Re: [DIYbio] Re: Ultra-Cheap DNA Printing/Sequencing

On Sun, Feb 23, 2014 at 12:01 PM, L <lakopa.palumbo@gmail.com> wrote:
> As for Ramen scattering and nanoscale lasers,
>
> Nanoscale lasers can be accomplished through focusing two photons in 180
> degree opposite phase at a single object. Destructive interference would
> cause the two photons to form an incredibly thin beam.
>
> I like the idea of Ramen spectroscopy, given that each base has its own
> highly unique vibrational signature. They probably do, but I personally
> don't know.

They do (old paper using UV excitation), sequencing has even been done
with Raman (Intel) based on concentration into and out of a PCR
reaction center.

> The reason I recommended using carbon nanotubes is because they have a
> highly controllable size and can be manufactured (relatively) easily. It
> makes them a nice candidate for such a small chip.

But you still have the issue of assembling them, and you haven't
really given a reason why a nanotube would be better than a nanopore
(which is much much more readily machined with something like a FIB,
or purchased off-the-shelf from SimPore, and integrated into a
layer-based microfluidic).

>
> Finally, if this chip became a reality, I wouldn't say it would be limited
> in its scope to impact the world if it were only manufactured by a few
> specialized facilities in the world. Again, virtually no one can make their

This sort of thing is getting quite common though, fabless IC
manufacturers are becoming more and more popular in everyday industry.

> own CPUs yet the modern computer is essentially the foundation of our
> civilization at this point. This is because it totally shifts who can
> produce data. The Internet world isn't about producing your own hardware,
> it's about producing your own software. With biotech, it's about producing
> your own wetware, which is a very convenient way to do both. At this point,
> though, it costs far too much to do even the simplest things. Making
> wild-type E. Coli glow should cost $1 at max. This chip would allow for
> that.
> I'm not saying its the end-all, though. It's just the beginning. With a
> whole world of bioengineers, the cost of synthetic biology will drop
> exponentially as they build on each other's technology. Eventually, a device
> that can do everything I want the sequencer/synthesizer we're talking about
> here to do and so much more could be produced using only a small culture of
> a few novel cells. Our sequence/synth machinery will eventually be made by
> what our sequence/synth machinery originally created, just as robots make
> robots today.
> BUT, for that to happen, we need a world already highly involved in
> synthetic biology. Kind of like chicken and egg, no?

I don't think so, the whole world wasn't drooling for computers and
yearning for some HP-type company to make it big in their garage...
the guy's starting HP in their garage were building the egg before a
chicken existed because they had a greater vision (whether it was to
further their own goals/desires or they were going for world-reaching
impact).

> So that's why I say we figure this out.

I'm less inclined to open-source something like this immediately,
since I've been incurring debt working on these and related ideas. I'd
have no problem doing that if I got something up and running, was able
to pay off my school debt and pool some money for further projects...
but at this point I'm quite wary of openly talking about the
secret-sauce I've been working on to this extent, as I genuinely fear
patent-trolls and companies that have the money to implement and take
to market stolen ideas.


I hope to have a nice relatively automated system up and running for
fabricating microfluidics sometime this summer, and I genuinely feel
that there is little need for new tech development, rather putting
existing pieces together in a novel fashion. It really is like how
Cathal was saying that no one has investigated agar purification
resin, or colicin self-selection... basically some people can only do
1 or 2 things in life, the people that might take longer but can do 3
or 4 things will be much more equipped to innovate. I.e. a biologist
can only count cells or pipette fluids, but combine that with computer
science and now they're a bioinformaticist or DNA gene function
hunter. If you add on Electrical Engineering or Optics, the scope and
possibilities for what they can accomplish grow tremendously (at the
cost of their increased time to learn, and often increased time being
a poor student, which arguably no one really enjoys).

There are lots of simply tricks buried in known science and
engineering, stuff that's so simple it blows your mind when you
realize it's beauty. Like all the crazy equations we used to have for
determining star future positions, all became much more unified with
some trickery of calculus. Sure the per-equation math got harder, but
the number of distinct equations dropped such that it more than offset
as far as cost-benefit.

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