
Synthetic Biology - jmelkington
https://axial.substack.com/p/axial-matrix-7-synthetic-biology
======
WhompingWindows
I worked in Syn Bio from 2008-2010, long before CRISPR came onto the scene. I
worked on a couple of iGEM projects, that's the international genetically
engineered machines conference at MIT.

The basic premise was we would design E. Coli "strains" or "models" that had
foreign DNA inserted via commonly-shared genetic tools. It is comparable to
using Linux as a shared OS, lots of other FOSS developers helping each
other... except that to get totally new DNA into your E. coli, you had to have
it shipped in on dry ice from a willing lab halfway around the world. So, you
can see why the field is much smaller and more niche than anything software-
related...downloading a library is WAY faster and cheaper than shipping in a
new genetic module.

CRISPR would've been a game changer for us. We could've much more easily
edited gene sequences, though it still would've been hard to get foreign DNA
from other labs...I don't believe CRISPR is good for writing huge new
sequences... But small changes, small modifications, would've been MUCH faster
with CRISPR. We could've gotten a foreign DNA sequence and then tried out 100
different mutations very simply, perhaps discovering an even better
functionality than nature's original code.

~~~
dnautics
Crispr is not necessary for e coli mutagenesis. For plasmids you really want
to use Gibson assembly. For chromosomal modification lambda red is as easy as
crispr.

Gibson assembly is basically foolproof. I trained an intern with almost no
molecular biology wetlab experience and in three months he designed DNA for
and made fifty mutants (I picked whuch mutations to try) and ran biochemistry
on half of them:

[https://pubmed.ncbi.nlm.nih.gov/24934472/](https://pubmed.ncbi.nlm.nih.gov/24934472/)

For yeast, you need neither. Just drop the DNA in and the yeast takes it up!

~~~
koeng
For doing mutagenesis on plasmids, you don't even need gibson. Overlapped
primers do some weird circularization during PCR, so for point mutations you
don't even need gibson mix.

I'm personally a big fan of synthesis + GoldenGate for building genetic
circuits. Gibson, IMO, destroys reproduciblity (how many different PCR kits
are there?) and leaning towards Gibson assembly over enzymatic assembly
methods (GoldenGate, maybe even BioBricks) makes biotech an Ivory-Tower
exercise, since not everyone has access to oligos.

~~~
vikramkr
How is gibson ivory tower? It's literally just based on overlapping sequences.
And how is it hard to reproduce? You select out colonies and verify with
sanger. These are not things that are inaccessible to most people, especially
if you live near a DIY bio hacker space, and if you get involved in the
biohacker community you'll get a sense of what providers ship to residential
address, where to get certain equiptment, and so on. Just googling will get
you information that can help you figure out how to get what you need.

[https://medium.com/@ThatMrE/a-guide-to-diybio-
updated-2019-a...](https://medium.com/@ThatMrE/a-guide-to-diybio-
updated-2019-abd0956cdf74)

~~~
koeng
Reordering of oligos is expensive, which makes people not reproduce. Sanger
sequencing is pretty expensive ($5 sure, but over 5kb on 3 different
constructs becomes pricey). PCR machines also ain’t that cheap (when you’re a
noob and don’t know what to buy), especially when you need to do more than 8
PCRs at a time.

In theory, works in practice, and in practice, works well in theory. Even for
experienced DIYbio folks, cloning isn’t just 1,2,3.

Also, PCRs themselves aren’t very reproducible. It’s not about the overlapping
sequence.

------
tbenst
SynBio in the 2020s smells a bit like green tech in the 2000s. I see a ton of
founders and funders with zero biology background thinking that they have the
vision and can just hire biology expertise.

Biology is ruthlessly unforgiving and complicated, and often times very low
efficiency. For example, it’s a bit amusing to see the ratio of CRISPR
mentions in startups vs the techniques actually being used by scientists. You
would never use CRISPR if you had the option of using Cre. I’ve made several
stable transgenic animal lines using Tol2 transgenisis, which is much higher
efficiency, too.

