[extropy-chat] Smalley, Drexler and the monster in Lake Michigan

[Robert J. Bradbury]

On Sun, 7 Dec 2003, Rafal Smigrodzki wrote:

> This introduces severe limits on the kind of chemical interactions
> between parts of a protein - they cannot be cross-linked for higher
> strength, except by the use of other proteins or the limited expedient of
> S-S bridges, so only select proteins are cross-braced (see collagen
> formation)

You could take 2 of the stop codons and use them to create 2 new
amino acids that crosslink with something much stronger than an S-S
bond, design/evolve 2 new tRNAs, then kludge up Venter's minimal
organism so it only uses the remaining stop codon, then verify/evolve
receptors that can absorb the new amino acids from the medium
(I'd suspect minimal microorganisms will use universal amino
acid pickup receptors).  Voila -- an orgainsm into which you can
put new genetic sequences that will allow you to build much
stronger proteins/enzymes.  (I believe scientists at UCSD have
done between 1/10th and 1/5th of this already).

It is worth pointing out in [1], Table 1, I point out an alternate
genetic code that would allow 63 building blocks rather than than
just 21.  The era of whole genome engineering would allow one
to construct a variety of organisms capable of working with
different genetic codes.

> or else you'd need to have a bunch of specialized
> post-translational modificators for each protein, and a bunch of
> modificators for each modificator, and ...

How does the selenocysteine modification work?  At the tRNA level
or at the protein level?

> (a cell couldn't store enzyme information for making e.g. 20 000
> building blocks instead of 21) and see if they survive.

Well that isn't true -- there are organisms like Amoeba dubia
that have 670 million BP genomes, 20,000 building blocks
gives them 33,000 bp/building block which is probably enough
for 1500+ bases for each enzyme in a 10 step assembly process
and that doesn't include any reuse of parts of pathways.

> This is a severe limitation on the amount of searching in the
> design space you can do, even in millions of years.

Particularly if you find a basic set that solves most of the
problems most of the time.  I think plants that can tolerate
great extremes of heat and cold would be interesting to study
as they may have copied the enzymes that worked and simply
evolved them sufficiently to work at alternate temperatures.

Robert

1.  Bradbury, R. J., "Protein Based Assembly of Nanoscale Parts", (July 2001)
http://www.aeiveos.com/~bradbury/Papers/PBAoNP.html