Biofuels are coming your way

When people hear about biofuels, they typically think of ethanol brewed from corn. That’s a reasonable association: this year the American corn crop is up nearly 20% from last year for this very reason. On the other hand, you might have also seen articles about the problems with the corn-to-ethanol process. Growing corn is, for example, so energy-intensive that it’s not clear you’re saving any greenhouse gas emissions or money by the time you’re done. It’s easy enough to see how the tractors and trucks required to harvest and transport corn use a lot of fuel, but many people don’t realize that the nitrogen-based fertilizer that gets dumped on cornfields by the ton is itself the product of a hot, expensive industrial process.

If that were where the story ended, it would all be quite sad. But there’s good news too. Life gets a lot better if you can make fuel out of stuff that we don’t eat, stuff like cornstalks, corncobs, cut grass, and wood chips. Life gets better still if the fuel you make isn’t ethanol, but something an awful lot like kerosene. This is exactly what a company called LS9 is doing. In fact there are several companies in this space: Amyris, Codon Devices, and Craig Venter’s Synthetic Genomics are all in the game.

As you can guess by the names, they’re not just using brewer’s yeast to do this. They’re doing serious microbial genetic manipulation. The results are very promising, and this will no doubt lead to some fascinating Green on Green violence. Quick: which is worse? Global warming or the widespread use of genetically modified organisms? Weeee’ll seeeee…

My source for this information is Rob Carlson’s excellent synthetic biology blog Synthesis. Here’s his latest post on LS9: LS9 – “The Renewable Petroleum Company”. Here’s a general one about synthetic biofuels: The Need for Fuels Produced Using Synthetic Biology.

What’s happening to the sharks?

In the continuing series of strange animal vs. animal YouTube videos, here is one from the Seattle Aquarium. Poor little octopus. Sitting defenseless in a tank full of sharks. Poor little guy.

I suppose that if sharks made their own version of a movie like Jaws, it would be called Eight Legs. “Just when you thought it was safe to swim close to the coral…”

Freeman Dyson’s biotech future

Freeman Dyson, the physicist, provocateur, and one-time colleague of Richard Feynman, has written a piece for the New York Review of Books called Our Biotech Future, and boy is it a doozy. This is no timid prediction about curing the common cold or even avoiding the next plague. It’s a full-on embrace of a bio-kaleidoscopic future. I’m not sure if he’s playing the I’m-old-and-I’ll-say-whatever-I-want card or if he’s always been this wild-eyed, but here’s a good sample quote:

The final step in the domestication of biotechnology will be biotech games, designed like computer games for children down to kindergarten age but played with real eggs and seeds rather than with images on a screen. Playing such games, kids will acquire an intimate feeling for the organisms that they are growing. The winner could be the kid whose seed grows the prickliest cactus, or the kid whose egg hatches the cutest dinosaur. These games will be messy and possibly dangerous.

You bet they will, Freeman! But that won’t stop us, right? Hey Mrs. Patterson! Billy’s cheating off my Ornithopsis genome!

Honestly, I admire him for writing this, and I admire the New York Review of Books for printing it. They must be taking bets in the editorial offices on how many letters this is going to draw. Someone needs to be talking like this, because the future of biotech is going to be a lot weirder than most people realize.

Things get really interesting when Dyson starts to compare the last few billion years of genomic evolution to evil proprietary software practices, as contrasted with a pre-Darwinian (and upcoming post-Darwinian) era of open-source horizontal gene transfer. For this last reference, he cites some fascinating papers by biologist Carl Woese. It’s wacky at times, but thoroughly thought provoking.

Unfortunately I don’t have time for further speculation… I’ve got to go tune the thagomizer on my dwarf stegosaur.

Fossil phones and genetic atrophy

I’m reading a biology book right now, The Making of the Fittest, that talks about how much information about the past we’re able to reconstruct from the forensic record of currently available DNA. One of the things that Sean Carroll, the author, talks about is the fossil genes to be found in our genome. Fossil genes are the cratered but identifiable remains of genes that no longer code for anything. They can arise when the protein they code for no longer does anything useful. For instance, the genes that help form eyes are no longer useful among cave fish. Eyeless mutants can thrive in a sunless sea, and their nonfunctional eye genes can persist in a recognizable form for millions of years before eventually being pulverized into genomic dust.

This weekend I went to a conference (Foo Camp), and at some point my cell phone went into an unrecoverable coma. Since I needed to coordinate an after-conference visit with some friends in the Bay Area, I had to make several phone calls. Old-school mesozoic landline phone calls. This means that I needed to find public pay phones in Berkeley on a Sunday afternoon. This brings me to the topic of fossil phones, which is closely related to the topic of fossil genes.

Since the rise of Homo mobilephonicus, the selection pressure to maintain working public phones has essentially vanished. This has allowed vandalism, neglect, and cosmic rays to do their worst to existing phones. Let me save you the trouble of walking into a liquor store on San Pablo Avenue and asking for the nearest pay phone. You will be looked at as though you just asked for the whereabouts of the neighborhood gramophone purveyor.

By the time I found a phone that worked, I had stopped at no fewer than five ostensible pay phone locations. Two of these had been simply ripped off of their mounts. They’ll all be dead soon. But the fossil record will betray our ancient love for gramophones and bakelite records to a thousand generations yet to come.

Creatures from the Deep

Movies that depict fictional encounters with alien life forms always seem so tame compared to the weird animals here on Earth. The deep sea is one of the best places to go looking for the unusual, and the good news is that we’re getting lots of snapshots these days.

