

Universal computing by DNA origami robots in a living animal - delackner
http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2014.58.html

======
yk
If I understand correctly, they demonstrated gates in living cells. Which
immediately raises further questions, can they also build circuits, where do I
get that stuff and how does IO work?

And to quote Gibson: the future is weird.

~~~
anigbrowl
Yes, they can build circuits. See the supplementary materials, which also
contain all the how-tos (ProTip: although most journal articles are behind
paywalls, the materials & methods stuff is often freely accessible, at least
for the _Nature_ and _Science_ journal families. It's also often a lot easier
to read and understand for the lay person who isn't already familiar with the
field in questions, assuming that your interest is more in the engineering
than the science end - I see many papers whose theoretical validity I am
incompetent to assess, but whose experimental process I am able to
understand.)
[http://www.nature.com/nnano/journal/vaop/ncurrent/extref/nna...](http://www.nature.com/nnano/journal/vaop/ncurrent/extref/nnano.2014.58-s1.pdf)

EDIT: I spoke too soon. Section 6 of the supplementary material, which
explores the idea of building more complex circuits and the scaling issues
therewith, is unfortunately missing right now. I notified the authors and I'm
sure that will be fixed soon. Meanwhile, here's what they say in the paper:

 _The architectures described here are capable of processing two input bits at
most. However, the outputs from two 'processors’ can be relayed to a third and
increase the processing capacity (limited by the possible number of unique
gate-key systems that can be designed). Importantly, the scaling of our design
is linear rather than logarithmic, with errors in robot activation propagating
in the order of the root sum square of the number of unique robot types in a
system (Supplementary Note 6). Figure 4 presents a schematic of a hypothetical
4-input bit architecture for an imaginary task of controlling three
therapeutic molecules simultaneously, where only the number of robots
comprising the system limits its capacity. The basic concept we describe can
be scaled plausibly to exceed the capacity of older 8-bit computers such as a
Commodore 64 or Atari 800, which many of us had experience of as children._

WTF |8-.

Where you get that stuff: the robots are designed with CADnano, which is free
software: [http://cadnano.org/](http://cadnano.org/) and programmed with
Visual DSD, a free project from Microsoft:
[http://boson.research.microsoft.com/webdna/](http://boson.research.microsoft.com/webdna/)
and [http://research.microsoft.com/en-
us/projects/dna/manual.pdf](http://research.microsoft.com/en-
us/projects/dna/manual.pdf)

(isn't it nice that 'webDNA actually means DNA programming on the web' instead
of some marketing department BS?) The raw material DNA strands are available
from commercial suppliers.

IO is currently done by fluorospectroscopy, which is very common in
experimental biology - you make compounds that flouresce inside the cell, then
pull out some blood/do a biopsy/chop up the host if it's something very
primitive and measure the degree of flourescence. So your unit testing is
basically probabilistic rather than deterministic.

~~~
Osmium
> Where you get that stuff: the robots are designed with CADnano, which is
> free software: [http://cadnano.org/](http://cadnano.org/)

I'm sorry, but there's CAD software for designing DNA structures now?! When
did this happen? As someone tragically unaware of recent advances in the
biosciences, I'd love to know more about this. I see the structures in
screenshots of their CAD software, and then micrographs of the resulting real
DNA(?) but how do you go from A to B?

Edit: Actually, for anyone reading this: what resources would you recommend
for getting up to speed on cell biology, modelling of DNA and the like for
someone with a solid science background? (I ask as someone who's done a lot of
computer modelling, but more from a solid state physics point of view) I'd
just like to be able to read articles like this with a slightly more critical
eye...

------
dnautics
by comparison, a transistor currently reliably scales down to 10 nm and the
theoretical limit is probably close to 2-5 nm, and can be flipped at a rate in
the range of Gigahertz. Being a designed system, the 100 nm scale is very
close to the absolute smallest you can design a DNA logic gate, and I
guarantee you it will never flip as fast as a electronic. And then just
handling DNA is not trivial in general.

~~~
Houshalter
From wikipedia:

>DNA computing is fundamentally similar to parallel computing in that it takes
advantage of the many different molecules of DNA to try many different
possibilities at once.[11] For certain specialized problems, DNA computers are
faster and smaller than any other computer built so far. Furthermore,
particular mathematical computations have been demonstrated to work on a DNA
computer. As an example, DNA molecules have been utilized to tackle the
assignment problem.[12] Aran Nayebi[13] has provided a general implementation
of Strassen's matrix multiplication algorithm on a DNA computer, although
there are problems with scaling. In addition, Caltech researchers have created
a circuit made from 130 unique DNA strands, which is able to calculate the
square root of numbers up to 15.

Perhaps it can be used in nanobots. Also being slow isn't necessarily a
disadvantage if it could be made much cheaper. Biology can rapidly self-
replicate out of everyday materials. It can also run efficiently on chemical
energy and even sunlight. Though these likely don't apply to this research,
just biocomputers in general.

~~~
dnautics
> Also being slow isn't necessarily a disadvantage if it could be made much
> cheaper.

silicon (processed sand) will always be cheaper. In order to make (nano)
artifical biological parts, you have to use really expensive chemical building
blocks, or, if it's biologically (and not petrochemically) derived go through
expensive finishing steps.

> Biology can rapidly self-replicate out of everyday materials.

Then you're adding at least a micron of space overhead.

> It can also run efficiently on chemical energy and even sunlight

Also true of mechanical parts, for example palladium nanoparticles running off
of peroxide, or light-driven silver nanoparticles. running off of sunlight is
a nontrivial process for biology (turns out oxygen wrecks a lot of really
important enzymes), and biology is actually not very good at it.

------
delackner
I wasn't sure which article to submit, since this was on gimodo, popular
science, and various other places, but this (albeit behind a paywall) is the
original journal article.

~~~
anigbrowl
That's always the best choice. Here's the paper itself: [http://life-
sciences.biu.ac.il/files/life-sciences/media/nna...](http://life-
sciences.biu.ac.il/files/life-sciences/media/nnano.2014.58.pdf)

Searching on the title and appending 'filetype:pdf' for Google will often
return a preprint or a copy from the authors' institutional website.

As for the content - wow, amazing work. I'm no biotechnologist but this seems
like the gateway to an algorithmic approach to medicine. I wonder if it could
be turned around to measure intra-cellular processes and send out signals by
producing nonreactive chemical tracers...oh yes, it's addressed on page 4.

How long before we see biological botnets? Fascinating stuff.

~~~
anon4
> biological botnets

What, you mean parasites that control their host's behaviour in order to
propagate themselves? Those already exist.

Granted, they don't mine bitcoins just yet.

~~~
zwegner
Yep. One of my favorite examples:
[https://en.wikipedia.org/wiki/Ophiocordyceps_unilateralis](https://en.wikipedia.org/wiki/Ophiocordyceps_unilateralis)

Part of a pretty cool Wikipedia category:
[https://en.wikipedia.org/wiki/Category:Mind-
altering_parasit...](https://en.wikipedia.org/wiki/Category:Mind-
altering_parasites)

------
rotten
Soon your cat can be your laptop!

~~~
andrewflnr
It will then find some way to sit on itself while you're working on it.

