A molecular assembler is a molecular machine capable of assembling other molecules given instructions, energy, and a supply of smaller "building block" molecules to work from. Ribosomes demonstrate the essential principles of a molecular assembler - they work within a cell's environment, and by reading strands of RNA they assemble specific large protein molecules out of more fundamental parts. Instead of being used in tiny stand-alone systems, large numbers of assembler-like mechanism could instead be integrated into a desktop-scale nanofactory able to build macroscopic products (without nanobots).

It is a matter of some debate among scientists whether more general, more "mechanical" molecular assemblers can exist, or whether naturally-evolved ribosomes are the only possible example. Richard Smalley seemingly takes this position, that any non-natural assembler is simply impossible. This appears to be carbon chauvinism.

Nonetheless, this has been an influential position in the US National Nanotechnology Initiative and the Texas Nanotechnology Initiative which have close ties to the US military-industrial complex, and seek to do molecular engineering of advanced materials for military use, with little or no scrutiny from any regulations. Greenpeace and the Foresight Institute however advocate strong controls.

K. Eric Drexler, founder of that Institute, asserts that such general assemblers are inevitable. Drexler and others assert that they could be used to build more dangerous devices that represent a clear competitive threat to all natural life in the form of grey goo which consumes carbon to make more of itself, potentially up to and including whole ecoregions or the whole Earth (ecophagy), or simply outcompetes natural life for carbon, ATP, or UV light (which some nanomotor examples run on), or the more likely green goo which co-opt a natural biologically-evolved infrastructure, as a virus or prion does, to make more of itself. Accordingly, Drexler advocates quite strict Foresight Guidelines for Research in Molecular Nanotechnology - including no creation of any such "replicator" in Earth's biosphere.

According to Smalley, of course, the regulations are unnecessary, since the replicators are impossible. However, he and the TNI advocate a regulations-free environment where presumably they can continue research in secret, including for military use. This parallels how the US biotechnology industry prevailed on George W. Bush to abandon treaties on biotechnology supervision, and on "dual-use technology", to prevent the use of either in weapons.

The UK Royal Society and UK Royal Academy of Engineering has commissioned a study to deal with the assembler question, other related issues and their larger social and ecological implications, led by mechanical engineering professor Ann Dowling. This is widely anticipated to take a strong position on these problems.

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