If you’re excited by the space, but don’t have a biology background, consider
joining an organization led by a biologist.

~~~
ros86
> I see a ton of founders and funders with zero biology background thinking
> that they have the vision and can just hire biology expertise.

Genuinely curious about your data here. The two first companies mentioned in
the article (Zymergen and Gingko) have founders with biology background. Many
other companies I know as well.

> You would never use CRISPR if you had the option of using Cre. I’ve made
> several stable transgenic animal lines using Tol2 transgenisis, which is
> much higher efficiency, too.

That probably depends on the organism you're working with. E.g. with baker's
yeast, my preference would definitely be CRISPR/Cas9 instead of cre
recombinase (see e.g.
[https://academic.oup.com/femsyr/article/15/2/fou004/534426](https://academic.oup.com/femsyr/article/15/2/fou004/534426)
).

~~~
tbenst
> Genuinely curious about your data here.

I invest a little in the space so have seen some pitches at IndieBio,
YCombinator, and talked with a bunch of companies. There are indeed some
really great founders with biology background as you point out. But have been
seeing more and more founders from software background. The enthusiasm is
great, and people with software backgrounds have a ton to contribute! Just
maybe shouldn’t be the CEO.

> baker's yeast, my preference would definitely be CRISPR/Cas9

I’ve never worked with yeast but was under the impression that you could just
give them plasmids and call it a day?

------
sangfroid_bio
A major issue with biology is the compensation. Biology compensation is
notoriously bad outside of accredited medicine.

~~~
1996
So you mean you can hire cheap?

Couple that with the recent fast technological advances (ex: rejuvenating stem
cells), the many possible applications, cheap capital, and I see all the
ingredients for a boom.

Just like the 2000s were about internet and the 2010s were about fintech and
cryptos, the 2020s may be about biohacking

~~~
roosterdawn
I (do not) look forward to seeing the results of "failing fast" here. The
conspiracy theorists are convinced that this is how we got to COVID19 in the
first place, and while I'm not really convinced there, I really do not enjoy
thinking about the potential of such technology to create bioweapons of a
scale never seen before.

~~~
Obi_Juan_Kenobi
Definitely don't look up 'gene drive' then :)

------
kharak
On a tangential note: I've seen the upcoming rise of Syn Bio for quite some
time now. But I've never figured out, how to participate / help its growth as
a pure SWE.

Job offers related to that field require a skill stack, that I have zero
investment in. I'm also in my thirties, so starting from scratch isn't really
an option. Someone else here from a similar background, who managed to get a
foot into the Syn Bio industry?

 _edit_ : Should have mentioned, I'm currently living in Europe. Although I
might give that up in order to break into the industry.

~~~
jfarlow
There is a niche of companies that are starting to let software eat biology.
It's one of the latecomers to utilize the improvements, but they do exist.

[My company is one - we have pure software engineers on our team, we build
synthetic therapeutic proteins]

Check out companies like Zymergen, Benchling, Synthego, Bolt Threads, Gingko,
Riffyn, & Teselagen.

In terms of pure software, helping open source scientific libraries, image
processing for science, and genomics software would help out what is otherwise
an under-funded field.

------
neural_thing
It mystifies me how often Amyris is omitted from posts about synbio. Sure it's
not a hot startup, but it has commercialized more molecules than anybody in
the industry (and possibly as many as everybody else combined).

------
carapace
I find synbio terrifying. Think about what you know about the dysfunctions of
our field, IT, but with hardware-that-is-software and can eat you or make you
sick. A _computer_ virus can infect the Internet, a _virus_ can infect the
real world.

We should study life for at least two to five hundred more years before
attempting applications via these methods.

Genetic engineering applications (except for human health) should be banned,
IMO, until we have enough information to do it responsibly.

We already have species and methods of creating new variations that answer our
needs.

> Luther Burbank (March 7, 1849 – April 11, 1926) was an American botanist,
> horticulturist and pioneer in agricultural science. He developed more than
> 800 strains and varieties of plants over his 55-year career.

[https://en.wikipedia.org/wiki/Luther_Burbank](https://en.wikipedia.org/wiki/Luther_Burbank)

