Sunday, March 26, 2006

More steps along the way

If one thinks about this stuff much, one must inevitably ask, what is the pathway to get from here to there? Ordinarily when attacking a big complicated task, one partitions it into many small subtasks. Then you can draw a big diagram with little boxes connected by lines, the boxes representing subtasks and the lines representing dependencies between subtasks, what the project management weenies call a PERT chart. So where is the PERT chart for developing advanced molecular manufacturing?

Rob Freitas took a stab at one a couple years ago, aimed specifically at diamondoid systems. At the most recent Foresight conference, Drexler and Damian Allis presented work on a tooltip similar in appearance to those described by Freitas, and also intended for extracting and depositing individual atoms on a work surface. More or less simultaneously the Foresight Institute announced their plan to develop a technology roadmap to get us to "productive nanosystems", which is basically the nanofactory shown in the animation. From there it's a relatively small step to any other form of nanotechnology. The nanofactory is the preferred concept today because there is no conceivable way that it could get loose or mutate or go out of control, and people worry about such things.

The people doing Foresight's technology roadmap stuff are talking to people with money, so that might turn out to be interesting. There is also the work by Schafmeister and Rothemund. So it's a pretty interesting time.

Monday, March 20, 2006

DNA origami

There is an MSNBC story about "DNA origami", a technique invented by Paul Rothemund at Caltech to form large complicated shapes by controlling folding patterns in long DNA chains.

Each of the two smiley faces are giant DNA complexes, imaged with an atomic force microscope. Each is about 100 nanometers across (1/1000th the width of a human hair), 2 nanometers thick, and comprised of about 14,000 DNA bases. 7000 of these DNA bases belong to a long single strand. The other 7000 of these bases belong to about 250 shorter strands, each about 30 bases long. These short strands fold the long strand into the smiley face shape. - Paul Rothemund

Rothemund's work is published in Nature, and the full text is available as a PDF at his website. Rothemund works in the DNA and Natural Algorithms Group headed by Erik Winfree.

Monday, March 06, 2006

Other peoples' related blogs

DNA computing progress

On February 24th, National Geographic reported on progress in DNA computing. This field began in 1994 with Leonard Adelman's work on solving the Hamiltonian path problem, and then I didn't hear much about it after that.

Ehud Shapiro and his colleagues at the Weizmann Institute in Israel have developed a DNA computer that can perform 3.3x1014 operations per second. A cubic centimeter of "computer soup" contains about 1.5x1016 individual computers, with a memory capacity of about 6x1020 bytes (ten billion 60-gigabyte hard drives). The two primary advances are that the system is generally programmable, and that the computation is powered by DNA rather than ATP.

"Autonomous bio-molecular computers may be able to work as 'doctors in a cell,' operating inside living cells and sensing anomalies in the host," said Shapiro. "Consulting their programmed medical knowledge, the computers could respond to anomalies by synthesizing and releasing drugs."
This approach appears applicable only to embarrassingly parallel problems involving no inter-processor communication. It should be able to tackle some problems in global optimization, though probably not very complicated ones like de-novo protein design, one of the possible pathways toward advanced nanotechnology. For the time being, it's not yet clear that this is a very useful technique.