DeepMind AlphaFold 3 - This Will Change Everything! 

Could it be also used as "chemtrails" to "eat" CO2 from the atmosphere to transform it into a harmless gas?

​@@Z0MBUSTER God designed molecular nanomachines to do that, it's called photosynthesis❗ No human involvement needed. If we have twice the Co2 in the air one day, plants will grow twice as fast. Co2 is a harmless gas --- and we would die without it. Don't believe the propaganda. Historically, Co2 levels have been much higher in the far past. ❗❗❗❗❗❗

We have done this foldingathome using gpu since 2002... hardforums team, especially. We used to teach people how to do it at home, long before bitcoin mining using gpu, which we did back when bitcoins were useless except to other bitcoiners.

​@@Z0MBUSTER co2 is not the issue, its methane... many commercial growers ON RU-vid dump co2 into grow areas, and a lot of it escapes. Methane from factories and smog byproducts is far worse....and a major concern, which breaks down into more co2, ironically.. you can capture it in a balloon shape object, and power generators. Methane is 28x worse greenhouse gas than co2.

​@@Z0MBUSTERone big problem with this kind of climate engineering is that it's hard to predict what long term side-effects it can have. I imagine that the plastic-digesting example can't be used outside of highly controlled environments.

I was literally about to make a joke lol

I've been waiting for BOINC to add dark mode for a while😂

"Dark Reader" extension for browser (free)

fairly big reason for why I've been using mostly linux since the 90s was inability to control blinding background colors in other OSes. now 20+ years later windows11 and macos are finally able to display most window contents with dark background, it was a pretty momentous achievement (their highly paid UI/usability "experts" are idiots)

Just imagine where we'll be just two papers down the line!

🙂

TwoMinutePapers be like: *sniffs white substance*, "lets read these papers!"

@@JohnDontFollowMe I think our man needs the white substance to get *down* after reading a really good paper.

@@JohnDontFollowMe 2MP needs not the "white substance". Bro Fahir has the spice melange..... he IS the Kwisatz Haderach! 😁

This really made my day. Thank you so much! 🙏

Artificial intelligence will study YOU!

you could already begin studying it! I started learning how to program even before high-school , and I now realize that although I didn't have a real clue of what I was doing back then, it actually helps a lot to already be in the water 😃

Why wait?! 🙂 A good grounding in high school maths will get you a long way in AI

This is where you learn to be a wizard, Harry! (PS: Ignore the trolls under the bridge, concentrate on your studies).

version 6 can out-pizza the hut

Wearing contacts keeps you from crying over dead onions

Version 8 will get the fusion reactor going,,,

well you don't award those until after the chickens hatch then you count them.

Dark Mode alone is enough for a Nobel Prize

I am 30 ad I too am amaized. I remember reading SCI-Fi books where we were able to simulate proteins and their interaction. And you could give a cancer genome to the computer and it would give you a blueprint for protein that is poisonous to the cancer, but not to the host. (So like a perfect cancer treatment, you just had to drink/inject the "poison" :D) And now I might live to see something like that come to life.

@@_sky_3123 I'm 66 :-) Need I say more? I hope I can extend my time being alive. Could it fix Long Covid please? I'm less than a bit alive at the moment, I'm after quality rather than length, but I'll be happy with both !

What could be a scenario that you could imagine happening now after this? And when? :)

20 smth college grads are developing AI lol

I'm 45 and hope that this means that our generation will not have to endure the chronic illnesses of old age that plagued our grandparents and are hitting our parents now. Maybe this means Alzheimer's and dementia will not end up costing TRIPLE what it currently does by 2050, which it will according to current predictions. And maybe even reverse aging to some extent. AlphaFold - 2018. AlphaFold 2 - 2020. AlphaFold 3 - 2024. Nobody saw anyo of this coming a whole _six years ago._Who even knows what's coming now.

not if it keeps being closed-source with carefully curated examples

It will fold my mind into smithereens.

