New E. coli strain will accelerate evolution of the genes of your choice | Hacker News Reader

New E. coli strain will accelerate evolution of the genes of your choice

arstechnica.com

50 pointsrbanffy30 comments

I think E. Coli needs a new publicist. Never having gotten into biology and coming from a food prep background, I assumed E. Coli was a single "bug" that caused foodborne illness... But there are apparently over 700 strains, many of them harmless or even beneficial. Some strains are used to make drugs and other things, some strains produce toxins that destroy your kidneys, this one can make stuff that runs in your genes, and others E. Coli strains only make stuff that runs in your jeans. Pretty amazing.

You also have something on the scale of pounds of e coli in you. It’s just you never hear about it except for illnesses.

I wish the news included like 10 percent segments of random facts. Maybe biased towards relevant current events but not entirely so. Like I want to see a 90 second documentary about ghengis khan, a how it’s made segment, and the etymology of the word bubble.

All of my feeds are way too focused, there’s not enough discovery. And the “news” is hot garbage. Same problem with Amazon, oh you just bought a printer? Here are fifty more just in case.

I don’t know if this is driven by real metrics or just bad algorithms. I want fewer suggestions within 0.2 sigma of what i liked before and more suggestions 1 or 2 sigma away. And for the love of all things holy if you’ve shown me the same thing fifty times, maybe set that aside and try something else.

I've been feeling particularly alienated by the algorithm sludge recently. I just don't feel comfortable being a part of this big automated closed knowledge/influence loop but it's pretty hard to avoid.

Sometimes I dont click youtube video I am a little bit interested in for the sole reason of knowing I will have to be marking "not interested" on associated reccomendations over next few days.

Its insane I have to click non-interested on 50 skiing vids instead of just telling it "I dont want skiing vids on my feed"

People are typically talking about pathogenic E. Coli when they talk about E. Coli in reference to food safety. I don't think that makes them wrong.

Also, there are over 700 identified serotypes.

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

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

In the context of food safety it's pretty unambiguous what E. Coli is referring to, and what to do about it. I was talking about my own knowledge having only really learned about it in that context working as a chef, and not in biology class.

I don't even know the distinction between a strain and a stereotype, so i guess I'll have to look it up.

https://www.helminthictherapywiki.org/wiki/Main_Page

Neat, I'll look into that.

Let's just say the path the researchers took aren't doing them any favors. Of all of the potential ways to explore this, they chose developing new antibiotic resistance in genes:

> The scientists then tweaked the mutation rate of the orthogonal DNA-replicating enzyme, eventually enhancing it 1,000-fold. To test if the system could be used to evolve new functions, they inserted a gene for resistance to one antibiotic and saw how long it took for that gene to mutate into one conferring resistance to a different antibiotic. Within twelve days, they got 150 times more resistance to the new antibiotic.

Back in ~2014-2015 I was looking at making this (worked in Chang Liu's orthorep lab) - the problem was that I couldn't get my hands on the PRD1 phage (which is a fascinating phage - protein primed replication, lipid membrane coliphage). They were clever about how they bootstrapped the system - they just expressed a whole lot of terminal protein and hoped that some would attach. And it did in VERY rare events.

Another potential mechanism to exploit is "somatic hyper mutation," which is employed by the immune system.

IIRC, taurine is degraded to uracil, then replaced by other base pairs.

Whoops, I was wrong, it's cytosine.

https://en.m.wikipedia.org/wiki/Somatic_hypermutation

Now I'm a little nervous about the idea that someone might be running a thyroidic bioreactor in a reckless manner, and we get the endemic Common-Substance-ivore microbe.

Common-subatance-ivore is something that already has quite a bit of evolutionary pressure to exist. If it doesn't already its probably because eating it is not energetically advantageous enough.

> If it doesn't already its probably because eating it is not energetically advantageous enough.

Counterexample: When trees developed the organic polymer lignin as a building block, it took 30 million years before something (a variety of fungi) evolved to decompose it. Some niches can exist long before they get filled.

Also, "evolutionary pressure to exist" is somewhat tricky idea, since one could say there's even more "pressure to exist" as a universe-spanning presence woven immortally into the fabric of spacetime and powered by vaccum-energy etc. While some organism may benefit by stumbling on it, there's no reason to expect they will given the long odds on whatever chain of transitions/developments are needed to get there. (See also: The Astrophage from Project Hail Mary, which has that One Weird Trick suns hate.)

We should be careful that we don't catalyze such transitions or adaptations when it isn't in our long-term interests.

Cautiously optimistic about bacteria being able to metabolize plastic at scale in my lifetime. Would be interesting if they are able to do so in the environment, no idea what the implications would be if most plastics suddenly gained a shelf life like natural materials.

> no idea what the implications would be if most plastics suddenly gained a shelf life like natural materials.

Wood basically doesn't have a shelf life as long as you aren't exposing it to the elements. This would be a problem for underground PVC piping, but not for bottled water, for the most part.

Plastics already photodegrade. Not being an expert I assume this would be one of the larger issues for bottled water expiration dates, for instance.

From here: https://www.pollutionsolutions-online.com/news/waste-managem...

The big issue seems to be the size of most plastics, not that bacteria can't already eat them.

: Eventually, the pieces of plastic will become small enough to be consumed by microorganisms, which are able to metabolise it and convert it to carbon dioxide (CO2) or absorb it into their own biomolecules.

> The big issue seems to be the size of most plastics, not that bacteria can't already eat them.

Yep, that's why it is super cool things like mealworms can consume styrofoam - they have microbes in there gut that do the actual digesting, but they can chew it up physically, which is very important.

Very neat. Gut microbes are what allow termites to digest wood so well.

Can I get some OTC capsules with these microbes ? Eating styrofoam would be great for winning barroom bets.

You can eat styrofoam without digesting it.

I'm not sure about mealworms, but insects generally have different gut pH levels than humans. I'm not certain their microbes would thrive in the human gut.

I would love for plastic to have a shelf life of exactly 100 years. That would make it robust enough for multiple lifetimes but wouldn’t litter the earth for the next 100,000.

I sincerely hope we never release these into the wild either accidentally or on purpose. It’s great to have microorganisms that can do work for you but they should be incapable of surviving outside a very controlled environment. We should only tackle a problem like plastic pollution with this by using a contained filter system where we feed the contaminated soil and water in and then take out the cleaned product and thoroughly sterilize it before returning it to the environment. Good God imagine how much worse it would be if the pollutant you had to deal with was alive and capable of self replication and evolving defences to your mitigation efforts!

Maybe make ecoli evolve to completely biodegrade nuclear waste as a challenge

You'd want to start with D. radiodurans, not E. coli. I'm not sure if this system would drop into D. radiodurans given the very different DNA repair mechanisms.

My thoughts, dreams, plots and my schemes….

Inching ever closer to that "this is how you get zombies" line :S

i want to be smarter and longer memory please

It can only evolve in new copies, so your offsprings will

Not a bad deal.

sign me up

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