

Synthetic biology is heading for the cloud - judegomila
http://www.judegomila.com/2012/08/synthetic-biology-is-heading-for-cloud.html

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mlerner
Intern from Teselagen here. <shameless plug> We have a private Beta that you
can sign up for on our website if editing your own DNA sequences is appealing
to you: <http://www.teselagen.com/user/registration> </shameless plug>

It's pretty cool to see Synthetic Biology getting coverage on HN. One of the
really interesting ideas that scientists are starting to grab a hold of is
that of "biological parts". People have started compiling these biological
circuit elements and figuring out how they work when exposed to different
stimuli [1]. The ultimate aim is to standardize the usage of these parts so
that you could design an organism in your browser, figure out whether it will
work or not (based on a super-secret algorithm), and get the resulting
functional organism shipped to your lab bench in a couple of days. As a
reference, right now it can take up to 2 months to even create an initial DNA
product with traditional methods. From there, it could take months to get your
organism working correctly. New DNA synthesis techniques will dramatically
speed up some of the initial steps (something Teselagen has done).

An addition to the article I'd make is that Teselagen is actually letting
people leverage new DNA synthesis techniques produced by a couple of groups
(the Venter institute is one) to design better biological circuits (as in
faster, better, stronger). If you are interested in reading about how
scientists have begun to overcome some of the many barriers to biological
circuit design, there's a good intro to advances in DNA synthesis techniques
here: <http://j5.jbei.org/j5manual/pages/1.html>

[1] partsregistry.org

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frisco
I've been waiting for an account for a couple months with you guys now... how
long until you start taking more people?

~~~
biohacker
My apologies frisco. I'm co-founder at TeselaGen. We've been running like
crazy, currently engaging with some of the largest biotech companies in the
world. We would love to have you as a user and get your input as well. We've
been holding invitations until we release our upcoming new version, later this
summer. We'll be contacting you soon!

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rflrob
> DNA needs to be read. If you want to identify the genetic code of something
> you need to sequence it. This is like being able to open the source code
> other people's programs to see how things work, debug your experiment and is
> the analogue of an oscilloscope in electronics.

While sequencing is incredibly useful for some applications (I spend my time
working on Illumina current-generation "Next-gen" sequencing), we don't
understand nearly enough about the regulation of genes for a sequencer to be
analogous to an oscilloscope. It is, at best, a wiring diagram, and really
much closer to a parts list. Oxford Nanopore seems really exciting, especially
for field biologists, but it's at best 1 order of magnitude better (in terms
of cost, speed, and sensitivity) than current technology; historical trends
have seen a Moore's law-style exponential increase in capabilities, though, so
Oxford Nanopore isn't really a quantum leap.

~~~
xaa
For RNAseq the analogy works pretty well.

~~~
siganakis
Isn't RNASeq more like looking at really verbose log messages? Where you only
sample 1% of the log messages and may be looking for an event that happens
0.01% of the time?

~~~
rflrob
The general assumption is that if you're looking for a transcript that falls
below the detection threshold of RNAseq, then it's likely to be so weakly
expressed as to be biologically negligible. Furthermore, with the bursty
nature of gene expression, an average of 2-3 copies per cell (about my limit
of detection in a reasonably sized experiment) could still have a sizable
fraction of cells with none at all.

That said, the downside of the Oxford Nanopore for RNA-seq is that, while you
get longer reads, it's not yet really clear how _many_ reads you get, which is
at least as important for trying to find those moderate-lowly expressed genes.

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jrkelly
As a founder of one of the companies mentioned (Ginkgo BioWorks), I have to
say this is actually a very nice outline of the industry. It's not clear yet
if there's enough of a market for individual services to be broken out and put
in the "synbio cloud". Not even clear if there is enough of a market for
platforms like Ginkgo that deliver a whole organism to spec vs application-
focused companies. Early days, but it's a great field for those interested in
getting out of the iphone app rat-race (no offense to the author). We hire
lots of programmers.

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jsmcgd
Does anyone have any good ideas on how we might mitigate the negative
consequences of this technology?

I recently dismissed the problems of people printing firearms in a 3d printer
as not really being much of a threat as currently firearms are already
ubiquitous. However having a potential personal bio-weapon design lab on your
desk, would seem to suggest were are entering a whole new paradigm in dangers
to humanity and our biosphere.

As an example and a serious question: why won't someone eventually create a
virus tailor made to target their enemies? Whether that's an entire race of
people, an individual or a family.

The genie is definitely already out of the bottle so I guess the only solution
is better defences. We're going to have to get good at identifying threats
(possibly in real time) and be able to create effective solutions near
instantaneously. Or isolate ourselves in self sufficient habitats as a
precaution.

In my mind's eye I can see Bill Joy tapping his watch and saying "Any minute
now ..."

