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Scientists are using AI to dream up revolutionary new proteins
- kirykl 4y agoThis seems incredibly risky, given the severity that prions present
- gus_massa 4y agoPrions don't build new prions form smaller parts, like virus do. Prions just change the shape of a complete protein that is already build. But each prion can change the shape of only one type of protein, not any protein that is floating around. I think the risk is almost almost almost zero.
- aetherspawn 4y agoUnless the prion is a quine, and then you have successfully ended the world.
- pyinstallwoes 4y agoOh bravo. Bingo. If only this was more understood.
- sudosysgen 4y agoI think everyone understands this, however fortunately that's not how prions work.
- mysterydip 4y agoI think you may be overestimating the understanding of "everyone". Sample size of 1 but I have no idea what either of those are.
- TOMDM 4y agoA prion is a misfolded protein, a quine is a program that can produce itself with no input. So a prion quine would be a self replicating nano machine, a semi popular doomsday scenario.
- r2_pilot 4y agoInterestingly enough, looking at the powdered form of retinal is a visual quine. (it is a chemical in your eyes that is produced during visual stimulation) https://arbesman.substack.com/p/a-visual-quine https://arbesman.substack.com/p/a-visual-quine
- danielheath 4y agoPrion disease isn't just any misfolded protein; it's a misfold that: * Has a lower bond energy than the correct fold (so can't readily be fixed), and * Can cause its correctly-folded version to also misfold. So far, as far as I'm aware, there have only ever been a handful of misfolds that fit this pattern.
- KaoruAoiShiho 4y agoHow can a prion be a quine? Is this a realistic thing?
- Teever 4y agonot quite. you need some RNA too. https://en.wikipedia.org/wiki/Ribosome#Structure https://en.wikipedia.org/wiki/Ribosome#Structure
- deleted 4y ago[deleted]
- flobosg 4y agoProtein design protocols usually favor globular, soluble proteins, where the sort of interactions generating amyloids and prions are absent.
- refulgentis 4y agoThis can't be true, many bioscience people have commented assuring us that because Deep Fold doesn't literally spit out new proteins, its nothing new, and saying otherwise is misleading
- elcomet 4y agoWhat do you mean? It certainly can fold new proteins that were not part of its training set, otherwise it is useless. Maybe you mean that it cannot fold proteins in new ways that were never seen in its training set though ? But new proteins might fold in known ways, right?
- bpodgursky 4y agoIt's sarcasm, every time DeepMind does something revolutionary in protein folding, some nominal biochemist jumps in and says "oh no, because it didn't literally automate 100% of my job today, this is overhyped"
- TaupeRanger 4y agoWell it hasn't improved the human condition one bit yet (except for researchers desperate for paper citations), so whether it lives up to the "hype" remains to be seen.
- flobosg 4y agoDeepMind has a website highlighting some of the applications of AlphaFold (https://unfolded.deepmind.com https://unfolded.deepmind.com), and apparently it has improved at least some lines of research.
- TaupeRanger 4y agoYes, again very good for the company's PR and padding researcher CVs. But no actual benefit to humankind has happened - again, the hype remains to be justified (or not). Notice the carefully vapid wording: doing [some nebulous thing] to "fight" [some terrible sounding thing], or "this could do [some holy grail amazing thing]".
- ohiovr 4y agoWizards are using something they have faith in and hope it will be useful.
- revolvingocelot 4y agoIndeed, a simple spell for animating an arbitrary number of broomsticks to fetch an amount of water given by argument. [0] Oh, and it was given to us by a demon whose output we don't really understand. What could go wrong? Thankfully, if I'm understanding the article properly, the broomsticks didn't properly animate, though both the demon and human researchers figured they would. I'm all for demon-assisted magical research, but I very much doubt that the next action taken will be "abandon this avenue of research until we understand the demon's process better". We should probably understand this kind of thing if we're going to be messing with it. [0] https://www.youtube.com/watch?v=VErKCq1IGIU https://www.youtube.com/watch?v=VErKCq1IGIU
- adriand 4y ago> But when they instructed microorganisms to make their creations in the labs, none of the 150 designs worked. “They didn’t fold at all: they were just gunk at the bottom of the test tube,” says Baker. When it works properly (when they fold), what do you see in the test tube instead? Does it no longer look like “gunk”? What I mean is, is this difference visible to the naked eye?
- flobosg 4y agoWhen you express recombinant proteins in bacteria, you grow them and then let them produce your protein of interest. Then you destroy the bacteria and separate the soluble parts (where you hope your protein stays) from the insoluble ones (protein aggregates, cell membrane components, etc.), usually by ultracentrifugation. The soluble portion (or supernatant) is a clear liquid, while the insoluble fraction (or precipitate) is a whiteish, gunky solid. So, to answer your question, soluble proteins would look clear. However, to actually check for the presence of your protein of interest in each fraction you load them in a polyacrylamide gel and pass current through it to separate all proteins in the mixture, using a method called electrophoresis[1]. [1]: https://en.wikipedia.org/wiki/Polyacrylamide_gel_electrophoresis https://en.wikipedia.org/wiki/Polyacrylamide_gel_electrophor.... In the first picture of the article each band represents one (or several, if you’re unlucky!) protein of a determined molecular weight or size.
