10/08/2005

The J Curve: Ode to Carbon

Sigh.. One day I will understand all that he says here... The few glimpses of comprehension I got show the ideas to be very interesting: Carbon based computers immitating live organisms / chemical reactions will be a lot more potent than the supercomputers we have today -- law

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....
The J Curve: Ode to Carbon

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