Future Ben

I am back in construct design mode, and a deeper lesson just dawned on me. I have been playing with a human protein in a human cell. It’s the metal transporter DMT1 that I will be talking about in Kyoto next week. Not surprisingly, this protein is tightly regulated at every level. How do I get around that problem?

I could edit out parts of the sequence and figure out what parts are regulatory, but that could take a long time. It turns out that a long time ago E.coli picked up the gene for DMT1 through horizontal gene transfer. All the regulatory parts have long since mutated away. Thanks for the help. I am going to use the Bacterial protein as a starting point, but of course it’s not that simple. First off bacteria prefer to use different codons for proteins. you can still get bacterial genes to express, they just don’t do it very efficiently. i have to synthesize the gene for mammalian expression. That’s not so tough these days. A trickier problem is the membrane. E.coli have a different thickness of membrane than a mammalian cell. I will have to do some serious sequence gazing and mental modeling to fix this problem. Sadly there is no structure to work with. If there was somebody else would have done this already.

I try not to repost boing boing material, but sometimes it’s to topical to pass up. Wired contributer Quinn Norton has posted her slides from her talk on Body Hacking. Body Hacking is admittedly just a catchphase that doesn’t really capture the embryonic state of post humanism we live in, but I can’t think of anything better so OK. So what makes body hacking different from piercings and tattoos? Ms. Norton makes the point that body hacking goes beyond the aesthetic and into enhanced functionality.

Already Lasik and ligament replacement surgeries are being used for enhacement in sports, and drugs like Provigil Aderol and Xanex enjoy vivrant trade on the black market. So what is the future of body hacking?
I would guess that surgical enhancements will grow as quickly as creative drug use and biological theraputics like viral gene transfer. I am waiting for somebody to use the Adenoviral treatment for CF on themselves to enhance their breathing capacity. I doubt it would do anything, but I still hope they try.

Everybody is talking about the Achitecture Exhibition in Venice! Admittedly nobody that I know or who would want to talk to me. Why don’t I have any architect friends? Is it me or is it a personality type that I don’t get along with? Maybe architects have to be too straightlaced… Oh I forgot I had a point.

From their site:

�More than half of the world�s population lives in cities�, states the Director of the 10th International Architecture Exhibition, Richard Burdett. �A century ago, it was less than 10%. The 21st century will be the first truly urban era, in which more than 75% of the world�s population will live in urban areas, much of it in mega-cities with more than 20 million inhabitants concentrated in the countries undergoing rapid development in Asia, Africa and South America. In the meantime, many Western and European cities are shrinking, or have been forced to re-invent themselves in order to adapt to a post-industrial condition.”

So the future is urban! That was my point! Is this really true that in an era where we can be completely mobile we all choose to congregate in dense little clusters. umm yes. A key feature of the urban landscape is public transport and access to public services. These features empower the disenfrachised, which is exactly why third world countries are urbanizing so rapidly. At a recent public health lecture I heard the shocking fact that 99% of the hospitals in China are within 300 miles of the coast. If you want access to any quality social services even in a communist country, you have to live in a city.

But what about the first world. I do know that NY is a few years away from another housing crash. But in general is America urbanizing or suburbanizing? I’m going to find out with an internet road trip across North America! Up next the future of the northeastern seaboard. NY, Boston and Halifax. Where are they going? An more importantly, where are they?

Scientists are on the verge of breaking the carbon barrier — creating artificial life and changing forever what it means to be human. And we’re not ready.

I just read this article on Salon. Its a little inflammatory but OK. I agree that we aren’t ready for a nanobiotech revolution, fortunately, it won’t be happening for quite a while. Our fear of the paradigm shifting technology will stave off a Neal Stephenson Diamond Age future through legislation and litigation.

Lets set aside the artifical life/inteligence “Matrix” stuff for a moment. What scares the status quo so much is the potential for bionanotech to be completely decentralized our economy to the point where governments and corporations will lose control. When they comes, new technologies will be user derived, open source and made by small design houses, or worse, individuals. How will that be regulated, bought or sold? When in home fabrication becomes routine. Economies will shift from delivering products to delivering commodities and generating content. If manufacturing turns into simply delivering raw materials, billions of first world dollars will have gone to waste on creating an obsolete infrastructure. Millions of skilled workers will have no future once their jobs have been replaced by an in home appliance. Of course, advertising and fashion will be as important as ever.

