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Foresight co-founder among panelists discussing role of technology in human existence

Foresight Institute Co-Founder and Past President Christine Peterson was among four panelists addressing the role of technology in human existence for a Stanford University Continuing Studies series. From a report in The Stanford Daily by Marshall Watkins “Bay Area thinkers ponder ‘life’“:

Christine Peterson, co-founder and president of The Foresight Institute, a public interest group seeking to educate the community on forthcoming technological advances, emphasized the increasingly prominent role that nanotechnology has come to play.

Peterson noted that nanotechnology has the potential to create new materials and make vast advances without the side effects, such as pollution, that would currently ensue. She allowed, however, that the near-invisible and highly sensitive technology might enable intrusions on privacy.

“We need to know what data is collected,” Peterson said, “how it is used and how long it is retained. We have those rights.”

Peterson highlighted the medical benefits of nanotechnology, noting, “The ability to control atoms and molecules would mean that there really isn’t a physical illness [that] we wouldn’t be able to address.”

The report quotes the moderator of the panel, author Piero Scaruffi, as stating that the four panelists were picked because “They discussed life as in the future, rather than life as in the past.” We can certainly expect that life after advanced nanotechnology has been developed will be fundamentally different from life up until that point.

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Crowd-sourced protein design a promising path to advanced nanotechnology

Less than four years ago we asked here whether online gamers playing Foldit could help perfect the de novo design of proteins that do not exist in nature. Four months ago we reported that Foldit players had succeeded where scientists had failed in solving the structure of an important viral enzyme. Now Scientific American reports that Foldit players have topped scientists in redesigning a protein—the challenge we suggested less than four years ago. From “Online gamers achieve first crowd-sourced redesign of protein“:

Obsessive gamers’ hours at the computer have now topped scientists’ efforts to improve a model enzyme, in what researchers say is the first crowdsourced redesign of a protein.

The online game Foldit, developed by teams led by Zoran Popovic, director of the Center for Game Science, and biochemist David Baker, both at the University of Washington in Seattle, allows players to fiddle at folding proteins on their home computers in search of the best-scoring (lowest-energy) configurations.

The researchers have previously reported successes by Foldit players in folding proteins, but the latest work moves into the realm of protein design, a more open-ended problem. By posing a series of puzzles to Foldit players and then testing variations on the players’ best designs in the lab, researchers have created an enzyme with more than 18-fold higher activity than the original. The work was published January 22 in Nature Biotechnology [abstract].

“I worked for two years to make these enzymes better and I couldn’t do it,” says Justin Siegel, a post-doctoral researcher working in biophysics in Baker’s group. “Foldit players were able to make a large jump in structural space and I still don’t fully understand how they did it.” …

The latest effort involved an enzyme that catalyses one of a family of workhorse reactions in synthetic chemistry called Diels-Alder reactions. Members of this huge family of reactions are used throughout industry to synthesize everything from drugs to pesticides, but enzymes that catalyze Diels-Alder reactions have been elusive. In 2010, Baker and his team reported that they had designed a functional Diels–Alderase computationally from scratch [abstract], but, says Baker, “it wasn’t such a good enzyme”. The binding pocket for the pair of reactants was too open and activity was low. After their attempts to improve the enzyme plateaued, the team turned to Foldit.

In one puzzle, the researchers asked users to remodel one of four amino-acid loops on the enzyme to increase contact with the reactants. In another puzzle, players were asked for a design that would stabilize the new loop. The researchers got back nearly 70,000 designs for the first puzzle and 110,000 for the second, then synthesized a number of test enzymes based on the best designs, ultimately resulting in the final, 18-fold-more-active enzyme.…

The article was written by Jessica Marshall and reprinted in Scientific American with permission from Nature, where it was originally published as “Victory for crowdsourced biomolecule design: Players of the online game Foldit guide researchers to a better enzyme.” The article does an excellent job of describing how researchers and game players collaborated to achieve the final result. The gamers explored much more radical changes to the protein than can be done by conventional molecular biology techniques such as directed evolution, which typic[a]lly explores only single amino acid substitutions. The researchers then physically constructed and characterized the enzyme designed by the gamers.