You are AlphaCreate 6 duhh this is what the Egyptians knew how to craft reality

Alphafold 6? More like Betafold 2

@@thegreenxeno9430 Sigmafold Ohio Rizz edition

It's gonna be massive once we can combine these, either a next gen chatGPT helping to create a next AlphaFold or direct chat to Protein 😂

Yup. A guy that's all talk but this is all bites

@@DreckbobBratpfanne "It's gonna be massive once we can combine these" Such AI -> AI bridges are already possible, and fine so long as you aren't bothered about communication latency vs a singukar multi modal AI. Tesla FSD was actually doing exactly that up to v11 I think, changing to a sort of multi modal approach for v12.

Well its takes 12 to 15 years become undisputable like the journey of iPhone 1 to iPhone 15 . They are just started there main objective is to make AGI if agi come it revolutionise the humanity .

It's not. Just a few % over last technique. The guy is presenting it as if it's a second coming of JC. Probably because he partnered with Google on this. Google has sunk Billions into Deep Mind and the shareholders start to ask questions. They are trying to make their investment look good.

This is made by an LLMs you know that right "Alphofold AI"

LLM*

@@tingtonggamer4901no, I was correct

@@tingtonggamer4901 Oh really? I haven't read the paper. Thanks for pointing it out, I'll check it out

LLMs are at the root of all these developments. Their emergence is an epochal event

Hey bud! While watching the video I had a question pop up, and seeing that you work in the field maybe you know the answer: From what I could understand, Alphafold is able to take "letters" as input (aminoacids or something like that I believe, but correct me if I'm wrong), and outputs the 3d shape of them right? If so, how does that helps with development of things like, the plastic eating enzyme, and other things? Wouldn't you already need to know which letters to use beforehand? How does knowing the shape of everything affects the development? Pardon me if I'm saying nonsense. I'm an automation engineer and know almost nothing about biology.

@@lucasreis6251you look slightly autistic

​@@lucasreis6251 answer of ChatGPT: Yes, you understood correctly. AlphaFold takes a sequence of amino acids (these are the "letters" in proteins) as input and predicts their three-dimensional structure. This can help in the development of various biological processes, such as creating a plastic-eating enzyme or other enzymes. Knowing the three-dimensional structure of a protein can help scientists understand how it interacts with other molecules and what changes in its structure could improve its functionality. Thus, even if we know the amino acid sequence beforehand, predicting the three-dimensional structure aids in understanding its function and designing improved versions of the protein.

@@lucasreis6251 So yes you are abselutly correct, you would need to know the amino acids beforehand. That is luckily a pretty standard thing to get to know. You can do a buch of differnet test (like mass spec) to figure out what amino acids and in which order they are placed. The almost impossible part to figure out is how the protein folds. It has been a core theory that the the chemistry of the aminoacid chain is what makes proteins fold in specific ways and hold their shape and activity. But breaching the gap from sequence to folding is a huge task that until alphafold many times took years of research to figure out. What most people did to get as accurate readings as alpha fold was to do crystalografi. That is a very complicated task that needs pure crystals of your specific target protein, which was almost more art than science to make work honestly. Alpha fold skips this years of wait and hard labor, letting us play with how mutations affect folding in a timeframe of hours. It is hard to overstate the impact of this ability in research. Hope this answered your question ^-^ edit: realized i didn't answer your question about how protein shape affects development. All proteins have basically the same amino acids in them. The amino acids are actually not what makes proteins able to interact in a biologically active manner. It is the shape of the protein that does. So to know how a protein interacts chemically you need to know how it folds, and not what amino-acids it has.