<http://www.wired.com/wired/archive/8.04/joy.html>

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fghh45sdfhr3
_I recently dismissed the problems of people printing firearms in a 3d printer
as not really being much of a threat as currently firearms are already
ubiquitous._

Your reasoning on guns was correct. Remember how almost every year we worry
about what kind of influenza we'll get? We all worry about a repeat of the
1918 flu, which is quite likely on any given year.

Remember how antibiotic resistance keeps getting worse and worse (or better
and better from the bacteria's perspective)?

HIV originated in nature, probably somewhere not too far from where Ebola is
natural brewing now.

Our number one threat is mother nature. Her and other humans living close to
domestic and wild animals around the world and air lines.

At any given time we might have to cope with an 1918 like flu.

Custom tailoring a virus to include one people but not other is going to be
extremely hard. We are all very closely related. Human conflict tends to be
between neighbors, and for example the people most genetically similar to the
Israelis are the Palestinians. So the probability of a custom tailored virus
is far, far, FAR lower than the probability of a natural don't-give-a-crap-
who-it-kills virus.

~~~
dedward
the same tools that would trivialize creating such a virus would also
trivialize a cure.

~~~
mckilljoy
I'd disagree, I think it is a lot easier to create a virus that wantonly
destroys life than it is to create a cure that puts everything back together.
I could email out a script that just executes "sudo rm -rf /" on everyone's
computer, and it would probably ruin a lot of people's lives.

Additionally, cures by their nature will always lag behind diseases, people
won't invest resources curing a disease that doesn't exist. A non-trivial
amount of damage would occur before society reacted to the threat.

~~~
graphene
The parent's reasoning would probably apply more to a vaccine than a cure.

Also, it's not illogical for there to be a demand for (research into)
protections against threats which have not materialized yet, but seem to have
a chance of doing so. As the prospect of portable bioweapons becomes more
likely, there will be increased incentive to come up with protections from
those weapons, even if they have not yet reached viability.

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c0nn0r
I'm a Co-Founder of Synbiota a startup in this area. We've shipped a beta of
GENtle, an open-source, web-based (HTML5) DNA editor that you can try right
now at:

<http://synbiota.com>

We're also in closed beta of our integrated environment for collaboration,
project management, file storage and DNA synthesis ordering etc. We have a
number of iGEM teams as well as some DIYBio groups that are currently using
the platform in their everyday work, which is pretty cool ;-)

We've been a part of Mozilla's WebFWD accelerator since last Fall which has
been a huge boost for us. Definitely check them out if you are working on a
web-standards based startup!

We also recently launched the S Prize - our contest to incentivize the
development of open-source plug-ins for GENtle (the DNA editor) - we have a
cash purse of $5k on the line for any developers who submit the most useful
and delightful contributions.

Check it out at:

<http://sprize.synbiota.com>

Please spread the word!

~~~
c0nn0r
Ahh, forgot to mention; we've also recently partnered with Genomikon
(<http://genomikon.ca>) to offer biological kits (think Arduino for bio)
through Synbiota (all documentation and DNA code is hosted and editable on the
platform).

So far we've only sent out one kit to a DIYBio group (still finalizing up
production), but we hope it's the first of many.

~~~
GregBuchholz
When do you anticipate having the kit available for sale to the general
public?

~~~
c0nn0r
We're shooting for September, but it will still be in limited release.

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GregBuchholz
Where does an engineer/programmer start to come up to speed on synthetic
biology? Are there any essential books in the field like "Learn Bio-hacking in
21 Days", "Bio-chemistry for Dummies", or "The Structure and Interpretation of
DNA"? Or do those still need to be written?

~~~
judegomila
"Synthetic Biology - a primer" [http://www.amazon.com/Synthetic-Biology-Paul-
S-Freemont/dp/1...](http://www.amazon.com/Synthetic-Biology-Paul-S-
Freemont/dp/1848168632)

~~~
GregBuchholz
The book seems to be out-of-stock/back-ordered everywhere, but I was able to
find a sample chapter, and it looks interesting:

[http://www.worldscientific.com/doi/suppl/10.1142/p837/suppl_...](http://www.worldscientific.com/doi/suppl/10.1142/p837/suppl_file/p837_chap01.pdf)

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jboggan
Transcriptic (<https://www.transcriptic.com/about/jobs>) is definitely another
company to watch in that space, and they are hiring. Hopefully the legions of
unemployed bioinformatics and cast-off pharmaceutical researchers will take
their expertise to these new enterprises and catalyze this nascent revolution.

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subrat_rout
The most part of synthetic biology is a brick and mortar science which will
need wet lab bench and fiddling fingers to do the development of the
prototypes to test the hypothesis. So Synthetic Biology in its entirety is not
going to cloud.

Synthetic biology involves several steps or components such as designing a
gene,synthesizing it, cloning it into appropriate vector and then expressing
it. Then studying the expressed gene product in the presence of multitude of
other gene products in an unknown environment poses it's unique challenges.
However several components of Synthetic biology can be moved to cloud. Take an
example of designing a gene of interest. It can be done taking a vast amount
of data/information of several similar genes from clouds and analyzing and
then optimally designing the gene of interest.

