Synthetic Biology
axial.substack.com
axial.substack.com
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.
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/
For yeast, you need neither. Just drop the DNA in and the yeast takes it up!
However, having worked with both prokaryotes and eukaryotes it definitely makes life easier. During my PhD (about metabolic engineering of S. cerevisiae) CRISPR started to get traction. Before I could incorporate one change at a time. Using CRISPR/Cas9 I could do up to 6 (at different places). That's a big deal!
I also PoC'ed CRISPR in a bacterium (C. glutamicum). Also there it opened up new avenues.
a 1:1 cloning is very much doable with terrible hands. You can reasonably do up to 8 pieces in the assembly, but as you get beyond 4 pieces it becomes important to follow the instruction exactly.
The craziest thing I did, though, was I cloned a (small) eukaryotic chromosome into an E Coli, by gibsoning against the telomere sequence.
At some point the difference becomes using very specially prepared competent cells and being very careful about how you get them in (the mechanism of electorporation is... not obvious), and of course one of the tricky things about gibson is that it's super salty, meaning that you have to be careful when electroporating.
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.
I don't know about that. I've bought 50-mer oligos at $20 a pop to do a 6-part assembly in my garage (I made a strain of yeast that generates cannabinoids). DNA oligos "basically last forever" if you handle them relatively correctly, even in a terrible defrost-cycling consumer freezer. Enzymes, especially specialty ones, not rock solid ones like modern TAQ, have a very short halflife in your freezer, especially if your freezer is consumer-grade.
> how many different PCR kits are there?
Yeah, just buy NEB. Seriously. Not worth screwing around with companies that have lower QC standards.
https://medium.com/@ThatMrE/a-guide-to-diybio-updated-2019-a...
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.
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.
If we look at the space, I think it is clear that biologist first companies have been the clear winners up to this point -- Gingko Bioworks being one clear example
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 ).
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?
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
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.
Disclaimer: I'm an investor in TeselaGen.
[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.
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.