Claire Nouvian is the author of a new book called The Deep: The Extraordinary Creatures of the Abyss. She was good enough to make a gallery of pretty pictures for those of us too cheap to buy the book. These creatures look funny, and they have funny names. If I’d gotten to name them, I’d have given them funny names too. Why, you may ask, do they call the noble Chondrochladia lampadiglobus a Ping Pong Tree Sponge? Go find the thing in the gallery and you will wonder no more.

All the while I’m gawking at these things, part of me realizes it’s just provincial bad manners to stare as I do. I imagine that somewhere in the Stygian depths there is a museum of all the strange stuff that’s drifted down from the surface.

Magnetic brain stimulation: the new drug

I just came across this Wired item on a magnetic brain stimulator that’s being discussed at the latest American Psychiatric Association meeting as a new therapeutic tool for treating depression.

It works like this: much of your brain activity is electrical. You can drive electrical activity by changing nearby magnetic fields. Thus, with cleverly designed electromagnets, you can push and pull the electrical activity deep in your brain through the process known as transcranial magnetic stimulation (TMS). This technique has been around for a while, but like all things technological, it’s gotten much better in the last few years. An article in the New York Times Magazine a few years ago made a splash by describing how an Australian researcher could turn anybody into a creative savant (temporarily) with TMS. These claims, it turns out, may have been overstated, but still, the news about TMS was starting to spread.

At the same MIT conference I mentioned here (H2.0 at the Media Lab) there was a brief presentation by neurological research wunderkind Ed Boyden. He’s doing all kinds of fascinating research, including using lasers to suppress and excite neuron activity in rats. But all anybody wanted to ask him about was his TMS research. Does it work? Does it hurt? Is it fun? It was obvious that there’s a fascination with this device that’s going to catapult it into the street when it becomes cheap. The whole thing vaguely reminded me of the period in the early 1960s when LSD escaped from the Stanford Psychology department. Not to suggest that this has the hitting power of LSD, but I know that anything that promises to give people a cheap thrill or even a dull buzz will be appropriated and abused in short order. The first thing that occurred to me was that researchers in this area should make sure they’re in a position to learn from the crazy shit people will do in their basements because nobody can stop them. I mentioned this to Ed Boyden, and I was impressed that he had already considered this. He’s created a wiki site called OpenStim that’s dedicated to letting people report on their research. Or their “research” as the case may be.

Synthetic life and corn starch babies

How close are we to truly playing Dr. Frankenstein and creating life from scratch? Watch this video to the end to find out. It starts off pretty tame, but stick with it. The ending is the most profoundly disturbing tub of damp cornstarch you will ever meet. Wet cornstarch is weird stuff. Even without divine intervention, you can run across a vat of the stuff without sinking. But if you stand on it, you’ll sink like a rock. And if you shake it at a high frequency, well… take a look.

In all seriousness, a lot of people are trying to create a living thing of some sort from scratch. I came across this cornstarch video and a summary of recent artificial life research at Biocurious, a biology blog written by physicists.

Evolving robots

Read this story and you may well conclude a robot uprising is right around the corner.

Carl Zimmer’s recent post Evolving Robotspeak describes robotics research done by social evolution researcher Laurent Keller in Switzerland. Plenty of folks have used genetic algorithms to “breed” robots, but this is the first time I’ve heard of someone using family and colony models for their genetics. In a nutshell, if you breed individual robots to find virtual food, they quickly get trained to do pretty well. But if you breed them as families, they do even better. To put it in anthropomorphic terms, their intermingled genetics help them understand the value of cooperation.

It’s fascinating to see the genetic theories of social behavior borne out in a colony of robotic organisms. This Darwin guy may have been on to something after all.

UC Berkeley molecular biology webcast

In the fall of 2002, MIT proudly announced its OpenCourseWare initiative. They were rightly praised at the time for putting course materials directly online and making them freely available to anyone with access to the web. I was interested in biology classes and poked around the site and came away a little disappointed. Not all the lectures were available as audio, the sound quality wasn’t good, and the lecture notes had images ripped out of every other slide along with some legal boilerplate about how copyrighted material had to be removed. In other words, wherever the lecture snipped a picture out of a textbook (which was often), they couldn’t distribute that slide to the internet masses. Taken all together, I was impressed with the notion of OpenCourseWare but not with the reality.

I forgot about open course ware for a long time, but recently found a page linking to podcast lectures from UC Berkeley. This time it was the real deal. I’m still interested in biology, so I’m watching the lectures for MCB 110: General Biochemistry and Molecular Biology. There’s audio, video, and PowerPoint slides, and the quality is very high. The slides are complete and unexpurgated. It’s a phenomenal resource. There’s just no doubt that free course material like this is going to transform lives.

I’ve since gone back and looked at MIT’s latest OpenCourseWare biology classes. I’m happy to report that now there’s plenty of good stuff there too, including video lectures in which Eric Lander, director of the Broad Institute and one of the more famous geneticists in the world, explains genetics to you. To get that delivered, at no cost, to the privacy and comfort of your sitting room, well… that’s remarkable.

Biology parody site

I’m not sure who’s behind NEXTgencode, but it’s a well done parody of the commercial promise of biotechnology. Some of the things they bring up in joke form are sure to be real issues at some point in the future. How much would you pay for a terminally cute PermaPuppy? How much is the gene for blond hair worth if it is disappearing “in the wild?” Since NEXTgencode links to the (more serious) Ethics in Genetics site, I assume the parody is intended to provoke as well as amuse.