​​@@lucasreis6251 As a biochemist I can answer this. These "letters" are just a human code for amino acids, amino acids are molecules that form polymers (polymers are long-chain molecules that consist of a certain number of repeating connected units). In the case of amino acids, almost all organisms have 20 different of them, using these 20 every protein in your body is created. Proteins can do things such as move your body (muscles), but basically everything else in your cells is done by proteins. Signal transduction in neurons, breaking down nutrients and synthesizing new structures, transport of molecules around your cells, the immune system is also dependent on a lot of proteins (antibodies for example are proteins). Now, a type of proteins are enzymes, these are nature's catalysts, they can speed up reactions drastically (up to *10^9 !!!). For example we have enzymes that break down sugars into food. It gets interesting when you study bacteria, fungi, plants... Often times they have very specialized enzymes, for example some that can break down polymers. Plastics are polymers as well with often very similar chemical bonds to molecules that bacterial enzymes would break down. If we can mutate/adjust these enzymes to be more efficient at breaking down plastic, they could be a very useful catalyst in such a reaction. This is just one potential use, the possibilities are endless. We can have enzymes that produce lab-grown meat, help with electricity production... It's very easy to get the sequence of a protein (the amino acids it's comprised of), but how these proteins look structurally (3D) is very hard to find out by traditional methods. Using AI trained on existing 3D models, it can find patterns, for example a code of a certain 10 aminoacids would always fold into a certain structure. This is how predictions are made. So, now imagine you discovered a new enzyme from some bacteria that can do X, you get its sequence and instead of spending years and thousands of dollars in finding its structure in the lab, you can just plug the sequence into alphafold and get very likely the same result. Based on this then you can find out more about the protein's function, the mechanism of function and the sequence to structure relationship. I hope it was understandable what I wrote.

This really made my day. Thank you so much! 🙏

Same for me.

it WILL HAPPEN.

Finding effective remyelination therapies to help people with MS like my daughter.

Are you talking about Lizard man

If that as a medicine can be programmed into a fruit or vegetable or maybe a group of fruit and vegetables eaten together that can be grown it would really be amazing. Also changing the snakes DNA so it can have hands and legs and fruit from a tree that can help women reduce the pain at child birth and robots that can do the hard labour in the sun whose hands cannot be pricked by thorns.

Death is inevitable and so is the timing of it. Will take u time to understand..

any sources?@@js_es209

​@js_es209 Death may just become a probability that can be mostly mitigate. One day you'll understand.

Our cells already contain proteins that repair damaged DNA. The reason we're even dealing with cancer nowadays is because we live long enough for one to eventually develop in our body, and our own repair systems can't keep up with the rising amount of damage we are now sustaining: carcinogens in the air and in our food, irregular lifestyles, and overexposure to substances and radiations that humanity had otherwise not have access to prior to technological advancement. Without those three conditions, our body's own proteins is probably more than good enough to protect us from cancer, although growing older still means increasing likelihood of developing cancer (because that's just the inevitably of aging).

​​​@@js_es209 not really. There are ways, at least in theory, to become what they call biologically immortal. So, while your assertion may still be true on this day and age, maybe in the future it won't. Ok, probably real eternal life won't be achieved or even desired, but, periods of time which we consider to be long enough might be in the future.

That's is a very cool concept 🎉🎉🎉

You just re-invented the field of pharmacogenomics, congrats. I can literally go do said test right now. It's just currently in its baby stages. I got offered to do said test for 500€ by my psychiatrist, with said disclaimer. The tech will only keep getting better though and once your genome is sequenced, they can just update the treatment with any new way to analyse it.

Do you have any need in mind ?

Yeah AI will revolutionize Biotechnology forever.

You’re our future and I wish you luck.

I recommend working with them now already!;)

Hary! AI will work alone when you finish the university! SUPERINTILIGANCE

I wanna dump truckloads of this on old landfills, come back in a few years and maybe it'll all be free compost...

@@JohnVance I guess that it won't work like this before some time.

100% agree, I think research on interventions to the aging process needs much more attention and funding.

Same, my dad is getting super old!

Pretty sure that would come with a rather large can of worms.

Nope. They will start on other animals first - likely significant life extension for domestic pets.

@@mnomadvfx Nope- they will take human volunteers on their death bed.

41 more folds to reach the moon!

I thought it’s impossible to fold paper more than 5 or 6 times?

Curing people doesn't make money. Creating new illnesses makes money..Guess which one is coming your way..

