With This CAD for Genomes, You Can Design New Organisms | Hacker News Reader

With This CAD for Genomes, You Can Design New Organisms

spectrum.ieee.org

70 pointsrbanffy24 comments

I would love to see this kind of application but I hate the way it's marketed here as something as "simple" as an informatics problem. I've seen phD student spending multiple years of their life dedicated to express one specific protein in one bacteria and it never worked. Saying that you can design a software that can do this for you in an universal way for any gene / pathway is a just a blatant lie to oversell another product which come from a non biologist who think that biology / genetic could be easily solved by good software practice and new technology.

I love that more and more companies are trying to resolve genome editing or related stuff, but it might be also a good time for people to accept that sequencing (the human) whole genomes was just the first step to a very long journey before fully understanding how it works. And that biology is not that easy.

Welcome to the bioinformatics-PR industrial complex. In BIOPR world, we've cured cancer, folded proteins, and solved gene therapy.

I met a traveller from an antique land

Who said: "Two vast and trunkless legs of stone

Stand in the dessert. Near them, on the goo,

Half sunk, a shattered visage lies, whose frown,

And wrinkled lip, and sneer of cold command,

Tell that its sculptor well those passions read

Which yet survive, stamped on these lifeless things,

The hand that mocked them and the heart that fed:

And on the pedestal these words appear:

"My name is Ozymandias, editor of engines of creations:

Look on my works, ye Mighty, and despair!'

Nothing beside remains. Round the decay

Of that colossal wreck, boundless and bare

The lone and level protein-goo stretch far away."

et sic transit gloria mundi

I'm gonna be super impressed if any custom goo outcompetes the incumbent goo with 3+ billion years of wins under its belt.

and yet mrna vaccines completely sidestep the immune system. We can break out of local minima just by the fact that we are coming at the problem of organism design from a different perspective.

There was a time period on earth (the Carboniferous period) where there was an immense amount of oxygen in the air and trees didn't break down, this is what allowed dinosaurs to grow so large.

Then fungi and bacteria appeared that could feed on lignin and cellulose and changed the world. If it happened once it could happen again.

https://www.nationalgeographic.com/science/article/the-fanta...

That's more like a config file for the existing, absolutely incredible, immune system sported by humans. Remember we can't even build a working single-celled organism yet (taking a natural organism and knocking genes out until you find a minimum viable set doesn't count.)

https://academic.oup.com/jxb/article/70/5/1425/5304601

We are on it :D

Looks neat for modelling but its just not that easy. Gene expression isn't as figured out as we might think. We know a lot ofcourse, enough that tools like this can be very useful if used with caution - like using lego to model a planet's biome. Neat.

Genetics seems like biological programming. It seems tools like these will help bridge the two fields of biology and computer science.

Genetics is only one piece of the pie. Take a look at how voltage gradients in an organism affect symmetries:

https://www.biotechniques.com/bioengineering-biophysics/the-...

another feel-good story about a system that will never work.

https://latticeautomation.com/solutions

"We make software solutions that enable synthetic biology workflows, pipelines, and best practices. We use experimental data and institutional knowledge to enable bio-design productivity and learning."

https://github.com/Lattice-Automation

https://tools.latticeautomation.com/seqviz/

see Zymergen's stock price + recent scandals if you think this is anything more than fantasy.

This is a very strange comment. Zymergen is a synthetic biology company selling bioengineered products and not a bioCAD company selling bioinformatics services.

These are completely different business models. This would be like looking at the Surfside condominium collapse in Miami and declaring autoCAD a “fantasy”. It makes no sense.

Now on to why Zermgen actually failed. The company has only one product out on the market called Hyaline. It is a synthetic bio based polymer film that is transparent but durable and bendable, meant to be used in products such as wearable sensors or foldable touch screen smartphones.

The company failed due to manufacturing limitations and not because using software to design synthetic bio is a “fantasy”. It’s hard for sure but people are working on it and making fantastic progress. For example see JBrowse: https://jbrowse.org/jb2/gallery

I’m going to quote the entire relevant section from the Forbes article regarding Zymergen’s collapse:

>We do not have our own commercial scale manufacturing capability,” the amended prospectus from March read, regarding Hyaline. “Currently we manufacture Hyaline and our other electronic films primarily in Japan but have established a (Contract Manufacturing Organizations) site for Hyaline in the United States. However, our U.S. CMO has informed us that we only have committed supply through the end of 2021. If we do not find and qualify an alternate source of manufacturing, are unable to increase capacity at our existing manufacturer in Japan, or do not invest in our U.S. CMO to support and increase production, acquire our U.S. CMO or otherwise manufacture Hyaline and our other films products on our own, we may not have the manufacturing capacity required to meet our commercial needs after the end of this year.”

https://www.forbes.com/sites/angelauyeung/2021/08/03/as-biol...

In fairness, it's the submitted article's connection rather than (or as well as) GP's.

> What does it mean to write a genome? [...] Pioneering synthetic biology companies such as Gingko Bioworks and Zymergen are already redesigning single-celled organisms like yeast and bacteria, turning them into microscopic factories that produce desirable substances.

I guess I read that part as “the bio side is ahead of the software side see these synthetic bio manufacturing companies are already big and they don’t use our cool tools”

Love the techno-optimist vibe. Let's empower every misanthrope on Earth to mix and match pathogens at scale. I was hoping the covid crisis taught us a lesson on the dangers of biohacking. Next: With this CAD for Warheads, You Can Design New Nukes.

https://en.wikipedia.org/wiki/Tokyo_subway_sarin_attack

Yes, misanthropes are a hazard, but I worry also about a scientifically sophisticated teenager who gets jilted or suffers some other emotional shock, and then decides to end it all for everyone. A species is in trouble when its entire future depends on the emotional stability of adolescents.

Unstated assumption: I am hoping the pricepoint is high enough to eliminate 'random teenager in their parents basement' category.

A single novel virus, possibly escaped from a one of a small number of elite professional labs, took down large swaths of the global economy and killed millions. Now multiply that by millions of amateurs playing genetic Russian Roulette in their parent's basement, with the rest of humanity in the cross hairs. This is the stuff of nightmares.

After covid crisis it boggles the mind that we don't have a global treaty on non-proliferation of genetic technology. For better or worse the damage of a single nuclear weapon is geographically localized, vs. the damage of a novel pathogen crossing borders in a global whirlwind of death and suffering.

https://en.wikipedia.org/wiki/Treaty_on_the_Non-Proliferatio...

A high price-point could eliminate random teenagers for some number of years, but it will not eliminate teenagers in well-to-do families -- especially if gene science experiments can get the teens into prestigious schools.

A treaty would be great, but there's too much medical benefit that would be lost by restricting the technology. Very hard to balance that against a nightmare.

I wonder how long it will be before we can knock up a batch of morphine producing bacteria? Or ecstasy? This could be the start of the end of the war on drugs.

I have libertarian leanings and have always been pretty confused that someone else is allowed to dictate what I put into my own body.

> I wonder how long it will be before we can knock up a batch of morphine producing bacteria?

(2016 Total biosynthesis of opiates by stepwise fermentation using engineered Escherichia coli)

https://www.nature.com/articles/ncomms10390

(2020 High-Efficiency Biocatalytic Conversion of Thebaine to Codeine )

https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7191831/

(2021 review)

https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8288269/

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