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Leap in DNA synthesis slashes time to build new genetic sequences

spectrum.ieee.org

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Re: Leap in DNA synthesis slashes time to build new genetic sequences

#21

Post by the__alchemist »

Bad-ass! Getting small seqs "oglios" is cheap/fast. (as stated in the article) (IDT or Sigma will courier it to you same or next day, and is ~$10 per) But longer ones is much more expensive!

So... is the "Generative AI" tie in (Mentioned many times, starting at the top of the article) used mainly get funding and press? The core part of this seems to have nothing to do with AI. I am sus this is bullshit marketing based on #1: How many times I've clicked an article, and have AI blasted all over it for sus reasons, and #2: Being able to cheaply and reliably synthesis custom DNA seqs longer than a few hundred/thousand bps is a broadly useful tech for current and future applications.

So: #1: This is really good news. #2: Do better with the hype/bull. It undermines your credibility. So now I start questioning whether this works as well as advertised, and what else they are being shady about.

Re: Leap in DNA synthesis slashes time to build new genetic sequences

#22

Post by biophysboy »

the__alchemist wrote: post #21

Bad-ass! Getting small seqs "oglios" is cheap/fast. (as stated in the article) (IDT or Sigma will courier it to you same or next day, and is ~$10 per) But longer ones is much more expensive! So... is the "Generative AI" tie in (Mentioned many times, starting at the top of the article) used mainly get funding and press? The core part of this seems to have nothing to do with AI. I am sus this is bullshit marketing base…

I used to order $10 oligos all the time. The extra length is cool, but I was honestly more impressed by the claims on sequence accuracy in the article. Even a single base pair change can affect the genetics and physics of DNA.

I broadly agree with you on the AI hyping. Data quality and quantity is not high enough in my opinion.

Re: Leap in DNA synthesis slashes time to build new genetic sequences

#24

Post by dnautics »

bonsai_spool wrote: post #9

This is not a practical challenge - I order DNA from Twist at these ‘large’ scales trivially without needing to do oligo hybridization magic. The DNA arrives in a month - but considering how many oligos sidewinder calls for, not clear how they could be faster.

12kb, you can get three gblocks in a week and change and have them assembled in two days.

Re: Leap in DNA synthesis slashes time to build new genetic sequences

#25

Post by dnautics »

cge wrote: post #13
bonsai_spool wrote: post #9

This is not a practical challenge - I order DNA from Twist at these ‘large’ scales trivially without needing to do oligo hybridization magic. The DNA arrives in a month - but considering how many oligos sidewinder calls for, not clear how they could be faster.

At a basic level, methods of combining oligos to produce long strands have been known for ages. The challenge is to be able to produce them with low enough error, high enough yield, and enough freedom on sequence. Low error improves your yield, reduces the amount of purification and amplification needed, and lets you make longer strands. Sequence constraints can be significant, too, especially around repeats. If you'…

> not-so-great sequence

are the limits on not-so-greatness for sidewinder known?

Re: Leap in DNA synthesis slashes time to build new genetic sequences

#26

Post by amirhirsch »

cge wrote: post #13
bonsai_spool wrote: post #9

This is not a practical challenge - I order DNA from Twist at these ‘large’ scales trivially without needing to do oligo hybridization magic. The DNA arrives in a month - but considering how many oligos sidewinder calls for, not clear how they could be faster.

At a basic level, methods of combining oligos to produce long strands have been known for ages. The challenge is to be able to produce them with low enough error, high enough yield, and enough freedom on sequence. Low error improves your yield, reduces the amount of purification and amplification needed, and lets you make longer strands. Sequence constraints can be significant, too, especially around repeats. If you'…

https://ansabio.com/ advertising 50 kb

Re: Leap in DNA synthesis slashes time to build new genetic sequences

#27

Post by mattbettinson »

vintermann wrote: post #14
Tade0 wrote: post #10

> Sequences of that length can encode entire biochemical pathways, laying the groundwork for engineered microbes that manufacture drugs, biofuels, or specialty chemicals, and eventually to the assembly of vast DNA constructs approaching complete artificial genomes. Never mind artificial genomes - let me have a snapshot of my DNA sequenced and re-created from scratch say 20 years later - telomeres and all.

What if the new one doesn't like you?

Just need the organs!

Re: Leap in DNA synthesis slashes time to build new genetic sequences

#28

Post by LarsDu88 »

mchinen wrote: post #3

Cool to see this from Brian Hie, who was doing interesting computational bio research at Meta's FAIR before they axed it. Interesting that this is work on the more physical/testing/manufacturing level than the computational, but it seems very useful. It's hard to quantify the impact of new foundational tools like this at launch. Most of the time it falls flat, but even the successes are difficult. For example, CRISPR…

I attended a talk by Brian at Stanford, and I asked why not just use Gibson assembly to stitch together 5 kb synthesized strands from a company like Twist Biosciences.

The answer I got was along the lines that they were simply going to get around to do the actual lab work at some point.

DNA synthesis technology hasn't really been a blocker for generative bio projects except at the full chromosome level.

And I think simply generating a full chromosome and booting it up without doing due diligence is probably a recipe for disaster.

We honestly aren't that far away from AI slop enzymes, AI slop ligases, and eventually AI slop bio weapons...

Re: Leap in DNA synthesis slashes time to build new genetic sequences

#29

Post by LarsDu88 »

amirhirsch wrote: post #26
cge wrote: post #13

Earlier quoted context omitted.

At a basic level, methods of combining oligos to produce long strands have been known for ages. The challenge is to be able to produce them with low enough error, high enough yield, and enough freedom on sequence. Low error improves your yield, reduces the amount of purification and amplification needed, and lets you make longer strands. Sequence constraints can be significant, too, especially around repeats. If you'…

https://ansabio.com/ advertising 50 kb

How is ANSA bio? I just got hit up by a recruiter for this company at random, and now I see them mentioned on Hackernews

Re: Leap in DNA synthesis slashes time to build new genetic sequences

#30

Post by BigTTYGothGF »

mchinen wrote: post #20
BigTTYGothGF wrote: post #11

Earlier quoted context omitted.

> Eventually one of these things will surface that will be GPU/transistor type innovations Why do you think that?

I just meant a big innovation that reshapes everything. I should have used 'level' instead of 'type' here. But there are a lot of analogies to computation in bio as a physical, atomic forces-driven, massively parallel computer, so it's possible there will be something related to electronics and computers that falls out. For example, there's also applications directly related to other fields including DNA storage of d…

> I just meant a big innovation that reshapes everything.

Biology has had many of these over the centuries.

> But there are a lot of analogies to computation

People have been saying this since pretty much the start of computation and I don't think anything's ever come of it.

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