The J Curve

Friday, March 25, 2005

Ode to Carbon

I took a close look at the benzene molecular model on my desk, and visions of nested snake loops danced in my head…

Is there something unique about the carbon in carbon-based life forms?

Carbon can form strong bonds with a variety of materials, whereas the silicon of electronics is more finicky. Some elements of the periodic table are quite special. Herein may lie a molecular neo-vitalism, not for the discredited metaphysics of life, but for scalable computational architectures that exploit three dimensions.

Why is the difference in bonding variety between carbon and silicon important? The computational power of nature relies on a multitude of shapes (in the context of Wolfram’s principle of computational equivalence whereby any natural process of interest can be viewed as a comparably complex computation).

“Shape based computing is at the heart of hormone-receptor hookups, antigen-antibody matchups, genetic information transfer and cell differentiation. Life uses the shape of chemicals to identify, to categorize, to deduce and to decide what to do.” (Biomimicry, p.194)

Jaron Lanier abstracts the computation of molecular shapes to phenotropic computation along conformational and interacting surfaces, rather than linear strings like a Turing Machine or a data link. Some of these abstractions already apply to biomimetic robots that “treat the pliability of their own building materials as an aspect of computation.” (Lanier)

When I visited Nobel Laureate Smalley at Rice, he argued that the future of nanotech would be carbon based, due to its uniquely strong covalent bond potential, and carbon’s ability to bridge the world of electronics to the world of aqueous and organic chemistries, a world that is quite oxidative to traditional electronic elements.

At ACC2003, I moderated a debate with Kurzweil, Tuomi and Prof. Michael Denton from New Zealand. While I strongly disagreed with Denton's speculations on vitalism, he started with the interesting proposition that "self-replication arises from unique types of matter and can not be instantiated in different materials... The key to self-replication is self-assembly by energy minimization, relieving the cell of the informational burden of specifying its 3D complexity... Self-replication is not a substrate independent phenomenon." (Of course, self-replication is not impossible in other physical systems, for that would violate quantum mechanics, but it might be infeasible to design and build within a reasonable period of time.)

Natural systems exploit the rich dynamics of weak bonds (in protein folding, DNA hybridization, etc.) and perhaps the power of quantum scanning of all possible orbitals (there is a probability for the wave function of each bond). Molecules snap together faster than predicted by normal Brownian interaction rates, and perhaps this is fundamental to their computational power.

For example, consider the chemical reaction of a caffeine molecule binding to a receptor (something which is top of mind =). These two molecules are performing a quantum mechanical computation to solve the Schrödinger equation for all of their particles. This simple system is finding the simultaneous solution for about 2^1000 equations. That is a task of such immense complexity that if all of the matter of the universe was recast into BlueGene supercomputers, they could not find the solution even if they crunched away for the entire history of the universe. And that’s for one of the molecules in your coffee cup. The Matrix would require a different approach. =)

A simultaneous 3D exploration of all possible bonds warps Wolfram’s classical computational equivalence into a neo-vitalist quantum equivalence argument for the particular elements and material sets that can best exploit these dynamics. A quantum computer with 1000 logical qubits could perfectly simulate the coffee molecule by solving the Schrödinger equations in polynomial time.

Of course this begs the question of how we would design and program these conformational quantum computers. Again, nature provides an existence proof – with the simple process of evolutionary search surpassing intelligent design of complex systems. Which brings us back the earlier blog prediction, that biology will drive the future of information technology – inspirationally, metaphorically, and perhaps, elementally.

Traditional electronics design, on the other hand, has the advantages of exquisite speed and efficiency. The biggest challenge may prove to be the hybridization of these domains and design processes.

Sunday, March 06, 2005

TED Reflections

TED is a wonderfully refreshing brain spa, an eclectic ensemble of mental exercise that helps rekindle the childlike mind of creativity.

This year’s theme was “Inspired by Nature”, which I believe has broad and interdisciplinary relevance, especially to the future of intelligence and information technology. By the end of the conference, there was a common thread running throughout the myriad talks, a leitmotif along the frontiers of the unknown. I felt as if I had been immersed in a fugue of biomimicry.

I am still trying to synthesize the discussions I had with Kurzweil, Venter and Hillis about subsystem complexity in evolved systems, but until then, I thought I’d share some of my favorite quotes and photos.

• Rodney Brooks, MIT robotocist:
“Within 2-3 weeks, freshmen are adding BioBricks to the E.Coli bacteria chassis. They make oscillators that flash slowly and digital computation agents. But the digital abstraction may not be right metaphor for programming biology.”

“Polyclad flatworms have about 2000 neurons. You can take their brain out and put it back in backwards. The worm moves backwards at first, but adapts over time back to normal. You can rotate its brain 180 degrees and put it in upside down, and it still works. Biology is changing our understanding of complexity and computation.”

• Craig Venter, when asked about the risks of ‘playing God’ in the creation of a new form of microbial life: “My colleague Hammie Smith likes to answer: ‘We don’t play.’”

“With Synthetic Genomics, genes are the design components for the future of biology. We hope to replace the petrochemical industry, most food, clean energy and bioremediation.”

“The sea is very heterogeneous. We sampled seawater microbes every 200 miles and 85% of the gene sequences in each sample were unique... 80% of all known gene data is new in the last year.”

“There are about 5*10^30 microbes on Earth. The Archaea alone outweigh all plants and animals... One milliliter of sea water has 1 million bacteria and 10 million viruses.”

• Graham Hawkes, radical submarine inventor, would agree:
“94% of life on Earth is aquatic. I am embarrassed to call our planet ‘Earth’. It’s an ocean planet.”

• Janine Benyus, author of Biomimicry (discussion):
“Our heat, beat and treat approach to manufacturing is 96% waste... Life adds information to matter. Life creates conditions conducive to life.”

• Kevin Kelly, a brilliant author and synthesizer:
“Organisms hack the rules of life. Every rule has an exception in nature.”

“Life and technology tend toward ubiquity, diversity, specialization, complexity and sociability…. What does technology want? Technology wants a zillion species of one. Technology is the evolution of evolution itself, exploring the ways to explore, a game to play all the games.”

• James Watson, on finding DNA's helix: “It all happened in about two hours. We went from nothing to thing.” (Photo and discussion)

• The Bill Joy nightmare ensemble: GNR epitomized in Venter (Genetics), Kurzweil (Nanotech) and Brooks (Robotics).

• The Feynman Fan club: particle diagrams take on human form =)
• GM’s VP of R&D on the importance of hydrogen to the auto industry.
• Amory Lovins on the inefficiency of current autos

And, for entertainment, a Grateful Dead drum circle, Pilobolus, and polypedal studies.

• Bono, Streaming video of his TED Prize acceptance speech:
“A head of state admitted this to me: There’s no chance this kind of hemorrhaging of human life would be accepted anywhere else other than Africa. Africa is a continent in flames.”