OK now the far future issues. Yes, we will start to let go of our definition of life and sentience, and there will be a backlash and conflict with fundamentalism. But there will be communities that are brave enough to face the dilution of our humanity and conciousness. This is likely to be an urban movement, but given that we will cease to be reliant on a centralized supply chain, there is every reason for nanobiotech friendly colonies to fluorish away from a culture less bold.

There is a lot to be afraid of from either end of the spectrum, from giant killer robots to torch bearing not-so-smart mobs. We have plenty to be afraid of right now, like AIDS cancer and ethnic religious violence. While we fear new technology, historically the greatest threats to our society have come from ignorance, hatred, prejudice and corruption. Should we be afraid of a potentially dagerous new technolgy or the ignorant and self rightous hand which would use it? What we shouldn’t fear is the future, or at least not specificly.

The J Craig Venter Institute is one of the most modern innovative research centers in the world today. Dr. Venter has stirred his share of controversy with his “shotgun” approach to sequencing. In the late 90’s there was a concern in the scientific community that there was too much data to be meaningful. This notion seems laughable today as Information Technology has caught up to the flood of data, yielding some incredible advances.

Already Dr. Venter has moved past Genomics into what is now called Metagenomics. His recent expedition on the Sorcerer II consisted of sampling seawater every 200 miles in an around the world sailing trip. A common reaction to this is rejection of the idea that anything meaningful could be gained from Venter’s around the world boondogle. But there is a genius behind the Sorcerer expedition. Venter’s thesis is that the ocean can be considered a single living organism with specialized genetics to handle environmental differences. In this view determining species is unimportant. What maters is the genome of the environment. The Metagenome.

What does this mean to the rest of the world? One of the major efforts of the Venter intitute is Synthetic Biology. Why? With a collection of environmental metagenomes a clever Biologist can determine just what genes are necesary to thrive and construct or modify organisms accordingly. Another application is biosynthesis or biogeneration. The Venter instute is working on generating Hydrogen as a fuel source.

This type of forward thinking will lead to biotech’s next great expansion. Data is the key. For this reason The Venter Institute has partnered with UCSD to start CAMMERA: Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis. Once completed this optical network will allow researcher from all over the world to datamine the ever growing sequence information being generated. What discoveries and innovations this will lead to is anyone’s guess.

I noticed a post on boingboing about computer designed antennas about to be used in a NASA experiment. It led me to The Evolvable Systems Group at NASA’s Ames research center. From their site:

“The Evolvable Systems Group investigates computer algorithms that automate the design and optimization of complex engineering systems for current and future NASA missions. Our overall goal is to dramatically increase mission reliability and science return through development and application of adaptive and evolutionary algorithms.”

This is the ultimate form of biomimicry. A human mind comes up with the specs and some seed designs for the algorithm and an evolutionary design and test series is played out virtually. To be clear about this, the algorithms can only optimize the parameters you have thought to model, so there are some limitations. This makes these methods immediately applicable to well worn models like molecular and electromagnetic force fields. I can think of dozens of engineering and systems biology problems that are still having their parameters worked out and would be great applications for these methods.

It is redundant to say that dirigibles are awesome. For me however they are even better than that. Blimps are so majestic, misunderstood, and underutilized. At one time they were a metaphor for our bold commitment to technology.

Then the Hindenburg happened and humanity showed its true face. Now blimps are a constant reminder of how spineless and sensationalistic we all are. Note that the Hindenburg did go up because of the hydrogen, but the powdered aluminum that coated the envelope didn’t help matters. And most people died from trying to jump out. Besides, come on! What do you want for 1937!
Anyway, Aeros may help lighter than air make a comeback. This one is helium filled, but it can still carry 1.6 million pounds of cargo. I am still waiting for a personal dirigible though.