
Biology's Master Programmers - llambda
http://www.technologyreview.com/featured-story/428187/biologys-master-programmers/
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Xcelerate
As a chemical engineer who loves programming just as much, I have had some
thoughts about bioengineering for a while now. Part of the problem is that the
immense complexity involved in living organisms is unpredictable, even with
today's computing technology.

Human-engineered circuits are easy to predict; they were designed in a way
that made the most sense. With biology however, something that appears to be
working may have a completely unrelated side effect that isn't noticed until
decades later, or even something so bizarre that it isn't noticed until
hundreds of years later in future generations.

The way we currently find treatments (grossly oversimplifying) is to grab some
substance that looks like it might work, test it in animals, test it in
humans, wait a while to make sure nothing really bad happened, and then
prescribe it as a drug.

If computers get advanced enough, I would much prefer the case where all of
these interactions are fully simulated. You can go through millions of
variations of substances all while tracking every change they make to each
part of the virtual organism. Obviously, this is a VERY long way off, but it
would be nice because we wouldn't have to worry about unknown side effects.

Of course, our current way is the best we've got, and it saves millions of
lives each year, so while there may be some future risk, we're doing the best
we can.

*On a somewhat related note, I've always thought it would be cool to have programmable blood filters. In other words, you could essentially provide the type of molecule or cell you are looking to trap, and then something like a ccd would either redirect it or let it pass through.

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Daniel_Newby
> ... I've always thought it would be cool to have programmable blood filters.

It is called flow cytometry. <http://en.wikipedia.org/wiki/Flow_cytometry>

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Xcelerate
Wow, that's pretty cool! I didn't realize people were already working on this.

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j_s
> Researchers today may alter, copy, and paste DNA with increasing ease, but
> they still struggle when it comes to actually composing DNA that does
> anything useful.

Leo Laporte did a TWiT Special on this recently: <http://twit.tv/show/twit-
live-specials/126>

The discussion centered around taking existing genomes and splicing in
functionality. The example given was setting up a Kickstarter project for
trees that glow in the dark. The government is aggressively pursuing this
tech.

[Edit] Direct links:

dna editor: <http://www.genomecompiler.com/>

dna printer: <http://angel.co/cambrian-genomics>

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corwinbad
Hi j_s, this is Omri from Genome Compiler - thanks for the mention!

Anyone can download our free gene/genome design software and start ordering
DNA today at genomecompiler.com

Omri

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lupatus
I checked-out your company. It seems really cool. And, I think that it is
really awesome that you are commercializing this tech and advocating it so
much on HN (seriously). But, the part I am having trouble understanding, as an
amateur, is what I do with the DNA once I order it.

With software, I double-click an executable or go to a web address, and BAM! I
can share pictures of kittens with my friends. How do I turn that DNA into a
bio-luminescent kitten, for example, that I can show off to my friends?

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corwinbad
Hi Lupatus, thanks!

Well, today you have to know some biology and have access to lab (or community
lab like bio-curious or genspace) to "execute" the biology. We are trying to
abstract biology to make it more accessible to people outside of the research
labs then you can order the DNA and transform living things in your kitchen
:-)

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grhino
"We use genomics and informatics to find a gene cluster. But that's an
information unit," Verdine says. "We have to get the molecule. Synthetic
biology involves coaxing the cluster into biosynthetic factories, which then
produce the molecules. If we don't have the molecule, the cluster is useless."

Once you have a scalable process for producing chemicals that are potential
drugs via DNA sequencing & analysis and bacterial synthesis, how do you figure
out what disease process to test those chemicals against? Do you shotgun them
against a large set of disease processes? Purify the product, analyze it, and
store it in a database and do theoretical work to pick out candidate diseases
for the chemical? Is there something about the gene cluster that gives clues
as to what the chemical might be doing for the organism?

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refurb
The knowledge of what the gene cluster does (by creating animals where that
gene is unnaturally over or underexpressed) gives insight into what the genes
product might do.

Not that different than what is currently done in biopharmaceutical research.

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pdelgallego
I will love to be able to switch career path at some point in the (far)
future, but I don't see how to start doing the move.

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username3
_Researchers today may alter, copy, and paste DNA with increasing ease, but
they still struggle when it comes to actually composing DNA that does anything
useful. They are still editing nature's code and learning from it. It turns
out that for now, nature is still the best programmer._

Sounds like Intelligent Design.

~~~
Lambdanaut
I tend to see the evolutionary process as a sort of pseudo intelligence,
constantly striving to make the best organism for the environment it's in.

