
Bacteria with synthetic gene circuit self-assemble into working device - isof4ult
http://pratt.duke.edu/news/pressure-sensor
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anon1253
This is so exciting! The field of synthetic biology is advancing rapidly, and
apart from the social stigma at times: it's a really promising technology.
When I was still an undergrad I was lucky enough to participate in the
International Genetically Engineered Machine (iGEM) competition. But that was
back in 2010, a lot has changed since then!

Check out the winners of my year:
[http://2010.igem.org/Team:Cambridge](http://2010.igem.org/Team:Cambridge) vs
this year
[http://2016.igem.org/Team:Imperial_College](http://2016.igem.org/Team:Imperial_College)

And these are just undergrads over the course of a summer!

[1]
[https://en.wikipedia.org/wiki/International_Genetically_Engi...](https://en.wikipedia.org/wiki/International_Genetically_Engineered_Machine)

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ballade
Does anyone with more expertise in this field know what resources/books there
are to learn more about systems and synthetic biology?

Also, what are the dozen or so subfields in biology that may have more
relevance than others such as epigenetics, evolutionary bio, comp. bio etc. to
engineering biological systems?

One last question, from your perspective, would it be more useful if one were
coming from an engineering background to synthetic biology or purely a biology
background to synthetic biology whilst learning some basics engineering
principles? I'm currently studying physics and mathematics.

~~~
jfarlow
I have built a company for designing proteins for use in therapeutic synthetic
biology (CRISPR/CAR/SynNotch/etc. systems). My undergrad background was more
chemistry/physics/philosophy while my graduate school was in
biochemistry/cell-bio, and I think that accidentally set me up well to work in
synthetic biology. The books have yet to be written :-)

The rules in synthetic biology are sloppy versions of the rules found in
chemistry and physics. The logical/statistical/mechanistic tools of the the
more mathematical sciences are extraordinarily useful to have in mind, however
you have to get comfortable with a lot fewer 'correct' answers and a lot more
unknown or even unknowable variables. Some tools like population level
statistics are really useful tool in biology, while complex logically
sequential steps used in programming really don't work so well in the wet
world of biology. Synthetic biology is very much parallel programming of
thousands of 10-line programs, rather than 10, thousand-line programs. To me
it seems the hardest part for people who haven't done biological lab work to
understand seems to be the intuition for how biological proteins interact with
each other, and the scale of their interactions in time and space, both
upwards and downwards - relative to the cell itself, as well as the chemistry
involved in the cell. That intuition at the 'meso-scale' is uncommon, and
building it without actually running experiments in lab is tricky.

It's still a new field, so it's not particularly well-articulated in terms of
sub-fields right now. But there are huge differences in terms of whether one
is studying prokaryotic systems, single-cell systems, or mammalian systems. Or
whether one is manipulating proteins, DNA itself, or biologically compatible
materials. Or whether you're building academic sensors, commercial systems, or
therapeutics. Though they all involve overlapping ideas, the edges to each
system are really pretty different to my mind. Another tricky thing for those
without the biological background is to be able to judge whether a synthetic-
biology tool is useful in the context of biology (and not just a toy). What is
a cool and useful trick for a digital computer or an physical robot can often
be either trivial or impossible in a cell, while engineering a cell to
biologically integrate a novel sensor can be an amazing breakthrough. Nano-
scale metal gears, robots and antennas with _massive_ energy reserves just
don't make sense in the warm, wet, energy-efficient, Brownian world of
biology.

iGEM is a great place to start - it's an academic competition for
undergraduates - a lot of exploration going on there that is relatively
accessible, if a bit unrefined. [1]

Our company, Serotiny, is trying to bring a plain-language understanding to
the synthetic design of novel proteins, which are often the payloads and tools
of synthetic systems like Cas9 in the article. [2]

Addgene is a non-profit physical repository of many of the genetic 'tools'
used, and they have some nice blog-posts and tutorials for beginning
scientists. [3]

SynBioBeta is the only real industry group around right now for the field, and
they keep pretty well up-to-date with interesting industry news - new
companies, new products, new events related to synthetic biology. [4]

[1] [http://igem.org](http://igem.org)

[2] [https://serotiny.bio/notes/proteins](https://serotiny.bio/notes/proteins)

[3] [http://blog.addgene.org/](http://blog.addgene.org/)

[4] [https://synbiobeta.com/](https://synbiobeta.com/)

~~~
ballade
Thank you for your detailed answer!

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verytrivial
For these nano construction techniques there always seems to be a _massive_
chasm between what they are demonstrating and a trivial _practical_
application. Like "we demonstrated cutting someones hair by running a combine
harvester over a field of dummy heads." Really? Oh. Keep me informed of
progress, I guess?

~~~
agumonkey
the realm of nanobiology is a bit different from our world; I talked to a dude
who makes DNA game of life based computers, couldn't resist asking him about
turing completeness, he said that's all fine but at 500 base-pair
thermodynamics conditions start to break the structures so "programs" can't be
long enough for such questions anyway.

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amelius
Bacteria _are_ already working devices.

~~~
unwind
I'm not a native speaker, but the primary meaning of "device" is "piece of
equipment made for a particular purpose" (see Wiktionary [1]).

I really don't think evolution counts, here.

1:
[https://en.wiktionary.org/wiki/device](https://en.wiktionary.org/wiki/device)

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lbill
This could become an interesting alternative to lithography!

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jlebrech
now make them build a self aware ai that also breeds them for survival, what
can go wrong?

~~~
tyingq
I don't think you need AI for anything to go wrong. Self-assemble is probably
enough for something to go wrong. If they could self-assemble from some
relatively abundant resource, and had a long enough lifespan, you get the grey
goo problem.
[https://en.wikipedia.org/wiki/Grey_goo](https://en.wikipedia.org/wiki/Grey_goo)

~~~
adrianN
Eh, with bacteria I wouldn't be too worried. The real world is a harsh place
for bacteria. All kinds of things want to eat them. Surely something would
provide balance before the whole planet is turned into a big E.coli colony.

~~~
noir_lord
> Surely something would provide balance before the whole planet is turned
> into a big E.coli colony.

Probably evolution has had a long run at evolving things to do that but how
badly would we screw ourselves and the planet in the meantime before an
equilibrium was reached.

The only thing that slightly cheers me up is that apart from when bacteria
wiped out almost everything by pumping out oxygen we haven't really seen that
situation again, if it was a low hill to climb you'd think we'd have seen it
already.

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colanderman
Bacteria _with a synthetic gene_. This is not a newly-discovered property of
naturally-occurring bacteria, as the title would lead you to believe.

~~~
dmichulke
Is there a systemic reason for why they can't or do you mean that only "none
of the known bacteria don't" (build sensors)?

~~~
colanderman
I mean, the article is about a gene that caused the bacteria to build sensors,
not anything else. I don't know what bacteria can or can't do. (E.g. Ants are
known to self-assemble into useful structures such as bridges. So that being
true of bacteria is believable, hence my confusion.)