The second example is testing the effect of the gene or its product in silico
( on a Lab-on-a-chip) before going to test it in real animal models thus
saving costs and time. So in-silico simulated lab animal software models
comprising of complex metabolic pathways can be stored in cloud for analysis
from several researcher groups or any groups across world. And this is just
the surface I am trying to scratch.....

~~~
danielrhodes
The wetlab component of synthetic biology seems unnecessary when a lot of that
work can be automated, which is where this idea of a cloud for biology has
merit. Of course if you can do accurate simulations as you describe, that
would be the best route.

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mckilljoy
I like how this summarized the state of the industry, but I feel like "the
cloud" angle was a bit forced for a lot of those companies. Most of these
companies had nothing to do with the internet / cloud.

~~~
jrkelly
I think by cloud he just meant "outsourced services." DNA synthesis definitely
has nothing to do with the internet.

~~~
mckilljoy
Hah, I agree, but when did "cloud" become synonymous with "outsourced
services"? That's kind of an abuse of the term :-)

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mckilljoy
I didn't realize YC was investing in bio companies now. Is that a recent
development?

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corwinbad
Hi, this is Omri, the founder of Genome Compiler (<http://genomecompiler.com>)
mentioned in the article. It's great to see many of my fellow entrepreneurs in
this field shamelessly plugging away their companies :-)

Anyhow, this is indeed a great field to be in and I'm happy HN is taking
notice.

I recommend this interview we gave for Leo Laporte (TwiT.tv) about this field:
[http://www.genomecompiler.com/news/2012/6/4/democratizing-
cr...](http://www.genomecompiler.com/news/2012/6/4/democratizing-
creation.html)

Feel free to contact us for more information: info@genomecompiler.com

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foobar2k
I like the comparison to the "building computers in your garage" era, this
really is the start of something huge.

Making a new technology space accessible to the masses is always the first
step in a revolution.

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tejaswiy
I have no idea how synthetic biology works, but have a couple of questions
from the applications section in the link.

They talk about designing vats of bacteria that extract gold from water. If
this level of customization is possible, is it also possible that you could
use this to create new disease strains ? For example, can you take a
Tuberculosis and engineer it to make it harder to cure? Or create entirely new
diseases with elements from different infections?

~~~
Cixelyn
yup that's one of the biggest fears with respect to bioterrorism.

engineering bacteria to produce new strains or even deadlier toxins is well
within realm of synthetic biology (although currently extremely nontrivial).

Falling synthesis prices and better assembly techniques however will make the
repeat-test cycle fast enough to debug and engineer such organisms.

~~~
mbreese
However, even if one _could_ produce such an organism with diybio technology,
not killing oneself in the process would still be non-trivial.

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caycep
Another thought is: how "wet" are a lot of the equipment being sold/marketed
to "home"/"bedroom" synth biologists? IIRC from college days, there was a huge
overhead in terms of, not only the apparatus (which I gather is coming down in
cost), but also the chemicals in use, which require all sorts of safety regs,
OSHA compliance, etc etc. How much of a barrier is this nowadays?

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caycep
i remember ginkgo bioworks in the news, along w/ the MIT mail order biobank.
Any pointers onto papers that have come out of this or new medicines, etc?

Has any synth organisms other than what's come out of Venter's lab been
created and proven viable?

~~~
jrkelly
>Has any synth organisms other than what's come out of >Venter's lab been
created and proven viable?

You should think of the Venter work as a technical demonstration of building a
_very_ large piece of DNA (>500 kilobases, a small genome) and transplanting a
whole genome into a microbe that had its original genome removed. Most of the
immediate practical applications of synthetic biology don't need pieces nearly
that large. If you want to add a genetic pathway to produce a chemical
product, it's typically <10 additional genes that need to be added to a
production microbe and that will be <50 kilobases typically.

> Any pointers onto papers that have come out of this or new > medicines, etc?

There are lots of industrial microbes out there now. For example, most Amino
Acids that go into food supplements are made at massive scale - >1M tons/year
by engineered microbes.

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skosuri
Are you also the PGA driving accuracy leader?
[http://espn.go.com/golf/statistics/_/type/type2/sort/driveAc...](http://espn.go.com/golf/statistics/_/type/type2/sort/driveAccuracyPct)

~~~
jrkelly
Sadly no, as I'd clearly be making more money. Sri, admit that this is the
best Synbio post you've seen on HN.

~~~
skosuri
Oh, Jason, not Jerry. This must be you then. <http://jasonkelly.com/>

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dminor14
Seriously cool and scary technology. "many of the startups are going for
"killer apps" first." he wrote this with no irony intended! I'm considering
getting a degree in "bio-informatics"