The choice as design target of an enzyme to catalyze Diels-Alder reactions is particularly interesting from the standpoint of developing advanced nanotechnology, also referred to as molecular manufacturing. As noted in the 2010 Science paper, this reaction is a “cornerstone” in organic synthesis, and no naturally occurring enzymes are known to catalyze this reaction. As early as 1994 Markus Krummenacker proposed the use of Diels-Alder cycloaddition in a strategy to develop molecular building blocks for molecular manufacturing (“Steps towards molecular manufacturing“).

What roles crowd-sourcing, citizen science, and de novo protein design will play in the development of molecular manufacturing, or productive nanosystems, remains to be seen, but this latest result looks like an important step alog the way.
—James Lewis

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Magnetic storage systems shrink from a million atoms per bit to twelve

Researchers at I.B.M.’s Almaden Research Center have used a scanning tunneling microscope to assemble an array of 96 iron atoms into an antiferromagnetic structure that encodes one byte (eight bits) of information. As reported in the NY Times by John Markoff “New storage device is very small, at 12 atoms“:

SAN JOSE, Calif. — Researchers at I.B.M. have stored and retrieved digital 1s and 0s from an array of just 12 atoms, pushing the boundaries of the magnetic storage of information to the edge of what is possible.

The findings, being reported Thursday in the journal Science, could help lead to a new class of nanomaterials for a generation of memory chips and disk drives that will not only have greater capabilities than the current silicon-based computers but will consume significantly less power. And they may offer a new direction for research in quantum computing. …

The group at I.B.M.’s Almaden Research Center here, led by Andreas Heinrich, has now created the smallest possible unit of magnetic storage by painstakingly arranging two rows of six iron atoms on a surface of copper nitride. …

Although the research took place at a temperature near absolute zero, the scientists wrote that the same experiment could be done at room temperature with as few as 150 atoms. …

The remainder of the article quotes Dr. Heinrich as saying that these tiny devices built with scanning tunneling microscopes are primarily of interest as a way to explore the quantum mechanical properties of the antiferromagnetic effect in the hope of developing novel nanomaterials that might lead to quantum computers. He also noted that many research groups are exploring self-assembly methods that could lead to practical manufacturing technologies to replace current microelectronic technologies.

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Advanced nanofactories in twenty years?

The potential of advanced nanotechnology is getting some attention from mainstream media. Late last year The Guardian web site posted a brief article on the prospects for nanofactories and atomically precise manufacturing, featuring quotes from Christine Peterson and Robert Freitas. From “Nanofactories – a future vision” by Penny Sarchet:

Mimicking nature is a recurring theme in nanotechnology and molecular nanotechnology, inspired by the natural nanostructures found in our own bodies, offers many exciting potential outcomes.

“Molecular nanotechnology is the expected ability to build our products with molecular-level precision, as nature can do,” says Christine Peterson, president of the Foresight Nanotech Institute in California. “It will bring unprecedented quality, energy efficiency and environmental sustainability”.

The recent development of an electron-powered molecular “nanocar”, by a team led by chemist Ben Feringa at the University of Groningen in the Netherlands, hints at the potential. Further indications that molecular nanotechnology is achievable are being found in the quest for ever-smaller computing.

Many of these efforts attempt to use nature’s own method of storing and transferring information – DNA. “DNA computing is the goal of building devices out of DNA that are able to act like computers, initially doing simple calculations but eventually doing everything that a macroscale computer can do,” says Peterson. …

One future prospect for molecular-scale nanotechnology is to build nanofactories. “The nanofactory is a proposed compact molecular manufacturing system that could build a diverse selection of large-scale, atomically precise products,” explains Robert Freitas Jr, senior research fellow at the Institute for Molecular Manufacturing, also in California. “The products of a nanofactory would be atomically precise, with every atom in exactly the right place, offering the ultimate in quality control. It could make products out of the strongest materials known to man – especially diamond, sapphire, and related ultra-strong ceramics. In manufacturing, it’s hard to do better than that.”

The first two-dimensional structure to be built atom-by-atom was made from silicon in 2003. However, Freitas says nanofactories are still a long way off. “We expect this will require a 20-year research and development effort and on the order of $1bn (£622m) in funding to achieve.” …

If anyone knows someone with a billion dollars they will not need for twenty years, ask them to contact Christine or Robert.

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