Just company bullshit. Protein folding accuracy needs much more than only this program. They just sell nonsense!

Hey bud! While watching the video I had a question pop up, and seeing that you work in the field maybe you know the answer: From what I could understand, Alphafold is able to take "letters" as input (aminoacids or something like that I believe, but correct me if I'm wrong), and outputs the 3d shape of them right? If so, how does that helps with development of things like, the plastic eating enzyme, and other things? Wouldn't you already need to know which letters to use beforehand? How does knowing the shape of everything affects the development? Pardon me if I'm saying nonsense. I'm an automation engineer and know almost nothing about biology.

@@lucasreis6251you are right，but same ‘letters’ can consist different shape and this shape detect different fraction.

​@@lucasreis6251i have a rough idea but lets wait for him His must be better

The highest of all high technologies; the final technology man will ever invent (because he can't be bothered with anything else after that).

It can make all the proteins but i dont think it can use them to build your cat girl

arxiv

I think it is merely bs. Protein folding by computer is not precise enough - a lot of interactions (h-h bridges) are just crudely approximated and you still would need a super computer as a neural network even bigger as every element of the universe to make it fold like in real time. The most precise models are when you combine protein x-ray crystallography with protein folding programs.

Amyloid plaques appear to be a symptom of AD, not a cause. They seem to be a kind of defensive or homeostatic mechanism in response to insufficient nutrition in brain cells, with the function of downsizing brain volume to keep more important areas of the brain well-supplied. Treatments which reduce or prevent amyloid plaques have shown to be ineffective, and in fact counterproductive, in halting or reversing the progression of the disease. Tau protein tangles and buildup of protein in cerebrospinal fluid during the prodrome of the disease seem to be more material to the pathogenesis.

@@4grammaton Interesting. I read (5+ years ago now) that the plaques naturally build up and eventually encroach on synapses. I will refresh my knowledge.

@@SteveRowe Please do, and feel free to inform me if what I said is inaccurate. I also remember reading that plaques are found even in the brains of young children.

This.

You should know (as a protein scientist) that those computer simulations are still not even close to predict accurate folding of a protein!

If you had a president take a space race approach to this technology you'd see a lot change. Something like "let's fundamentally eliminate biological failure as a cause of death within 10 years", and throw space race money at it, and you'd probably be able to pull it off. Would require a lot of planning though. Problem is that much more is *possible* than anyone has the authority or administrative capacity to implement, when it comes to all that sci fi stuff. Would require a society making a decision, which is a bigger barrier than the technology itself at this point.

Our politicians do not work for the people. They work for corporations. That's why they're trying to be careful not to eliminate just worker jobs but also not make their industry or business obsolete in the future. They are going slow not only to be safe but to line their pockets with profit

I mean, we said the same thing about the internet and the smartphone. Sure we have hype about eventual flops like NFTs, but you can't say something like email hasn't fundamentally changed the world in 30 years. And even stuff like enzymes are all in your detergents and your cosmetics. It doesn't change until it does, all at once.

@@adissentingopinion848 Sure, but one just tires of the constant rhetoric that everything is always being revolutionised while day to day life is more of a struggle than ever. I think we just need to tone down the rhetoric a little.

It is also a game of patience. Lots of these are like designer custom made parts. You'd need to market it to scale it up enough for people to afford it, and that requires large initial funding... Which requires a Monetary incentive to do it. Basically, unless the enzymes break plastic into gold or companies/people(worst case) are taxed for plastic waste accumulated, there is no incentive to break down plastic until it is a dire threat

😂😂😂😂

How dare you! Only a human is capable of sounding this stilted and unnatural! XD

I want Dr Károly's voice in GPT-4o.

I want Dr Károly's voice in GPT-4o.

A friend of mine is curious to know, too.

In a nutshell: To predict correct protein folding is absolutely insane. In reality: You need actually to concentrate the real protein and use x-ray crystallography and a simulation like this to get a quite precise glimpse how it fold. I think this advertising for this program just ignores that. A solely simulation can’t predict folding of a protein (not even close). Peptides (very short proteins) are eventually possible so take this advertising with a grain of salt. Yes it will fold your proteins and give you some insights but no real scientist would put their hand into fire that he/she trusts a program like this.

