Using AI to design proteins is now easy. Making enzymes remains hard.

Enzyme mechanisms can be complex, and getting them to work is tricky.

See full article...

 

[ColdWetDog]

So... whatever is wrong with using fungus? Too slow?

https://www.sciencealert.com/scient...can-break-down-tough-plastic-in-just-140-days

Nothing wrong with that approach at all. In fact, if the result is repeatable and useful in something other than a lab setting, it may be this AI project to the punch. But they are complementary approaches.

The fungi approach is to throw the entire kitchen at the problem (the organism) and see what sticks. This approach is much more sophisticated (and complicated and slow). It does offer the advantage of being able to do things that natural processes simply cannot or will not.

But, I, for one, welcome our plastic eating fungal overlords. They have to be able to clean things up better than humans are managing it.

 

[ColdWetDog]

Thing is we could literally use mushrooms to eat plastic (see my previous post), basically free and it won't cost the trillions invested in Ai.

The only downside us that the plastic eating mushrooms are slower the upside is price and the fact thar under the right weather conditions you can set those plastic eating mushrooms anywhere.

Industrial scale mushrooms are a problem. Not insurmountable, but difficult. Industrial enzymes are also a problem but different ones.

But your logical fallacy is to assume that just because you can solve a problem without AI that you don't need AI to solve other problems or, more succinctly in this environment, to make money.

 

[ColdWetDog]

A few years ago this article would have used ML instead of AI, and in my mind ML would still be a better fit. I'm not quite sure how forcing the AI to learn to go back a workable state is "generative AI" of the sort I normally think of as "Generative AI". Sure, this generates results, but so did any original ML algorithm. Random trees generate outputs, so is it a generative AI? The use of AI rather than ML, and especially generative AI, feels like more buzzword use rather than accurate description (but that's without reading the original paper).

Ok, sure. But where are all the enzymes that this 'old' process kicked out? Genuinely curious since Google, at least, has been trying to figure out how to make enzymes on demand for some time. And even if the 'old' system worked, perhaps the LLMs would do better? No idea, not in my wheelhouse. Not even the same boat. But different approaches to the same problem are often useful.

 

[ColdWetDog]

There are hundreds, more likely many thousands, of enzymes which do this with a single protein. The basic chemistry is very simple, but the details are complex. The biggest problem for unnatural substrates is having the enzymes actually recognizing the molecules they are supposed to catalyze a reaction of. This is particularly true for plastics, which are long polymers, usually of very low water solubility, and from the perspective of enzymes largely featureless. A multi-enzyme complex would make the chemistry steps more complex, and you would have to get the various component enzymes to recognize one another. There are many such enzyme complexes in nature, but they are usually doing something much more sophisticated than simple ester hydrolysis.

Oh, just give it a few billion years.......

 

[ColdWetDog]

According to that article:

“More than 400 microorganisms have so far been found to degrade plastic naturally, with fungi attracting a fair bit of attention for their versatility and ability to degrade all sorts of synthetic substrates with a powerful concoction of enzymes.”

Yet in the Ars article:

“Unfortunately, there isn't an enzyme for many reactions we would sorely like to catalyze—things like digesting plastics.”

So which is it?

The fungi that can process plastics likely use a multi enzyme pathway, probably attached to a cell membrane to work. And, being fungi, the process is slow (they don't care, they don't have to). Doing a quick search about molecular mechanisms of fungal plastic degradation doesn't yield anything I can either read or access (anybody got some references?). My WAG is that fungal biochemistry isn't well studied* and the particular metabolic pathways even less so.

So it isn't and either / or here. While there always seems to be promise of myco remediation for plastics, fungal biochemistry really hasn't yielded any commercially viable systems. So doing it in vitro (literally in glass, outside of the organism) is certainly a way to go and yes, TFA is correct, we don't have a specific enzyme that does that.

* Actually doing a bit more research, there is a bunch of stuff being done at the molecular level, mostly at the 'neat metabolite' stage (think penicillin, psilocybin, etc.). However, none of it seems easily available and since I retired I don't have access to any institutional libraries and even if I did I'd probably fall asleep reading the stuff so there...

 

[ColdWetDog]

Something like:

We finally decomposed all the hydrocarbons in our landfills!..

And released gigatonnes of CO2 in the process..?

The advantage of doing this step by step outside an organism is you can (probably) control it. You don't have to make CO2, maybe CH4 (which is useful) or octanol or butanol or whatever. We're pretty far away from this but if you can control the enzymatic pathway with that degree of precision, the world is your oyster. Or hydrocarbon.

Further, this is really just a test system for designing an enzyme to do some particular, specific, controlled function. Harness this and you have the Diamond Age. Or The Stand.