-lit front, I just read Nicholson Baker’s, The Anthologist—a really terrific book about a down-at-the-heels poet who’s trying to get it together to write a longish introduction for an anthology of rhyming poetry. It’s written in the first person, with the poet going on and on about his theories on rhyme and meter, larded with gossip about poets of the past, and with the gossamer thread of a love story running through it.

The big deal in The Anthologist is the voice and the poetry of the prose. Here the narrator is describing a book of poems by John Ashbery that he just bought in an (unrealistically) well-stocked airport book store, “…although the poems themselves weren’t heartbreakers, the book made me think of the sound of someone closing the door of a well-cared-for pale blue Infiniti on a late-summer evening in the gravel overflow parking lot of a beach hotel that had once been painted by Gretchen Dow Simpson.”

I love how that description unfolds and unpacks and runs on. To really appreciate it, you have to know that Gretchen Dow Simpson’s paintings used to appear fairly often on the cover of the New Yorker, which Nicholson (and his character) tend rather to fetishize.

More high lit: This summer, I reread all four of John Updike’s Rabbit novels, Rabbit Run, Rabbit Redux, Rabbit is Rich, Rabbit at Rest, assembled into a nice good-sized-print edition of two volumes. And I read his novelette postlude, “Rabbit Remembered,” which, rather chintzily, the publisher make you buy in a separate collection with the off-putting title Licks of Love.

I don’t have the time and energy to describe what I find so great about the Rabbit books, suffice it to say that it’s like wallowing in a giant soap opera that’s also high literature. A secret history of an unknown America. A true modeling of a mind. The whole thing assembled from poetic yet demotic passages tiled together into a seamless whole. And with in-your-face humor that won’t quit.

Like—Rabbit is at the funeral of a woman he had an off-and-on affair with for years. Self-involved in hiw own grief, and meaning (perhaps) to comfort her husband, Ron, Rabbit blurts out something like “She was a great lay, Ronnie.” Ron doesn’t speak to Rabbit for quite some time after that…but eventually Ron—well, read “Rabbit Remembered.”

I see Updike falling out of his chair laughing when he wrote that “great lay” line…like Franz Kafka would do when he’d read “The Metamorphosis” to his pal Max Brod.

Updike really should have gotten the Nobel Prize…in his later years he somewhat touchingly and even pathetically wrote a story about his alter ego writer-character Henry Bech getting the Prize, which reminded me of the impoverished Edgar Allan Poe launching into a very long description of the treasure trove of gold, silver and jewels that his characters unearth in “The Gold Bug.”