The only thing that's really changing is the increasing level of fakeness.

It feels like where in the bubble phase of this technology where people see potential everywhere but there is no actual use, so there’s a race to find it. It reminds a lot of the dotnet bubble. People claimed the Internet would change everything for years and only after the bubble popped and a small number of products survived did change start to happen. Well and now its hard to find a place in everyday life where the internet didn’t change something.

I ain't a guy that does much personal work with AI, but from what I gather it's mainly because this AI model can "intuit" to approximations and skip over many steps, then go back and verify it, and adjust its answer until it's as close as it can get. rather than having to work through the calculations done for a physics based interaction with many points of failure that can cause a cascade of inaccuracies to develop due to small errors and the like. Again, take it with a grain of salt, that's just my best guess

I'm flattered on behalf of humanity that you decided to interact with humans before consulting with an AI, My human reply would be that I guess the physics based algorithms are based on physics as we understand them and are more limited as they're only as good as we understand physics. A full general AI can take inspiration from any element in the world that would boost the chance of success. So less precise because it's not rooted in physics yet more precise because of the insane amount of datapoints as inspiration. Chatgpt 3.5 Machine learning models like AlphaFold 3 outperform physics-based approaches in protein folding due to their ability to learn complex patterns from vast amounts of data. While physics-based methods rely on rigid rules and principles, they often struggle with the inherent complexity of biological systems. ML models, on the other hand, can capture subtle relationships and nuances in the data, leading to more accurate predictions. However, it's essential to note that both approaches have their strengths and weaknesses, and a hybrid approach combining the best of both worlds may yield even better results in the future. PS, this is just me trying to come up with an answer to your question because it was a good question and I'm curious.

I'm definitely no expert but from my engineering experience when it comes to simulating complex processes with algorithms errors tend to stack quickly and so your result loses reliability the more iterations are ran. Artificial intelligence systems have the benefit of "knowing" roughly what the output result should be expected as, whilst an algorithm has to be tuned either by the operator or a separate algorithmic process (With much the same issues as before). The intelligence model is probably never going to be exactly accurate as it doesn't solve the problem as a series of fundamental physical rules of nature but instead through user defined rules. The physics model will probably never be exactly accurate because noise is inherent in the system. A weird analogy I think of is if the two systems are both set out to solve a jigsaw puzzle the intelligence algorithm takes premade data (That may not be neccesarily accurate) in the form of puzzle pieces and tries to make the picture as you and I would, but will always lose data in the gaps and overall accuracy. On the other hand the physics algorithm attempts to cut out its own pieces which can sometimes be effective but compounds errors as it goes. As I say tho, I am no expert, just having some fun with the ideas

We simply do no have the compute, because these calculations scale unfavorable. These new models seem to somehow compress the data. Its like the game of life, simple rules can create complexity

From what I understand it isn’t a problem of accuracy but of computing power. If an AI gets decent at learning the higher order ‘rules’ which govern protein folding it can look at a sequence of amino acids and give an educated guess on the shape it would likely take under certain conditions without having to calculate millions interactions between hundreds of thousands of physics objects. It makes it viable for a researcher to identify promising novel drug candidates within a search field of millions of possible amino acid sequences without needing to invest in thousands of years of supercomputing time or the obscene amount of lab time and resources that would be required in order to to test each novel substance in vitro.

Exactly! The complexity is just insane and just brute force AI won’t give any precision to it. They might get better when it comes to longer peptides but protein chains and yes post translated ones will be a real pain to computerize and simulate.

The thing is, we already understand a lot - if not most - of the mechanics at play here. We just haven’t had computationally efficient algorithms to do it.

Okay, obviously I dont know anything about protein folding algorithms, so to simplify and generalize my comment - i wish ai would make us smarter, enhance us, make us able to produce whatever wonderful results