- radicalOH 4y agoIs SDS-PAGE the normal way or do they actually do a western or ELISA?
- throwawaymaths 4y agoThe first step of a western is SDS-PAGE.
- DrAwdeOccarim 4y agoTo follow on, typically proteins produced this way have a tag, or handle, to specifically pull it out from all the other proteins. A typica tag is 6 x Histidine amino acids at the beginning of the protein. These histidines bind to nickel, which is immobilized on a resin. You can use antibodies against the 6xHis to Western for your protein of desire without needing a protein specific antibody.
- adastra22 4y agoAs a solution to the inverse folding problem, this is THE enabling technology for molecular nanotechnology. I suggest anyone interested in this read Drexler’s Radical Abundance which talks about what is possible with atomically precise manufacturing built with custom designed proteins. Radical Abundance in video form: https://m.youtube.com/watch?v=1bw6Zi17DBI https://m.youtube.com/watch?v=1bw6Zi17DBI If anyone is interested in making this happen, contact me.
- 0x1062 4y agoHi, I'd love to chat -- could you please email me jordan[at]astro[dot]codes?
- adastra22 4y agoSent. Nice domain btw.
- dsign 4y agoI'm gonna check that book, I bet I will learn a lot. I sometimes wonder how we are going to solve the scaling problems around silicon and energy for this kind of AI applications. Think about this: a life-saving cancer drug may need to be custom-designed for a patient by using a few Giga-joules of energy to feed a data-center.
- adastra22 4y agoMost of the energy goes into building these models. Applying the model takes orders of magnitude less energy, and can run on efficient hardware that is optimized for that purpose. It's not going to take a gigaojoules of energy to infer custom solutions from a prompt.
- spacecity1971 4y agoWould love to contribute, please contact me at variofab(at)icloud(dot)com
- 4y ago
- LostFutures 4y agoThis news is so shocking I created an account here after lurking for like a decade. I've yet to read the paper itself but if this is legitimate and not "New battery chemistry is 1000x better!!" type clickbait then holy shit. I'm surprised the article doesn't mention nanotechnology. The potential applications of this are insane and go well beyond medicine.
- fartsucker69 4y agodoesn't the article say that the proteins they dreamed up didn't work
- ac29 4y agoThe lab created a protein based Covid vaccine that works and was approved a few months ago: https://www.ipd.uw.edu/2022/06/covid-19-vaccine-skycovione-wins-full-approval-abroad/ https://www.ipd.uw.edu/2022/06/covid-19-vaccine-skycovione-w...
- LostFutures 4y agoTwo attempts. The first failed, the second succeeded. >When Baker and his team applied this second network to their hallucinated protein nanoparticles, it had much greater success making the molecules experimentally. The researchers determined the structure of 30 of their new proteins using cryo-electron microscopy and other experimental techniques, and 27 of them matched the AI-led designs2. The team’s creations included giant rings with complex symmetries, unlike anything found in nature. In theory, the approach could be used to design nanoparticles corresponding to almost any symmetric shape, says Lukas Milles, a biophysicist who co-led the effort. “It is electrifying to see what these networks can do.
- ImPleadThe5th 4y agoWhat are the usecases for designer proteins outside of medicine? The article mentions pollution cleanup. Anybody have any resources to learn about the mechanisms involved in a use case like that?
- flobosg 4y agoOne goal of protein design is to create bespoke enzymes that catalyze reactions of interest, such as the degradation of target compounds. Keep in mind that the vast majority of de novo designed proteins to date lack a defined function and have been used to showcase structure rather than functionality.
- dsign 4y agoAny bio-processes that you can think of. For example, spiders fabricate ultra-strong fibers using a few cubic millimeters. Compare that volume to the smallest Kevlar factory we can set up. A lot of applications will be about designing or adapting biological processes; so they wouldn't be enabled by just protein design but would need way more "tooling". It's worth noting that the computational viability of much of that tooling is boosted by AI as well. That I think is the main value and the "new thing": we got a new, powerful class of "hacks" that we can use to shortcut and scale in-silico bio-research.
- dekhn 4y agoLaundry detergent. Genentech, a biotech company, engineered a version of a protease (a protein that cuts other proteins) to work at high temps, then formed a spinoff with Corning to license that tech for billions to laundry detergent companies. https://en.wikipedia.org/wiki/Genencor https://en.wikipedia.org/wiki/Genencor