Arnold G. Reinhold writes:
> I am not sure I understand the difference between "random" and
> "pseudorandom" as you are using it here. In any case, I expect more
There is no difference from an attacker's point of view. He can't tell
random from pseudorandom without extra knowledge. But he sure can tell
a high-entropy sequence from a segment encoding, say, a vanilla
transmembrane protein. Check out the genome of a real critter, a
standard model nematode C. elegans
http://elegans.swmed.edu/genome.shtml
Doesn't look exactly random, does it?
It would be interesting to analyse the genome from a cryptoanalyst's
point of view. Any takers?
> sensitive cryptoanalytic tools for DNA can be developed if the need
> (and funding) arise. For example, has anyone done an n-tuple
> frequency analysis on natural DNA? Probes targeting n-tuples that are
> significantly less likely to occur in nature could be used to find
> human generated DNA strings without total sequencing. It might even
Indeed. There are short subsequences which never or almost never occur
in biology. This is the reason why you need to camouflage/steganograph
as a biological sequence. Which, of course, dramatically reduces your
payload, if you want to stay below individual/species variability
threshold.
> The problem seems to be error rates. Here is what one DNA synthesis
> company has to say: http://www.alphadna.com/special.html#long
Error-correction/redundant encoding.
> A mer (as in polymer) is a DNA base pair. There are four
> possibilities, so a mer encodes two bits. A 200-mer chain holds 400
> bits. That's long enough to start thinking about packet technology.
> You could use ECC to deal with the base errors, or just assume you
> will have enough copies of each packet to do majority voting.
>
> Anyway, I expect Moore's law will apply here as it does in
> electronics. Price per base might be a good number to chart over
Sure, designer enzymes and palmtop sequencers will be the vogue.
> time. I don't think that Moore's time constant is due to the peculiar
> nature of semiconductors, but rather it is results from the
> so-far-unlimited richness of the technology. DNA technology is just
> as rich in possibilities as semiconductors. I think Moore's 18 months
DNA is just a particular instance of molecular nanotechnology. There
is a very rich set of opportunities there, whether
solvated/biologically inspired or dry/machine phase. Even a partial
closure would make pretty useful things.
> is the limit as resources go to infinity of the time needed for
> humans to understand the limitations of the last innovation and come
> up with an approach to overcome them.
One of the bottlenecks of molecular manufacturing is a decent fully
interactive realtime molecular dynamics simulator, and another which
has enought quantum clue do reliably predict chemistry. We do have the
hardware power for that already (at least in form of clusters), it is
really the question of writing the codes.
> You are right, of course, about density, but I'd be reluctant to rely
> on DNA's destructibility. On the contrary, I am told that PCR can
> reliably detect ten molecules and has a good chance of detecting a
> single molecule. If you are synthesizing 160 nmole, that is 10**20
> molecules. You must completely destroy every one with high certainty.
The whole point about DNA is that you can have few 100-1000 molecules,
and yet still reliably amplify from these microscopic amounts. A drop
of such DNA solution dropped into 98% HClO4 has a half life time of
seconds at best.
